水稻成熟胚组织培养能力遗传机制的相关研究
|
摘要
植物组织培养和遗传转化是转基因育种技术发展和应用的重要基础,而植物离体培养能力的高低是决定转基因效率的关键。已有诸多证据表明,基因型是决定植物组织培养能力的主要因素。水稻是人类的主要粮食作物之一,对水稻组织培养能力遗传机制的研究具有举足轻重的意义。
93-11和日本晴分别是籼、粳稻的代表性品种,也是转基因难易程度高低的两个典型范例。本研究对93-11以及源自于日本晴×93-11的重组自交系群体(RIL)进行了成熟胚组织培养能力的详细评估,结合基于SNP的群体深度测序的基因型数据对组培再生相关性状进行了QTL定位,并对部分主效QTL区段注释基因进行了表达水平分析,缩小了候选基因的筛选范围。同时对亲本日本晴和93-11各生长时期的愈伤展开了抗氧化能力方面的生理生化分析。结果如下：
1.通过不同愈伤诱导培养基(MS和NBm诱导培养基)和植株再生培养基(MSB、MSW、NBm和DL3)对93-11成熟种子胚进行组织培养能力的考察,发现：(1)NBm诱导培养基更适于对93-11愈伤的诱导；(2)以每粒愈伤平均出苗数(NRS)考察分化能力时,17天的93-11愈伤再生能力最强,之后随继代培养时间的延长逐渐下降,其中DL3再生培养基对于培养40天以内的93-11愈伤具有最好的植株再生表型,但对于50天的愈伤已无优势；而以植株再生率(RR)考察时,不同培养基对不同培养时间的93-11愈伤的再生能力影响不大。
2.将愈伤诱导、分化和植株再生过程分解为十个性状(ICC、ICS、ICF、ICR、 CIR、CPA、CBA、CGA、NRS和RR)对RIL进行组培能力考察,结果表明：(1)本实验的表型鉴定过程具有良好的可重复性,且各性状评价指标之间大都存在显著或极显著的相关性；(2)群体各株系组培能力表现各异,大部分性状各株系表型差异呈现连续分布状态,且均出现超亲分离现象,其中CBA、CGA、 NRS、RR呈现出严重偏态分布,预示着控制相关性状的主效基因的存在。
3.结合SNP为基础的bin图谱和RIL的九个表型进行QTL定位,共找到25个QTL,分布在除1,4,8,11以外的其它8条染色体上,LOD值介于3.12和9.09之间,表型贡献率从5.99%至21.91%,两个亲本对部分表型都有不同程度的贡献,以第7号染色体上QTL区域效应值最高。此外,还发现了8组QTL共定位现象。
4.通过对与性状CGA、NRS和RR相关定位存Chr.7上的主效QTL共定位区域(95%置信区间)内的注释基因进行RNA表达水平分析,发现27个基因在日本晴和93-11间有明显差异表达,大大缩小了候选基因的范围。
5.对日本晴和93-11不同时期愈伤的酶活性水平进行测定,包括：总抗氧化能力(T-AOC)、过氧化物酶(POD)活性和超氧化物歧化酶(SOD)活性。结果表明,T-AOC受基因型影响,93-11愈伤分化后期T-AOC活性的大幅增加与这时期愈伤的褐化死亡有关。
The development and application of transgenic breeding technology is deeply depended on the success of plant tissue culture and genetic transformation, and the genetic transformation efficiency of plant is largely rest with it's tissue culturability. It has been evidenced in numerous cases from previous studies that the tissue culture response of plant was strongly genotype-dependent. Since rice is one of major cereal crops for human, the study on the genetic mechanism of tissue culture capability in rice has very important significance.
93-11(Oryza sativa ssp. indica) and Nipponbare (Oryza sativa ssp.japonica) are not only the representatives for the sub-species of indica and japonica, but also the typical varieties as the most difficult and the easiest host genotype for gene transformation in rice, respectively. In this study, the tissue culture response of93-11on different culture medium was firstly investigated. In order to clarify the genetic mechanisms of tissue culture, the quantitative trait loci (QTLs) associated with in vitro tissue culture response from mature seed were then identified by using a high quality genetic map based on the SNPs generated from deep sequencing of140recombinant inbred lines (RILs) derived from Nipponbare×93-11. The expression patterns of candidate genes existes in the genomic region of the major QTL with great effect were analyzed and physiological and biochemical characteristics mainly about the level of reactive oxygen species of two parent calli in various phases were also conducted. The results are summarized as follows:
1. Two callus-induced media (MS and NBm) and four plant-regenerated media (MSB, MSW, NBm and DL3) were tested to survey the tissue culture capability of93-11mature seed, and it was found that:(1) NBm callus-induced medium is more suitable for callus induction of93-11mature seed than MS callus-induced medium;(2) When the parameter of the mean number of regenerated shoots (NRS) was used for investigating the differentiation ability of callus, DL3plant-regenerated medium is the best one among four media for93-11callus cultured less than40days; however, no obvious discrepancy was found when the parameter of regeneration rate (RR) was employed to valuate the callus differentiation ability no matter which kind of medium was used and how long the subculture was taken place.
2. The process of callus growth (induction and differentiation) for the whole RIL was dissected into and investigated from ten indices, including ICC (induced-callus colour), ICS (induced-callus size), ICF (induced-callus friability), ICR (induced-callus rigidity), CIR (callus induction rate), CPA (callus proliferation ability), CBA (callus browning ability), CGA (callus greening ability), NRS and RR, respectively. The results indicated:(1) Reproducibility of phenotypic evaluations has satisfactorily achieved in this study, which is evidenced by the high correlations between the data generated from the replicates, and also the different indices.(2) Various phenotypes of the rice RIL were observed, and the population difference for most of indices presented continuous distribution. Moreover, transgressive segregation was found for all indices and even severe skew distributions were discovered in four indices (CBA, CGA, NRS and RR).
3. A total of25QTLs,2each for ICC, ICS, ICF, CIR and CBA,3for CPA,4each for CGA, NRS and RR, respectively, were detected and located on eight rice chromosomes except chromosome1,4,8and11. The LOD value of all QTLs ranged from3.12(gNRS-12) to9.09(qCGA-7), and phenotypic effect (R2) variances explained by the individual QTL were in a rang between5.99%(qCPA-10) and21.91%(qCGA-7). Eight groups of QTL co-location were identified for eight indices and the additive effects came from both Nipponbare and93-11, respectively.
4. In order to reduce the number of candidate genes responsible for major QTL associated with CGA, NRS and RR, the candidate genes were screened in the genomic region located on Chromosome7with95%confidence, and27candidate genes were found with differential expression.
5. Total-antioxidative capacity (T-AOC), peroxidase (POD) activity and superoxide dismutase (SOD) activity of callus in various phases for Nipponbare and93-11were assessed to survey their situation of reactive oxygen species. The results revealed that T-AOC was clearly genotype-dependent and, the drastically increase of T-AOC in later period of differentiation for93-11callus was closely related with callus drowning and death.
93-11和日本晴分别是籼、粳稻的代表性品种,也是转基因难易程度高低的两个典型范例。本研究对93-11以及源自于日本晴×93-11的重组自交系群体(RIL)进行了成熟胚组织培养能力的详细评估,结合基于SNP的群体深度测序的基因型数据对组培再生相关性状进行了QTL定位,并对部分主效QTL区段注释基因进行了表达水平分析,缩小了候选基因的筛选范围。同时对亲本日本晴和93-11各生长时期的愈伤展开了抗氧化能力方面的生理生化分析。结果如下：
1.通过不同愈伤诱导培养基(MS和NBm诱导培养基)和植株再生培养基(MSB、MSW、NBm和DL3)对93-11成熟种子胚进行组织培养能力的考察,发现：(1)NBm诱导培养基更适于对93-11愈伤的诱导；(2)以每粒愈伤平均出苗数(NRS)考察分化能力时,17天的93-11愈伤再生能力最强,之后随继代培养时间的延长逐渐下降,其中DL3再生培养基对于培养40天以内的93-11愈伤具有最好的植株再生表型,但对于50天的愈伤已无优势；而以植株再生率(RR)考察时,不同培养基对不同培养时间的93-11愈伤的再生能力影响不大。
2.将愈伤诱导、分化和植株再生过程分解为十个性状(ICC、ICS、ICF、ICR、 CIR、CPA、CBA、CGA、NRS和RR)对RIL进行组培能力考察,结果表明：(1)本实验的表型鉴定过程具有良好的可重复性,且各性状评价指标之间大都存在显著或极显著的相关性；(2)群体各株系组培能力表现各异,大部分性状各株系表型差异呈现连续分布状态,且均出现超亲分离现象,其中CBA、CGA、 NRS、RR呈现出严重偏态分布,预示着控制相关性状的主效基因的存在。
3.结合SNP为基础的bin图谱和RIL的九个表型进行QTL定位,共找到25个QTL,分布在除1,4,8,11以外的其它8条染色体上,LOD值介于3.12和9.09之间,表型贡献率从5.99%至21.91%,两个亲本对部分表型都有不同程度的贡献,以第7号染色体上QTL区域效应值最高。此外,还发现了8组QTL共定位现象。
4.通过对与性状CGA、NRS和RR相关定位存Chr.7上的主效QTL共定位区域(95%置信区间)内的注释基因进行RNA表达水平分析,发现27个基因在日本晴和93-11间有明显差异表达,大大缩小了候选基因的范围。
5.对日本晴和93-11不同时期愈伤的酶活性水平进行测定,包括：总抗氧化能力(T-AOC)、过氧化物酶(POD)活性和超氧化物歧化酶(SOD)活性。结果表明,T-AOC受基因型影响,93-11愈伤分化后期T-AOC活性的大幅增加与这时期愈伤的褐化死亡有关。
The development and application of transgenic breeding technology is deeply depended on the success of plant tissue culture and genetic transformation, and the genetic transformation efficiency of plant is largely rest with it's tissue culturability. It has been evidenced in numerous cases from previous studies that the tissue culture response of plant was strongly genotype-dependent. Since rice is one of major cereal crops for human, the study on the genetic mechanism of tissue culture capability in rice has very important significance.
93-11(Oryza sativa ssp. indica) and Nipponbare (Oryza sativa ssp.japonica) are not only the representatives for the sub-species of indica and japonica, but also the typical varieties as the most difficult and the easiest host genotype for gene transformation in rice, respectively. In this study, the tissue culture response of93-11on different culture medium was firstly investigated. In order to clarify the genetic mechanisms of tissue culture, the quantitative trait loci (QTLs) associated with in vitro tissue culture response from mature seed were then identified by using a high quality genetic map based on the SNPs generated from deep sequencing of140recombinant inbred lines (RILs) derived from Nipponbare×93-11. The expression patterns of candidate genes existes in the genomic region of the major QTL with great effect were analyzed and physiological and biochemical characteristics mainly about the level of reactive oxygen species of two parent calli in various phases were also conducted. The results are summarized as follows:
1. Two callus-induced media (MS and NBm) and four plant-regenerated media (MSB, MSW, NBm and DL3) were tested to survey the tissue culture capability of93-11mature seed, and it was found that:(1) NBm callus-induced medium is more suitable for callus induction of93-11mature seed than MS callus-induced medium;(2) When the parameter of the mean number of regenerated shoots (NRS) was used for investigating the differentiation ability of callus, DL3plant-regenerated medium is the best one among four media for93-11callus cultured less than40days; however, no obvious discrepancy was found when the parameter of regeneration rate (RR) was employed to valuate the callus differentiation ability no matter which kind of medium was used and how long the subculture was taken place.
2. The process of callus growth (induction and differentiation) for the whole RIL was dissected into and investigated from ten indices, including ICC (induced-callus colour), ICS (induced-callus size), ICF (induced-callus friability), ICR (induced-callus rigidity), CIR (callus induction rate), CPA (callus proliferation ability), CBA (callus browning ability), CGA (callus greening ability), NRS and RR, respectively. The results indicated:(1) Reproducibility of phenotypic evaluations has satisfactorily achieved in this study, which is evidenced by the high correlations between the data generated from the replicates, and also the different indices.(2) Various phenotypes of the rice RIL were observed, and the population difference for most of indices presented continuous distribution. Moreover, transgressive segregation was found for all indices and even severe skew distributions were discovered in four indices (CBA, CGA, NRS and RR).
3. A total of25QTLs,2each for ICC, ICS, ICF, CIR and CBA,3for CPA,4each for CGA, NRS and RR, respectively, were detected and located on eight rice chromosomes except chromosome1,4,8and11. The LOD value of all QTLs ranged from3.12(gNRS-12) to9.09(qCGA-7), and phenotypic effect (R2) variances explained by the individual QTL were in a rang between5.99%(qCPA-10) and21.91%(qCGA-7). Eight groups of QTL co-location were identified for eight indices and the additive effects came from both Nipponbare and93-11, respectively.
4. In order to reduce the number of candidate genes responsible for major QTL associated with CGA, NRS and RR, the candidate genes were screened in the genomic region located on Chromosome7with95%confidence, and27candidate genes were found with differential expression.
5. Total-antioxidative capacity (T-AOC), peroxidase (POD) activity and superoxide dismutase (SOD) activity of callus in various phases for Nipponbare and93-11were assessed to survey their situation of reactive oxygen species. The results revealed that T-AOC was clearly genotype-dependent and, the drastically increase of T-AOC in later period of differentiation for93-11callus was closely related with callus drowning and death.
引文
巩振辉,申书兴(2007)植物组织培养.北京：化学工业出版社.
李卫,董文,周菲,郭光沁,郑国锠(2003)参与在农杆菌介导遗传转化过程中的植物因子研究进展.中国生物工程杂志23(12)：62-67.
李卫,郭光沁,郑国铝(2000)根癌农杆菌介导遗传转化研究的若干新进展.科学通报45(8)：798-807.
马欣荣,刘华玲,谈心(2007)植物生物技术在黑麦草遗传改良中的应用.应用于环境生物学部13(6)：881-887.
钱前,程式华主编(2006)水稻遗传学和功能基因组学.北京：科学出版社.
孙正文,黄兴奇,李维蛟,钟巧芳,余腾琼,郭怡卿,李定琴,殷富有,程在全(2011)分子标记技术及其在水稻基因定位上的应用.基因组学与应用生物学,30(1)：78-86.
王关林,方宏筠(2002)植物基因工程.北京：科学出版社.
王永勤,肖兴国,张爱民(2002)农杆菌介导的小麦遗传转化几个影响因素的研究.遗传学报29(3)：260-265.
吴林森,戴养富(2004)植物生物技术在茶叶育种生产中的应用.安徽农业科学32(3)：563-564,588.
杨邵华(2011)植物QTL研究进展.中国农学通报27(03)：226-231.
叶兴国,Sato S,徐惠君,杜丽璞,Clemente T(2001)小麦农杆菌介导转基因植株的稳定获得和检测.中国农业科学34(5)：469-474.
章元明(2006)作物QTL定位方法研究进展.科学通报19：2223-2231.
周永国,尹中明,沈忠伟,李建粤(2007)籼稻9311成熟胚再生体系.上海师范大学学报(自然科学版)36(4)：71-77.
朱军(1998)数量性状基因定位的混合线性模型分析方法.遗传20(增刊)：137-138.
Aldemita RR, Hodges TK (1996) Agrobacterium tumefaciens-mediated transformation of japonica and indica rice varieties. Planta 199:612-617.
Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25(4):95-203.
Apel K, Hirt H (2004) Reactive oxygen species:metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373-99.
Armstrong CL, Romero-Severson J, Hodges TK (1992) Improved tissue culture response of an elite maize inbred through backcross breeding and identification of chromosomal regions important for regeneration by RFLP analysis. Theor Appl Genet 84:755-762.
Asada K (1994) Production and action of active oxygen species in photosynthetic tissues. In:Causes of photooxidative stress and amelioration of defense systems in plants. pp:77-104.
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735):741-745.
Bajaj S, Mohanty A (2005) Recent advances in rice biotechnology-towards genetically superior transgenic rice. Plant Biotechnol J 3:275-307.
Bartlett JG, Alves SC, Smedley M, Snape JW, Harwood WA (2008) High-throughput Agrobacterium-mediated barley transformation. Plant Methods 4:22.
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick EM, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3:e13.
Ben Amer IM, Worland AJ, Korzun V, Borner A (1997) Genetic mapping of QTL controlling tissue-culture response on chromosome 2B of wheat (Triticum acstivum L.) in relation to major genes and RFLP markers. Theor Appl Genet 94:1047-1052.
Bentsink L, Jowett J, Hanhart CJ, Koornneef M (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Aca Sci 103:17042-17047.
Bergmann L (1959) A new technique for isolating and cloning cells of high plants. Nature 184:648-9.
Bolibok H, Rakoczy-Trojanowska M (2006) Genetic mapping of QTLs for tissue-culture response in plants. Euphytica 149:73-83.
Bolibok H, Gruszczynska A, Hromadajudycka A, Rakoczy-Trojanowska M (2007) The identification of QTLs associated with the in vitro response of rye(Secale cereale L.). Cell Mol Biol Lett 12 (4):523-535.
Bregitzer P, Campbell RD (2001) Genetic markers associated with green and albino plant regeneration from embryogenic barley callus. Crop Sci 41:173-179.
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl:QTL mapping in experimental crosses. Bioinformatics 19:889-890.
Cano MS de, Zaccaro MC, Garcia I, Stella AM, Caire GZ de (2003) Enhancing rice callus regeneration by extracellular products of Tolypothrix tenuis (Cyanobacteria). World J Microb Biotech 19:29-34.
Carvalho CHS, Zehr UB, Gunaratna N, Anderson JM, Kononowicz HH, Hodges TK, Axtell JD (2004) Agrobacterium-mediated transformation of sorghum:factors that affect transformation efficiency. Genet Mol Biol 27:259-269.
Cheng M, Joyce EF, Pang SZ, Zhou HP, Hironaka CM, Duncan DR, Conner TW, Wan YC (1997) Genetic transformation of wheat mediated by Agrobacterium tumefaciens. Plant Physiol 115:971-980.
Chu CC, Wang CC, Sun CS, Hsu C, Yin CK, Chu CY, Bi FY (1975) Establishment of an efficient medium for anther culture of rice through comparative experiments on the nitrogen source. Sci Sin 18:659-668.
Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e 122. doi:10.1093/nar/gkn502.
Dabul ANG, Belefant-Miller H, RoyChowdhury M, Hubstenberger JF, Lorence A, Phillips GC (2009) Screening of a broad range of rice (Oryza sativa L.) germplasm for in vitro rapid plant regeneration and development of an early prediction system. In Vitro Cell Dev Biol-Plant 45:414-420.
Delseny M, Han B, Hsing YI (2010) High throughput DNA sequencing:The new sequencing revolution. Plant Sci 179:405-422.
Doke N (1985) NADPH-dependent O2- generation in membrane fractions isolated from wounded potato tubers inoculated with Phytophtora infestans. Physiol Plant Pathol 27:311-22.
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1 a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18(8):926-936.
Elstner EF (1991) Mechanism of oxygen activation in different compartments. In: E.J. Pell, K.L. Steffen (Eds.), Active Oxygen/Oxidative Stress and Plant Metabolism. Am Socienty Plant Physiologists, Roseville 13-25.
Ezhova TA (2003) Genetic control of totipotency of plant cells in an in vitro culture. Rus J Devel Biol 34(3):197-204.
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmenbrane protein. Theor Appl Genet 112:1164-1171.
Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan JP, Wu M, Zhang RQ, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing:lessons and rationales. Trends in Plant Sci 16(2):77-88.
Flores Berrios E, Gentzbittel L, Kayyal H, Alibert G, Sarrafi A (2000a) AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower (Helianthus annuus L.). Theor Appl Genet 101:1299-1306.
Flores Berrios E, Sarrafi A, Fabre F, Alibert G, Gentzbittel L (2000b) Genotypic variation and chromosomal location of QTLs for somatic embryogenesis revealed by epidermal layers culture of recombinant inbreed in the sunflower (Helianthus annuus L.). Theor Appl Genet 101:1307-1312.
Frary A, Nesbitt TC, Frary A, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw 2.2:A quantitative trait locus key to the evolution of tomato fruit size. Science 289:85-88.
Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484bp within an invertase gene. Proc Natl Aca Sci 97:4718-4723.
Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151-158.
Gautheret RJ (1985) History of plant tissue and cell culture. In:Vasil IK (ed) Cell culture and somatic cell genetics of plants. Cell growth, nutrition, cytodifferentiation. and cryopreservation. Academic Press, New York 2:1-59.
Ge XJ, Chu ZH, Lin YJ, Wang SP (2006) A tissue culture system for different germplasms of indica rice. Plant Cell Rep 25:392-402.
Gibson G, Weir B (2005) The quantitative genetics of transcription. Trends Genet 21(11):616-623.
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean P, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Machlma T, Pliphant A, Briggs S (2002) A draft sequence of the rice genome(Oryza sativa L. ssp. japonica). Science 296(5565): 92-100.
Gonzalez JM, Mufiiz LM, Jouve N (2005) Mapping of QTLs for androgenetic response based on a molecular genetic map of Triticosecale Wittmack. Genome 48: 999-1009.
Gould J, Devey M, Hasegawa O, Ulian EC, Peterson G, Smith RH (1991) Transformation of Zea mays L. using Agrobacterium lumefaciem and the shoot apex. Plant Physiol 95:426-434.
Grimsley N, Hohn T, Davis JW, Hohn B (1987) Agrobacterium-mediated delivery of infectious maize streak virus into maize plants. Nature 325:177-179.
Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, Cambisano N, Mni M, Reid S, Simon P, Spelman R, Georges M, Snell R (2002) Positional candidate cloning of a QTL in dairy cattle:identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res 12:222-231.
Grosse BA, Deimling S, Geiger HH (1996) Mapping of genes for anther culture ability in rye by molecular markers. Vortrage fur Pflanzenzuchtung 35:282-283.
Haberlandt G (1902) Kulturversuche mit isolierten Pflanzenzellen. Sitzungsber K Preuss Akad Wiss Wien. Math-Naturwiss 111:69-92.
Haley CS, Andersson L (1997) Linkage mapping of quantitative trait loci in plants and animals. In:P.H. Dear, (Ed) Genome Mapping A Practical Approach. Oxford University Press, Oxford,49-71.
Han KH, Bradshaw HD, Gordon J, Gordon MP (1994) Adventitious root and shoot regeneration in vitro is under major gene control in an F2 family of hybrid poplar (Populus trichocarpa × P. deltoids). Forest Genet 1:139-146.
Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330-333.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z (2008) Single-molecule DNA sequencing of a viral genome. Science 320: 106-109.
Harwood WA, Bartlett JG, Alves SC, Perry M, Smedley MA, Leyl N, Snape JW (2009) Barley Transformation using Agrobacterium-mediated techniques. Methods Mol Biol, Transgenic Wheat, Barley and Oats 478:137-147.
He G, Luo X, Tian F, Li K, Zhu Z, Su W, Qian X, Fu Y, Wang X, Sun C, Yang J (2006) Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res 16:618-626.
He P, Sheng L, Lu C, Chen Y, Zhu L (1998) Analysis of quantitative trait loci, which contribute to anther culturability in rice (Oryza sativa L.). Mol Breed 4: 165-172.
Henry Y, Vain P, Buyser JD (1994) Genetic analysis of in vitro plant tissue culture response and regeneration capacities. Euphytica 79:45-58.
Hiei Y, Komari T (2008) Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nat Protoc 3:824-834.
Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271-282.
Holme IB, Torp AM, Hansen LN, Andersen SB (2004) Quantitative trait loci affecting plant regeneration from protoplast of Brassica oleracea. Theor App Genet 108:1513-1520.
Huang XH, Feng Q, Qian Q, Zhao Q, Wang L, Wang AH, Guan JP, Fan DL, Weng QJ, Huang T, Dong GJ, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068-1076.
Howe A, Sato S, Dweikat I, Fromm M, Clemente TE (2006) Rapid and reproducible Agrobacterium-mediated transformation of sorghum. Plant Cell Rep 25:784-791.
Ikram-ul-Haq, Zhao CX, Mukhtar Z, Jaleel CA, Azooz MM (2009) Effect of physical desiccation on plant regeneration efficiency in rice (Oryza sativa L.) variety wuper basmati. Journal Plant Physiol 166:1568-1575.
Inz6 D, Montagu MV (1995) Oxidative stress in plants. Curr Opin Biotech 6:153-158.
Ishida Y, Saito H, Ohta S, Hiei Y, Komari T, Kumashiro T (1996) High efficiency transformation of maize (Zea mays L.) mediated by Agrobacterium tumefaciens. Nat Biotechnol 14:745-750.
Jia H, Yi D, Yu J, Xue S, Xiang Y, Zhang C, Zhang Z, Zhang L, Ma Z (2007) Mapping QTLs for tissue culture response of mature wheat embryos. Mol Cells 23(3): 323-330.
Jia H, Yu J, Yi D, Cheng Y, Xu W, Zhang L, Ma Z (2009) Chromosomal intervals responsible for tissue culture response of wheat immature embryos. Plant Cell Tiss Organ Cult 97:159-165.
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365-1369.
Jones LE, Hildebrandt AC, Riker AJ. (1960) Growth of somatic tobacco cells in microculture. Am J Bot 47:468-475.
Kao CH, Zeng ZB (1997) General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics 53:359-371.
Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203-1216.
Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants, where are we now? Heredity 80:137-142.
Khaleda L, Ahmed AMA, Marzan LW, Al-Forkan M (2007) Identification of callus induction and plant regeneration responsiveness in presence of NaCl in in vitro culture of some deepwater rice(Oryza sativa L.) cultivars. Asian J Plant Sci 6(1): 36-41.
Khanna HK, Raina SK (1999) Agrobacterium-mediated transformation of indica rice cultivars using binary and superbinary vectors. Aust J Plant Physiol 26:311-324.
Khanna HK, Raina SK (2002) Elite indica transgenic rice plants expressing modified Cry 1 Ac endotoxin of Bacilllus thuringiensis show enhanced resistance to yellow stem borer (Scirpophaga incertulas). Transgenic Res 11:411-423.
Kogl F, Haagen-Smit AJ, Erxleben H (1934) Uber ein neues auxin ("Heteroauxin") aus Harn. Z Physiol Chem 228:90-103.
Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43(10): 1096-1105.
Komatsuda T, Annaka T, Oka S (1993) Genetic mapping of a quantitative trait locus (QTL) that enhances the shoot differentiation rate in Hordeum vulgare L.. Theor Appl Genet 86:713-720.
Konishi S, Izawa T, Lin SY, Ebana K. Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312(5778): 1392-1396.
Koornneef M, Bade J, Hanhart C, Horsman K, Schel J, Soppe W, Verkerk R, Zabel P (1993) Characterization and mapping of a gene controlling shoot regeneration in tomato. Plant J 3(1):131-141.
Krens FA, Molendijk L, Wullems GJ, Schilperoot RA (1982) In vitro transformation of plant protoplasts with Ti-plasmid DNA. Nature 296:72-74.
Kumar KK, Maruthasalam S, Loganathan M, Sudhakar D, Balasubramanian P (2005) An improved Agrobacterium-mediated transformation protocol for recalcitrant elite indica rice cultivars. Plant Mol Biol Rep 23:67-73.
Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V (2001) Genetic transformation of Hela cells by Agrobacterium. Proc Natl Aca Sci 98:1871-1876.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12. doi:10.1186/gb-2004-5-2-rl2.
Kwon YS, Kim KM, Eun MY, Sohn JK (2000) Quantitaive trait loci mapping associated with plant regeneration ability from seed derived calli in rice (Oryza saliva L.). Mol Cells 11(1):64-67.
Kwon YS, Eun MY, Sohn JK (2002) Marker-assisted selection for identification of plant regeneration ability of seed-derived calli in rice (Oryza sativa L.). Mol Cells 12(1):103-106.
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics,121:185-199.
Lee K, Jeon H, Kim M (2002) Optimization of a mature embryo-based in vitro culture system for high-frequency somatic embryogenic callus induction and plant regeneration from japonica rice cultivars. Plant Cell Tiss Org Cult 71:237-244.
Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science, 311(5769):1936-1939.
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858.
Li RQ, Li YR, Fang XD, Yang HM, Wang J, Kristiansen K, Wang J (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124-1132.
Li Z, Duan SH, Kong J, Li SQ, Li YS, Zhu YG (2007) A single genetic locus in chromosome 1 controls conditional browning during the induction of calli from mature seeds of Oryza sativa ssp. indica. Plant Cell Tiss Organ Cult 89:237-245.
Liao PY, Lee KH (2010) From SNPs to functional polymorphism:The insight into biotechnology applications. Bilchem Eng J 49:149-158.
Lin Z, Hattori K (1998) Inheritance of high shoot regeneration ability from seed callus in a rice cultiva Joshu. Breeding Sci 48:41-44.
Lin YJ, Zhang QF (2005) Optimising the tissue culture conditions for high efficiency transformation of indica rice. Plant Cell Rep 23:540-547.
Liu J, Eck JV, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Aca Sci 99:13302-13306.
Liu RH, Meng JL (2003) MapDraw:a Microsoft Excel macro for drawing genetic linkage maps based on given genetic linkage data. Heraditas (Beijing) 25(3):317-321.
Low PS, Merida JR (1996) The oxidative burst in plant defense:function and signal transduction. Physiol Plant 96:533-42.
Loyola-Vargas VM, De-la-Pefia C, Galaz-Avalos RM, Quiroz-Figueroa FR (2008) Plant tissue culture. Molecular Biomethods Handbook.2nd Edition 875-904.
Lu L, Wu X, Yin X, Morrand J, Chen X, Folk WR, Zhang Z (2009) Development of marker-free transgenic sorghum [Sorghum bicolour (L.) Moench] using standards binary vectors with bar as a selectable marker. Plant Cell Tiss Organ Cult 99:97-108.
Luo Z, Ray W (1988) A simple method for the transformation of rice via the pollen-tube pathway. Plant Mol Biol Reporter 6:165-174.
Manninen OM (2000) Associations between anther-culture response and molecular markers on chromosomes 2H.3H and 4H of barley (Hordeum vulgare L.). Theor Appl Genet 100:57-62.
Mano Y, Takahashi H, Sato K, Takeda K (1996) Mapping genes for callus growth and shoot regeneration in barley. Breeding Sci 46:137-142.
Mano Y, Komatsuda T (2002) Identification of QTLs controlling tissue-culture traits in barley (Hordeum vulgare L.). Theor Appl Genet 105(5):708-715.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim KB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg J,M (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
Matthews PR, Wang MB, Waterhouse PM, Thornton S, Fieg SJ, Gubler F, Jacoben JV (2001) Marker gene elimination from transgenic barley, using co-transformation with adjacent'twin T-DNAs'on a standard Agrobacterium transformation vector. Mol Breeding 7:195-202.
McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) (2008) Gene Nomenclature System for Rice. Rice 1(1):72-84.
Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31-46.
Millicent E, Thoday JM (1960) Gene flow and divergence under disruptive selection. Science 131(3409):1311-1312.
Mir KU (2009) Sequencing genomes:from individuals to populations. Briefings Funct Genomics & Proteomics 8(5):367-378.
Mohanty A, Kathuria H, Ferjani A, Sakamoto A, Mohanty P, Murata N, Tyagi AK (2002) Transgenics of an elite indica rice variety Pusa Basmati I harbouring the codA gene are highly tolerant to salt stress. Theor Appl Genet 106:51-57.
Mouchel CF, Briggs GC, Hardtkel CS (2004) Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. Genes & Dev 18:700-714.
Muir WH, Hildebrandt AC, Riker AJ. (1954) Plant tissue cultures produced from isolated single cells. Science 119:877-8.
Mufioz-Amatriain M, Castillo AM, Chen XW, Cistue L, Valles MP (2008) Identification and validation of QTLs for green plant percentage in barley(Hordeum vulgare L.) anther culture. Mol Breeding 22:119-129.
Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473-497.
Murigneux A, Bentolila S, Hardy T, Baud S, Guitton C, Jullien H, Tahar SB, Freyssinet G, Beckert M (1994) Genotypic variation of quantitative trait loci controlling in vitro androgenesis in maize. Genome 37(6):970-976.
Nadeau JH, Frankel WN (2000) The roads from phenotypic variation togene discovery:mutagenesis versus QTLs. Nat Genet 25:381-384.
Nadolska-Orczyk A, Malepszy S (1989) In vitro culture of Cucumis sativus L.7. Genes controlling plant regeneration. Theor Appl Genet 78:836-840.
Nayak P, Basu D, Das S, Basu A, Ghosh D, Ramakrishnan NA, Ghosh M, Sen SK (1997) Transgenic elite indica rice plants expressing CrylAc-endotoxin of Bacillus thuringiensis are resistant against yellow stem borer (Scirpophaga incertulas). Proc Natl Acad Sci 94:2111-2116.
Nickerson DA, Taylor SL, Weiss KM, Clark AG, Hutchinson RG, Stengard J, Salomaa V, Vartiainen E, Boerwinkle E, Sing CF (1998) DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat Genet 19:233-240.
Ning Z, Cox AJ, Mullikin JC (2001) SSAHA:A fast search method for large DNA databases. Genome Res 11:1725-1729.
Nishimura A, Ashikari M, Lin S, Takashi T, Angeles ER, Yamamoto T, Matsuoka M (2005) Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. Proc Natl Acad Sci 102:11940-11944.
Nishimura A, Aichi I, Matsuoka M (2007) A protocol for Agrobacterium-mediated transformation in rice. Nat Protoc 1:2796-2802.
Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J, Purugganan MD (2004) Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167:1361-1369.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriew IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Paterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556.
Paterson AH (1995) Molecular dissection of quantitative traits:progress and prospects. Genome Res (5):321-333.
Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721-726.
Peng JJ, Hodges TK (1989) Genetic analysis of plant regeneration in rice(Oryza sativa L.). In Vitro Cell Dev Biol 25(1):91-94.
Peleman JD, Wye C, Zethof J, S(?)rensen AP, Verbakel H, Oeveren J, Gerats T, Voort JR (2005) Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis:A Method for High-Resolution Mapping of QTL Within a Single Population. Genetics 171:1341-1352.
Price HA (2006) Believe it or not, QTLs are accurate. Trends Plant Sci 11(5): 213-216.
Rao AQ, Bakhsh A, Kiani S, Shahzad K, Shahid AA, Husnain T, Riazuddin S (2009) The myth of plant transformation. Biotechnology Adv 27:753-763.
Rashid H, Yokoi S, Toriyama K, Hinata K (1996) Transgenic plant production mediated by Agrobacterium in incdica rice. Plant Cell Rep 15:727-730.
Raveendar S, Premkumar A, Ignacimuthu S, Agastian P (2008) Effects of sea water on callus induction and regeneration of rice genotypes. Int J Integ Biol 3(2): 92-95.
Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37(10):1141-1146.
Rice P, Longden I, Bleasby A (2000) EMBOSS:the European Molecular Biology Open Software Suite. Trends Genet 16:276-277.
Rothberg JM, Leamon JH (2008) The development and impacts of 454 sequencing. Nat Biotechnol 28:426-428.
Raveendar S, Premkumar A, Ignacimuthu S, Agastian P (2008) Effect of sea water on callus induction and regeneration of rice genotypes. In J Integrative Biol 3(2):92-95.
Saika H, Toki S (2010) Matur seed-derived callus of the model indica rice variety Kasalath is highly competent in Agrobacterium-mediated transformation. Plant Cell Rep 29(12):1351-1364.
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463-5467.
Schiantarelli E, Pena AD, Candela M (2001) Use of recombinant inbred lines (RILs) to identify, locate and map major genes and quantitative trait loci involved with in vitro regeneration ability in Arabidopsis thaliana. Theor Appl Genet 102:335-341.
Schlappi M, Hohn B (1992) Competence of immature maize embryos for Agrobacterium-mediated gene transfer. Plant Cell 4:7-16.
Schleiden MJ (1838) Beitrage zur Phytogenesis. Arch Anat Physiol Wiss Med (J Muller):137-76.
Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pastemak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Mink P, Reily AD, Courtney L, Krschowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson AM, Gillam B, Chen WZ, Yan L, Higginbotham J, Cardenas M, Waligorski J, Allpebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane M, Henke J, Wang T, Ruppet J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse L, Collura K, Kudrna D, Currie K, He RF, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dijmic Z, Kim W, Talag J, Ziccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento, Zutavem T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMchan L, Buren PV, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carptia NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Plnnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome:complexity, diversity, and dynamics. Science 326:1112-1115.
Schwann T (1839) Mikroscopische Untersuchungen fiber die Ubereinstimmung in der Struktur und dem Wachstum des Tiere und Pflanzen. W Engelmann:Leipzig:No 176.
Sergeeva LI, Keurentjes JJB, Bentsink L, Vonk J, Plas LHW, Koornneef M, Vreugdenhil D (2006) Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis. Proc Natl Acad Sci 103: 2994-2999.
Shan XJ, Zhu MZ, Shi M, Gao JP, Lin HX (2009) Fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice(Oryza rufipogon Griff). Theor Appl Genet 119:827-836.
Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135(3):1198-1205.
Shendure J, Porreca GJ, Reppas NB, Lin XX, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732.
Shendure J, Li H (2008) Next generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP:The NCB1 database of genetic variation. Nucleic Acids Res 29: 308-311.
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023-1028.
Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39(5):623-630.
Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316:112-115.
Taguchi-Shiobara F, Lin SY, Tanno K, Komatsuda T, Yano M, Sasaki T, Oka S (1997a) Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L.. Theor Appl Genet 95:823-833.
Taguchi-Shiobara F, Komatsuda T, Oka S (1997b) Comparison of two indices for evaluating regeneration ability in rice (Oryza sativa L.) through a diallel analysis. Theor Appl Genet 94:378-382.
Taguchi-Shiobara F, Yamamoto T, Yano M, Oka S (2006) Mapping QTLs that control the performance of rice tissue culture and evalution of derived near-isogenic lines. Theor Appl Genet 112:968-976.
Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the a subunit of protein kinase CK2. Proc Natl Acad Sci USA 98(14):7922-7927.
Takeuchi Y, Abe T, Sasahara T (2000) RFLP Mapping of QTLs influencing shoot regeneration from mature seed-derived calli in rice. Crop Sci 40:245-247.
Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360-1364.
Thimann KV (1935) On the plant hormone produced by Rhizopus suinus. J Biol Chem 109:279-291.
Tingay S, McElroy D, Kalla R, Fieg S, Wang M, Thornton S, Brettell R (1997) Agrobacterium tumefaciens-mediated barley transformation. Plant J 11:1369-1376.
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphism associate with variation in flowering time. Nat Genet 28:286-289.
Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J 47:969-976.
Toledano MB, Fourquet S, D'Autrdaux B (2010) Cellular Signaling by Reactive Oxygen Species:Biochemical Basis and Physiological Scope.In:Ari Sitaramayys. Signal transduction:Pathways, Mechanism and Diseases:313-314.
Torp AM, Hansen AL, Andersen SB (2001) Chromosomal regions associated with green plant regeneration in wheat(Triticum aestivum L.) anther culture. Euphytica 119:377-387.
Travella S, Ross SM, Harden J, Everett C, Snape JW, Harwood WA (2005) A comparison of transgenic barley lines produced by particle bombardment and Agrobacterium-mediated techniques. Plant Cell Reports 23:780-789.
Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC Gene Regulating Senescence Improves Grain Protein, Zinc, and Iron Content in Wheat. Science 314:1298-1301.
Ueda T, Sato T, Hidema J, Hirouchi T, Yamamoto K, Kumagai T, Yano M (2005) qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase. Genetics 171(4):1941-1950.
Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Halet CS, Buys N, Tally M, Andersson G, Georges M, Andersson L (2003) A regulatory mutation in IGF2 causes a major QTL dffect on muscle growth in the pig. Nature 425:832-836.
Van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JNAMR, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato:Providing a framework for accelerate gene isolation and a genomewide physical map. Genetics 173:1075-1087.
Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522-530.
Vasil V, Castillo AM, Fromm ME, Vasil IK (1992) Herbicide resistant fertile transgenic wheat plants obtained by microprojectile bombardment of regenerable embryogenic callus. Nat BioTechnol 10:667-674.
Vasil V, Hildebrandt AC (1965) Differentiation of tobacco plants from single, isolated cells in microcultures. Science 150:89-892.
Vasil V, Hildebrandt AC (1967) Further studies on the growth and differentiation of single, isolated cells of tobacco in vitro. Planta 75:139-151.
Vasil IK (2008) A history of plant biotechnology:from the cell theory of Schldiden and Schwann to biotech crops. Plant Cell Rep 27:1423-1440.
Vasil IK, Vasil V (1992) Advances in cereal protoplast research. Physiol Plant 85:279-283.
Verdeil JL, Alemanno L, Niemenak N, Tranbarger TJ (2007) Pluripotnet versus totipotent plant stem cells:dependence versus autonomy. Trends Plant Sci 12(6):245-252.
Wan Y, Rocheford TR, Widholm JM (1992) RFLP analysis to identify putative chromosomal regions involved in the anther culture response and callus formation of maize. Theor Appl Genet 85:360-365.
Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H, Ma H, Zhang G, He Z (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genet 40(11):1370-1374.
Wang L, Wang AH, Huang XH, Zhao Q, Dong GJ, Qian Q, Sang T, Han B (2010) Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theor Appl Genet 122:327-340.
Wang S, Basten CJ, Zeng ZB (2007) Windows QTL Catergrapher 2.5 Department of Statistics. North Carolina State University, Raleign.
Wei Chi (2006) Enhancement of NADP-Malic Enzyme in Transgenic Rice Induced the Accumulation of Reactive Oxygen Species. Russ J Plant Physl 53(3):325-331.
Went FW (1928) Wuchstoff und Wachstum. Rec Trav Bot Neerl 25:1-116.
White PR (1943) A handbook of plant tissue culture. Jacques Cattell Press, Tempe, Arizona.
White PR (1963) The cultivation of animal and plant cells,2nd edn. The Ronald Press. New York.
Wu WR, Li WM, Tang DZ, Lu HR, Worland AJ (1999) Time-Related Mapping of Quantitative Trait Loci Underlying Tiller Number in Rice. Genetics 151:297-303.
Xia GM, Li ZY, He CX, Chen HM, Brettell R (1999) Transgenic plant regeneration from wheat(Triticum aestivum L.) mediated by Agrobacterium tumefaciens. Acta Phytophologica Sinica 25(1):22-28.
Xu JJ, Zhao Q, Du PN, Xu CW, Wang BH, Feng Q, Liu QQ, Tang SZ, Gu MH, Han B, Liang GH (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 11:656-669.
Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705-708.
Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu s, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761-767.
Yan JQ, Zhu J, He CX (1998) Quantitative trait loci analysis for the developmental behavior of tiller number in rice(Oryza sativa. L.) Theor Appl Genet 97:267-274.
Yang C, Zhao T, Yu D, Gai J (2011) Mapping QTLs for tissue culture response in soybean (Glycine max (L.) Merr.) Mol Cells 32:337-342.
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000)Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12(12):2473-2484.
Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145-153.
Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, Xie D, Sun C (2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891-898.
Yu HH, Xie WB, Wang J, Xing YZ, Xu CG, Li XH, Xiao JH, Zhang QF (2011) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE 6(3):e17595.
Yu J, Hu SN, Wang J, Wong GKS, Li WG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Huang XG, Li WJ, Li J, Liu ZW, Li L, Liu JP, Qi QH, Liu JS, Li L, Li T, Wang XG, Lu H, Wu TT, Zhu M, Ni PX, Han H, Dong W, Ren XY, Feng XL, Cui P, Li XR, Wang H, Xu X, Zhai WX, Xu Z, Zhang JS, He SJ. Zhang JG, Xu JC, Zhang KL, Zheng XW, Dong JH, Zeng WY, Tao L, Ye J, Tan J, Ren XD, Chen XW, He J, Liu DF, Tian W, Tian CG, Xia HA, Bao QY, Li G, Gao H, Cao T, Wang J, Zhao WM, Li P, Chen W, Wang XD, Zhang Y, Hu JF, Wang J, Liu S, Yang J, Zhang GY, Xiong YQ, Li XJ, Mao L, Zhou CS, Zhu Z, Chen RS, Hao BL, Zheng WM, Chen SY, Guo W, Li GJ, Liu SQ, Tao M, Wang J, Zhu LH, Yuan LP, Yang HM (2002) A draft sequence of the rice genome (Oryza saliva L. ssp. indica). Science 296 (5565):79-92.
Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17:155-160.
Zaidi MA, Narayanan M, Sardana R, Taga I, Postel S, Johns R, McNulty M, Mottiar Y, Mao J, Loit E, Altosaar I (2006) Optimizing tissue culture media for efficient transformation of different indica rice genotypes. Agronomy Res 4(2): 563-575.
Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci 90:10972-10976.
Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
Zeng ZB, Kao CH, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279-289.
Zhang J, Chiodini R, Badr A, Zhang GF (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38:95-109.
Zhang Z, Ober JA, Kliebenstein DJ (2006) The Gene Controlling the Quantitative Trait Locus EPITHIOSPECIFIER MODIFIER1 Alters Glucosinolate Hydrolysis and Insect Resistance in Arabidopsis. Plant Cell 18:1524-1536.
Zhang J, Xu RJ, Elliott MC, Chen DF (1997) Agrobacterium-mediated transformation of elite indica and japonica rice cultivars. Mol Biotechnol 8:223-231.
Zhao LN, Zhou HJ, Lu LX, Liu L, Li XH, Lin YJ, Yu SB (2009) Identification of quantitative trait loci controlling rice mature seed culturability using chromosomal segment substitution lines. Plant Cell Rep 28:247-256.
Zhao ZY, Cai T, Tagliani L, Miller M, Wang N, Pang H, Rudert M, Schroeder S, Hondred D, Seltzer J, Pierce D (2000) Agrobacterium-mediated sorghum transformation. Plant Mol Biol 44:789-798.
Zhao ZY, Glassman K, Sewalt V, Wang N, Miller M, Chang S, Thompson T, Catron S, Wu E, Bidney D, Kedebe Y, Jung R (2003) Nutritionally improved transgenic sorghum. In:Vasil IK (ed) Plant biotechnology 2002 and beyond. Proceedings of the 10th IAPTC & B Congress. Kluwer Academic Publishers, pp 413-416.
Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Yong ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123-1134.
李卫,董文,周菲,郭光沁,郑国锠(2003)参与在农杆菌介导遗传转化过程中的植物因子研究进展.中国生物工程杂志23(12)：62-67.
李卫,郭光沁,郑国铝(2000)根癌农杆菌介导遗传转化研究的若干新进展.科学通报45(8)：798-807.
马欣荣,刘华玲,谈心(2007)植物生物技术在黑麦草遗传改良中的应用.应用于环境生物学部13(6)：881-887.
钱前,程式华主编(2006)水稻遗传学和功能基因组学.北京：科学出版社.
孙正文,黄兴奇,李维蛟,钟巧芳,余腾琼,郭怡卿,李定琴,殷富有,程在全(2011)分子标记技术及其在水稻基因定位上的应用.基因组学与应用生物学,30(1)：78-86.
王关林,方宏筠(2002)植物基因工程.北京：科学出版社.
王永勤,肖兴国,张爱民(2002)农杆菌介导的小麦遗传转化几个影响因素的研究.遗传学报29(3)：260-265.
吴林森,戴养富(2004)植物生物技术在茶叶育种生产中的应用.安徽农业科学32(3)：563-564,588.
杨邵华(2011)植物QTL研究进展.中国农学通报27(03)：226-231.
叶兴国,Sato S,徐惠君,杜丽璞,Clemente T(2001)小麦农杆菌介导转基因植株的稳定获得和检测.中国农业科学34(5)：469-474.
章元明(2006)作物QTL定位方法研究进展.科学通报19：2223-2231.
周永国,尹中明,沈忠伟,李建粤(2007)籼稻9311成熟胚再生体系.上海师范大学学报(自然科学版)36(4)：71-77.
朱军(1998)数量性状基因定位的混合线性模型分析方法.遗传20(增刊)：137-138.
Aldemita RR, Hodges TK (1996) Agrobacterium tumefaciens-mediated transformation of japonica and indica rice varieties. Planta 199:612-617.
Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25(4):95-203.
Apel K, Hirt H (2004) Reactive oxygen species:metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373-99.
Armstrong CL, Romero-Severson J, Hodges TK (1992) Improved tissue culture response of an elite maize inbred through backcross breeding and identification of chromosomal regions important for regeneration by RFLP analysis. Theor Appl Genet 84:755-762.
Asada K (1994) Production and action of active oxygen species in photosynthetic tissues. In:Causes of photooxidative stress and amelioration of defense systems in plants. pp:77-104.
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735):741-745.
Bajaj S, Mohanty A (2005) Recent advances in rice biotechnology-towards genetically superior transgenic rice. Plant Biotechnol J 3:275-307.
Bartlett JG, Alves SC, Smedley M, Snape JW, Harwood WA (2008) High-throughput Agrobacterium-mediated barley transformation. Plant Methods 4:22.
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick EM, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3:e13.
Ben Amer IM, Worland AJ, Korzun V, Borner A (1997) Genetic mapping of QTL controlling tissue-culture response on chromosome 2B of wheat (Triticum acstivum L.) in relation to major genes and RFLP markers. Theor Appl Genet 94:1047-1052.
Bentsink L, Jowett J, Hanhart CJ, Koornneef M (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Aca Sci 103:17042-17047.
Bergmann L (1959) A new technique for isolating and cloning cells of high plants. Nature 184:648-9.
Bolibok H, Rakoczy-Trojanowska M (2006) Genetic mapping of QTLs for tissue-culture response in plants. Euphytica 149:73-83.
Bolibok H, Gruszczynska A, Hromadajudycka A, Rakoczy-Trojanowska M (2007) The identification of QTLs associated with the in vitro response of rye(Secale cereale L.). Cell Mol Biol Lett 12 (4):523-535.
Bregitzer P, Campbell RD (2001) Genetic markers associated with green and albino plant regeneration from embryogenic barley callus. Crop Sci 41:173-179.
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl:QTL mapping in experimental crosses. Bioinformatics 19:889-890.
Cano MS de, Zaccaro MC, Garcia I, Stella AM, Caire GZ de (2003) Enhancing rice callus regeneration by extracellular products of Tolypothrix tenuis (Cyanobacteria). World J Microb Biotech 19:29-34.
Carvalho CHS, Zehr UB, Gunaratna N, Anderson JM, Kononowicz HH, Hodges TK, Axtell JD (2004) Agrobacterium-mediated transformation of sorghum:factors that affect transformation efficiency. Genet Mol Biol 27:259-269.
Cheng M, Joyce EF, Pang SZ, Zhou HP, Hironaka CM, Duncan DR, Conner TW, Wan YC (1997) Genetic transformation of wheat mediated by Agrobacterium tumefaciens. Plant Physiol 115:971-980.
Chu CC, Wang CC, Sun CS, Hsu C, Yin CK, Chu CY, Bi FY (1975) Establishment of an efficient medium for anther culture of rice through comparative experiments on the nitrogen source. Sci Sin 18:659-668.
Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e 122. doi:10.1093/nar/gkn502.
Dabul ANG, Belefant-Miller H, RoyChowdhury M, Hubstenberger JF, Lorence A, Phillips GC (2009) Screening of a broad range of rice (Oryza sativa L.) germplasm for in vitro rapid plant regeneration and development of an early prediction system. In Vitro Cell Dev Biol-Plant 45:414-420.
Delseny M, Han B, Hsing YI (2010) High throughput DNA sequencing:The new sequencing revolution. Plant Sci 179:405-422.
Doke N (1985) NADPH-dependent O2- generation in membrane fractions isolated from wounded potato tubers inoculated with Phytophtora infestans. Physiol Plant Pathol 27:311-22.
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1 a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18(8):926-936.
Elstner EF (1991) Mechanism of oxygen activation in different compartments. In: E.J. Pell, K.L. Steffen (Eds.), Active Oxygen/Oxidative Stress and Plant Metabolism. Am Socienty Plant Physiologists, Roseville 13-25.
Ezhova TA (2003) Genetic control of totipotency of plant cells in an in vitro culture. Rus J Devel Biol 34(3):197-204.
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmenbrane protein. Theor Appl Genet 112:1164-1171.
Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan JP, Wu M, Zhang RQ, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing:lessons and rationales. Trends in Plant Sci 16(2):77-88.
Flores Berrios E, Gentzbittel L, Kayyal H, Alibert G, Sarrafi A (2000a) AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower (Helianthus annuus L.). Theor Appl Genet 101:1299-1306.
Flores Berrios E, Sarrafi A, Fabre F, Alibert G, Gentzbittel L (2000b) Genotypic variation and chromosomal location of QTLs for somatic embryogenesis revealed by epidermal layers culture of recombinant inbreed in the sunflower (Helianthus annuus L.). Theor Appl Genet 101:1307-1312.
Frary A, Nesbitt TC, Frary A, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw 2.2:A quantitative trait locus key to the evolution of tomato fruit size. Science 289:85-88.
Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484bp within an invertase gene. Proc Natl Aca Sci 97:4718-4723.
Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151-158.
Gautheret RJ (1985) History of plant tissue and cell culture. In:Vasil IK (ed) Cell culture and somatic cell genetics of plants. Cell growth, nutrition, cytodifferentiation. and cryopreservation. Academic Press, New York 2:1-59.
Ge XJ, Chu ZH, Lin YJ, Wang SP (2006) A tissue culture system for different germplasms of indica rice. Plant Cell Rep 25:392-402.
Gibson G, Weir B (2005) The quantitative genetics of transcription. Trends Genet 21(11):616-623.
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean P, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Machlma T, Pliphant A, Briggs S (2002) A draft sequence of the rice genome(Oryza sativa L. ssp. japonica). Science 296(5565): 92-100.
Gonzalez JM, Mufiiz LM, Jouve N (2005) Mapping of QTLs for androgenetic response based on a molecular genetic map of Triticosecale Wittmack. Genome 48: 999-1009.
Gould J, Devey M, Hasegawa O, Ulian EC, Peterson G, Smith RH (1991) Transformation of Zea mays L. using Agrobacterium lumefaciem and the shoot apex. Plant Physiol 95:426-434.
Grimsley N, Hohn T, Davis JW, Hohn B (1987) Agrobacterium-mediated delivery of infectious maize streak virus into maize plants. Nature 325:177-179.
Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, Cambisano N, Mni M, Reid S, Simon P, Spelman R, Georges M, Snell R (2002) Positional candidate cloning of a QTL in dairy cattle:identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res 12:222-231.
Grosse BA, Deimling S, Geiger HH (1996) Mapping of genes for anther culture ability in rye by molecular markers. Vortrage fur Pflanzenzuchtung 35:282-283.
Haberlandt G (1902) Kulturversuche mit isolierten Pflanzenzellen. Sitzungsber K Preuss Akad Wiss Wien. Math-Naturwiss 111:69-92.
Haley CS, Andersson L (1997) Linkage mapping of quantitative trait loci in plants and animals. In:P.H. Dear, (Ed) Genome Mapping A Practical Approach. Oxford University Press, Oxford,49-71.
Han KH, Bradshaw HD, Gordon J, Gordon MP (1994) Adventitious root and shoot regeneration in vitro is under major gene control in an F2 family of hybrid poplar (Populus trichocarpa × P. deltoids). Forest Genet 1:139-146.
Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330-333.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z (2008) Single-molecule DNA sequencing of a viral genome. Science 320: 106-109.
Harwood WA, Bartlett JG, Alves SC, Perry M, Smedley MA, Leyl N, Snape JW (2009) Barley Transformation using Agrobacterium-mediated techniques. Methods Mol Biol, Transgenic Wheat, Barley and Oats 478:137-147.
He G, Luo X, Tian F, Li K, Zhu Z, Su W, Qian X, Fu Y, Wang X, Sun C, Yang J (2006) Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res 16:618-626.
He P, Sheng L, Lu C, Chen Y, Zhu L (1998) Analysis of quantitative trait loci, which contribute to anther culturability in rice (Oryza sativa L.). Mol Breed 4: 165-172.
Henry Y, Vain P, Buyser JD (1994) Genetic analysis of in vitro plant tissue culture response and regeneration capacities. Euphytica 79:45-58.
Hiei Y, Komari T (2008) Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nat Protoc 3:824-834.
Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271-282.
Holme IB, Torp AM, Hansen LN, Andersen SB (2004) Quantitative trait loci affecting plant regeneration from protoplast of Brassica oleracea. Theor App Genet 108:1513-1520.
Huang XH, Feng Q, Qian Q, Zhao Q, Wang L, Wang AH, Guan JP, Fan DL, Weng QJ, Huang T, Dong GJ, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068-1076.
Howe A, Sato S, Dweikat I, Fromm M, Clemente TE (2006) Rapid and reproducible Agrobacterium-mediated transformation of sorghum. Plant Cell Rep 25:784-791.
Ikram-ul-Haq, Zhao CX, Mukhtar Z, Jaleel CA, Azooz MM (2009) Effect of physical desiccation on plant regeneration efficiency in rice (Oryza sativa L.) variety wuper basmati. Journal Plant Physiol 166:1568-1575.
Inz6 D, Montagu MV (1995) Oxidative stress in plants. Curr Opin Biotech 6:153-158.
Ishida Y, Saito H, Ohta S, Hiei Y, Komari T, Kumashiro T (1996) High efficiency transformation of maize (Zea mays L.) mediated by Agrobacterium tumefaciens. Nat Biotechnol 14:745-750.
Jia H, Yi D, Yu J, Xue S, Xiang Y, Zhang C, Zhang Z, Zhang L, Ma Z (2007) Mapping QTLs for tissue culture response of mature wheat embryos. Mol Cells 23(3): 323-330.
Jia H, Yu J, Yi D, Cheng Y, Xu W, Zhang L, Ma Z (2009) Chromosomal intervals responsible for tissue culture response of wheat immature embryos. Plant Cell Tiss Organ Cult 97:159-165.
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365-1369.
Jones LE, Hildebrandt AC, Riker AJ. (1960) Growth of somatic tobacco cells in microculture. Am J Bot 47:468-475.
Kao CH, Zeng ZB (1997) General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics 53:359-371.
Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203-1216.
Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants, where are we now? Heredity 80:137-142.
Khaleda L, Ahmed AMA, Marzan LW, Al-Forkan M (2007) Identification of callus induction and plant regeneration responsiveness in presence of NaCl in in vitro culture of some deepwater rice(Oryza sativa L.) cultivars. Asian J Plant Sci 6(1): 36-41.
Khanna HK, Raina SK (1999) Agrobacterium-mediated transformation of indica rice cultivars using binary and superbinary vectors. Aust J Plant Physiol 26:311-324.
Khanna HK, Raina SK (2002) Elite indica transgenic rice plants expressing modified Cry 1 Ac endotoxin of Bacilllus thuringiensis show enhanced resistance to yellow stem borer (Scirpophaga incertulas). Transgenic Res 11:411-423.
Kogl F, Haagen-Smit AJ, Erxleben H (1934) Uber ein neues auxin ("Heteroauxin") aus Harn. Z Physiol Chem 228:90-103.
Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43(10): 1096-1105.
Komatsuda T, Annaka T, Oka S (1993) Genetic mapping of a quantitative trait locus (QTL) that enhances the shoot differentiation rate in Hordeum vulgare L.. Theor Appl Genet 86:713-720.
Konishi S, Izawa T, Lin SY, Ebana K. Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312(5778): 1392-1396.
Koornneef M, Bade J, Hanhart C, Horsman K, Schel J, Soppe W, Verkerk R, Zabel P (1993) Characterization and mapping of a gene controlling shoot regeneration in tomato. Plant J 3(1):131-141.
Krens FA, Molendijk L, Wullems GJ, Schilperoot RA (1982) In vitro transformation of plant protoplasts with Ti-plasmid DNA. Nature 296:72-74.
Kumar KK, Maruthasalam S, Loganathan M, Sudhakar D, Balasubramanian P (2005) An improved Agrobacterium-mediated transformation protocol for recalcitrant elite indica rice cultivars. Plant Mol Biol Rep 23:67-73.
Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V (2001) Genetic transformation of Hela cells by Agrobacterium. Proc Natl Aca Sci 98:1871-1876.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12. doi:10.1186/gb-2004-5-2-rl2.
Kwon YS, Kim KM, Eun MY, Sohn JK (2000) Quantitaive trait loci mapping associated with plant regeneration ability from seed derived calli in rice (Oryza saliva L.). Mol Cells 11(1):64-67.
Kwon YS, Eun MY, Sohn JK (2002) Marker-assisted selection for identification of plant regeneration ability of seed-derived calli in rice (Oryza sativa L.). Mol Cells 12(1):103-106.
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics,121:185-199.
Lee K, Jeon H, Kim M (2002) Optimization of a mature embryo-based in vitro culture system for high-frequency somatic embryogenic callus induction and plant regeneration from japonica rice cultivars. Plant Cell Tiss Org Cult 71:237-244.
Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science, 311(5769):1936-1939.
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858.
Li RQ, Li YR, Fang XD, Yang HM, Wang J, Kristiansen K, Wang J (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124-1132.
Li Z, Duan SH, Kong J, Li SQ, Li YS, Zhu YG (2007) A single genetic locus in chromosome 1 controls conditional browning during the induction of calli from mature seeds of Oryza sativa ssp. indica. Plant Cell Tiss Organ Cult 89:237-245.
Liao PY, Lee KH (2010) From SNPs to functional polymorphism:The insight into biotechnology applications. Bilchem Eng J 49:149-158.
Lin Z, Hattori K (1998) Inheritance of high shoot regeneration ability from seed callus in a rice cultiva Joshu. Breeding Sci 48:41-44.
Lin YJ, Zhang QF (2005) Optimising the tissue culture conditions for high efficiency transformation of indica rice. Plant Cell Rep 23:540-547.
Liu J, Eck JV, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Aca Sci 99:13302-13306.
Liu RH, Meng JL (2003) MapDraw:a Microsoft Excel macro for drawing genetic linkage maps based on given genetic linkage data. Heraditas (Beijing) 25(3):317-321.
Low PS, Merida JR (1996) The oxidative burst in plant defense:function and signal transduction. Physiol Plant 96:533-42.
Loyola-Vargas VM, De-la-Pefia C, Galaz-Avalos RM, Quiroz-Figueroa FR (2008) Plant tissue culture. Molecular Biomethods Handbook.2nd Edition 875-904.
Lu L, Wu X, Yin X, Morrand J, Chen X, Folk WR, Zhang Z (2009) Development of marker-free transgenic sorghum [Sorghum bicolour (L.) Moench] using standards binary vectors with bar as a selectable marker. Plant Cell Tiss Organ Cult 99:97-108.
Luo Z, Ray W (1988) A simple method for the transformation of rice via the pollen-tube pathway. Plant Mol Biol Reporter 6:165-174.
Manninen OM (2000) Associations between anther-culture response and molecular markers on chromosomes 2H.3H and 4H of barley (Hordeum vulgare L.). Theor Appl Genet 100:57-62.
Mano Y, Takahashi H, Sato K, Takeda K (1996) Mapping genes for callus growth and shoot regeneration in barley. Breeding Sci 46:137-142.
Mano Y, Komatsuda T (2002) Identification of QTLs controlling tissue-culture traits in barley (Hordeum vulgare L.). Theor Appl Genet 105(5):708-715.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim KB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg J,M (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
Matthews PR, Wang MB, Waterhouse PM, Thornton S, Fieg SJ, Gubler F, Jacoben JV (2001) Marker gene elimination from transgenic barley, using co-transformation with adjacent'twin T-DNAs'on a standard Agrobacterium transformation vector. Mol Breeding 7:195-202.
McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) (2008) Gene Nomenclature System for Rice. Rice 1(1):72-84.
Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31-46.
Millicent E, Thoday JM (1960) Gene flow and divergence under disruptive selection. Science 131(3409):1311-1312.
Mir KU (2009) Sequencing genomes:from individuals to populations. Briefings Funct Genomics & Proteomics 8(5):367-378.
Mohanty A, Kathuria H, Ferjani A, Sakamoto A, Mohanty P, Murata N, Tyagi AK (2002) Transgenics of an elite indica rice variety Pusa Basmati I harbouring the codA gene are highly tolerant to salt stress. Theor Appl Genet 106:51-57.
Mouchel CF, Briggs GC, Hardtkel CS (2004) Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. Genes & Dev 18:700-714.
Muir WH, Hildebrandt AC, Riker AJ. (1954) Plant tissue cultures produced from isolated single cells. Science 119:877-8.
Mufioz-Amatriain M, Castillo AM, Chen XW, Cistue L, Valles MP (2008) Identification and validation of QTLs for green plant percentage in barley(Hordeum vulgare L.) anther culture. Mol Breeding 22:119-129.
Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473-497.
Murigneux A, Bentolila S, Hardy T, Baud S, Guitton C, Jullien H, Tahar SB, Freyssinet G, Beckert M (1994) Genotypic variation of quantitative trait loci controlling in vitro androgenesis in maize. Genome 37(6):970-976.
Nadeau JH, Frankel WN (2000) The roads from phenotypic variation togene discovery:mutagenesis versus QTLs. Nat Genet 25:381-384.
Nadolska-Orczyk A, Malepszy S (1989) In vitro culture of Cucumis sativus L.7. Genes controlling plant regeneration. Theor Appl Genet 78:836-840.
Nayak P, Basu D, Das S, Basu A, Ghosh D, Ramakrishnan NA, Ghosh M, Sen SK (1997) Transgenic elite indica rice plants expressing CrylAc-endotoxin of Bacillus thuringiensis are resistant against yellow stem borer (Scirpophaga incertulas). Proc Natl Acad Sci 94:2111-2116.
Nickerson DA, Taylor SL, Weiss KM, Clark AG, Hutchinson RG, Stengard J, Salomaa V, Vartiainen E, Boerwinkle E, Sing CF (1998) DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat Genet 19:233-240.
Ning Z, Cox AJ, Mullikin JC (2001) SSAHA:A fast search method for large DNA databases. Genome Res 11:1725-1729.
Nishimura A, Ashikari M, Lin S, Takashi T, Angeles ER, Yamamoto T, Matsuoka M (2005) Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. Proc Natl Acad Sci 102:11940-11944.
Nishimura A, Aichi I, Matsuoka M (2007) A protocol for Agrobacterium-mediated transformation in rice. Nat Protoc 1:2796-2802.
Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J, Purugganan MD (2004) Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167:1361-1369.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriew IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Paterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556.
Paterson AH (1995) Molecular dissection of quantitative traits:progress and prospects. Genome Res (5):321-333.
Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721-726.
Peng JJ, Hodges TK (1989) Genetic analysis of plant regeneration in rice(Oryza sativa L.). In Vitro Cell Dev Biol 25(1):91-94.
Peleman JD, Wye C, Zethof J, S(?)rensen AP, Verbakel H, Oeveren J, Gerats T, Voort JR (2005) Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis:A Method for High-Resolution Mapping of QTL Within a Single Population. Genetics 171:1341-1352.
Price HA (2006) Believe it or not, QTLs are accurate. Trends Plant Sci 11(5): 213-216.
Rao AQ, Bakhsh A, Kiani S, Shahzad K, Shahid AA, Husnain T, Riazuddin S (2009) The myth of plant transformation. Biotechnology Adv 27:753-763.
Rashid H, Yokoi S, Toriyama K, Hinata K (1996) Transgenic plant production mediated by Agrobacterium in incdica rice. Plant Cell Rep 15:727-730.
Raveendar S, Premkumar A, Ignacimuthu S, Agastian P (2008) Effects of sea water on callus induction and regeneration of rice genotypes. Int J Integ Biol 3(2): 92-95.
Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37(10):1141-1146.
Rice P, Longden I, Bleasby A (2000) EMBOSS:the European Molecular Biology Open Software Suite. Trends Genet 16:276-277.
Rothberg JM, Leamon JH (2008) The development and impacts of 454 sequencing. Nat Biotechnol 28:426-428.
Raveendar S, Premkumar A, Ignacimuthu S, Agastian P (2008) Effect of sea water on callus induction and regeneration of rice genotypes. In J Integrative Biol 3(2):92-95.
Saika H, Toki S (2010) Matur seed-derived callus of the model indica rice variety Kasalath is highly competent in Agrobacterium-mediated transformation. Plant Cell Rep 29(12):1351-1364.
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463-5467.
Schiantarelli E, Pena AD, Candela M (2001) Use of recombinant inbred lines (RILs) to identify, locate and map major genes and quantitative trait loci involved with in vitro regeneration ability in Arabidopsis thaliana. Theor Appl Genet 102:335-341.
Schlappi M, Hohn B (1992) Competence of immature maize embryos for Agrobacterium-mediated gene transfer. Plant Cell 4:7-16.
Schleiden MJ (1838) Beitrage zur Phytogenesis. Arch Anat Physiol Wiss Med (J Muller):137-76.
Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pastemak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Mink P, Reily AD, Courtney L, Krschowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson AM, Gillam B, Chen WZ, Yan L, Higginbotham J, Cardenas M, Waligorski J, Allpebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane M, Henke J, Wang T, Ruppet J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse L, Collura K, Kudrna D, Currie K, He RF, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dijmic Z, Kim W, Talag J, Ziccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento, Zutavem T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMchan L, Buren PV, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carptia NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Plnnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome:complexity, diversity, and dynamics. Science 326:1112-1115.
Schwann T (1839) Mikroscopische Untersuchungen fiber die Ubereinstimmung in der Struktur und dem Wachstum des Tiere und Pflanzen. W Engelmann:Leipzig:No 176.
Sergeeva LI, Keurentjes JJB, Bentsink L, Vonk J, Plas LHW, Koornneef M, Vreugdenhil D (2006) Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis. Proc Natl Acad Sci 103: 2994-2999.
Shan XJ, Zhu MZ, Shi M, Gao JP, Lin HX (2009) Fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice(Oryza rufipogon Griff). Theor Appl Genet 119:827-836.
Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135(3):1198-1205.
Shendure J, Porreca GJ, Reppas NB, Lin XX, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732.
Shendure J, Li H (2008) Next generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP:The NCB1 database of genetic variation. Nucleic Acids Res 29: 308-311.
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023-1028.
Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39(5):623-630.
Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316:112-115.
Taguchi-Shiobara F, Lin SY, Tanno K, Komatsuda T, Yano M, Sasaki T, Oka S (1997a) Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L.. Theor Appl Genet 95:823-833.
Taguchi-Shiobara F, Komatsuda T, Oka S (1997b) Comparison of two indices for evaluating regeneration ability in rice (Oryza sativa L.) through a diallel analysis. Theor Appl Genet 94:378-382.
Taguchi-Shiobara F, Yamamoto T, Yano M, Oka S (2006) Mapping QTLs that control the performance of rice tissue culture and evalution of derived near-isogenic lines. Theor Appl Genet 112:968-976.
Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the a subunit of protein kinase CK2. Proc Natl Acad Sci USA 98(14):7922-7927.
Takeuchi Y, Abe T, Sasahara T (2000) RFLP Mapping of QTLs influencing shoot regeneration from mature seed-derived calli in rice. Crop Sci 40:245-247.
Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360-1364.
Thimann KV (1935) On the plant hormone produced by Rhizopus suinus. J Biol Chem 109:279-291.
Tingay S, McElroy D, Kalla R, Fieg S, Wang M, Thornton S, Brettell R (1997) Agrobacterium tumefaciens-mediated barley transformation. Plant J 11:1369-1376.
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphism associate with variation in flowering time. Nat Genet 28:286-289.
Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J 47:969-976.
Toledano MB, Fourquet S, D'Autrdaux B (2010) Cellular Signaling by Reactive Oxygen Species:Biochemical Basis and Physiological Scope.In:Ari Sitaramayys. Signal transduction:Pathways, Mechanism and Diseases:313-314.
Torp AM, Hansen AL, Andersen SB (2001) Chromosomal regions associated with green plant regeneration in wheat(Triticum aestivum L.) anther culture. Euphytica 119:377-387.
Travella S, Ross SM, Harden J, Everett C, Snape JW, Harwood WA (2005) A comparison of transgenic barley lines produced by particle bombardment and Agrobacterium-mediated techniques. Plant Cell Reports 23:780-789.
Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC Gene Regulating Senescence Improves Grain Protein, Zinc, and Iron Content in Wheat. Science 314:1298-1301.
Ueda T, Sato T, Hidema J, Hirouchi T, Yamamoto K, Kumagai T, Yano M (2005) qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase. Genetics 171(4):1941-1950.
Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Halet CS, Buys N, Tally M, Andersson G, Georges M, Andersson L (2003) A regulatory mutation in IGF2 causes a major QTL dffect on muscle growth in the pig. Nature 425:832-836.
Van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JNAMR, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato:Providing a framework for accelerate gene isolation and a genomewide physical map. Genetics 173:1075-1087.
Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522-530.
Vasil V, Castillo AM, Fromm ME, Vasil IK (1992) Herbicide resistant fertile transgenic wheat plants obtained by microprojectile bombardment of regenerable embryogenic callus. Nat BioTechnol 10:667-674.
Vasil V, Hildebrandt AC (1965) Differentiation of tobacco plants from single, isolated cells in microcultures. Science 150:89-892.
Vasil V, Hildebrandt AC (1967) Further studies on the growth and differentiation of single, isolated cells of tobacco in vitro. Planta 75:139-151.
Vasil IK (2008) A history of plant biotechnology:from the cell theory of Schldiden and Schwann to biotech crops. Plant Cell Rep 27:1423-1440.
Vasil IK, Vasil V (1992) Advances in cereal protoplast research. Physiol Plant 85:279-283.
Verdeil JL, Alemanno L, Niemenak N, Tranbarger TJ (2007) Pluripotnet versus totipotent plant stem cells:dependence versus autonomy. Trends Plant Sci 12(6):245-252.
Wan Y, Rocheford TR, Widholm JM (1992) RFLP analysis to identify putative chromosomal regions involved in the anther culture response and callus formation of maize. Theor Appl Genet 85:360-365.
Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H, Ma H, Zhang G, He Z (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genet 40(11):1370-1374.
Wang L, Wang AH, Huang XH, Zhao Q, Dong GJ, Qian Q, Sang T, Han B (2010) Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theor Appl Genet 122:327-340.
Wang S, Basten CJ, Zeng ZB (2007) Windows QTL Catergrapher 2.5 Department of Statistics. North Carolina State University, Raleign.
Wei Chi (2006) Enhancement of NADP-Malic Enzyme in Transgenic Rice Induced the Accumulation of Reactive Oxygen Species. Russ J Plant Physl 53(3):325-331.
Went FW (1928) Wuchstoff und Wachstum. Rec Trav Bot Neerl 25:1-116.
White PR (1943) A handbook of plant tissue culture. Jacques Cattell Press, Tempe, Arizona.
White PR (1963) The cultivation of animal and plant cells,2nd edn. The Ronald Press. New York.
Wu WR, Li WM, Tang DZ, Lu HR, Worland AJ (1999) Time-Related Mapping of Quantitative Trait Loci Underlying Tiller Number in Rice. Genetics 151:297-303.
Xia GM, Li ZY, He CX, Chen HM, Brettell R (1999) Transgenic plant regeneration from wheat(Triticum aestivum L.) mediated by Agrobacterium tumefaciens. Acta Phytophologica Sinica 25(1):22-28.
Xu JJ, Zhao Q, Du PN, Xu CW, Wang BH, Feng Q, Liu QQ, Tang SZ, Gu MH, Han B, Liang GH (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 11:656-669.
Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705-708.
Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu s, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761-767.
Yan JQ, Zhu J, He CX (1998) Quantitative trait loci analysis for the developmental behavior of tiller number in rice(Oryza sativa. L.) Theor Appl Genet 97:267-274.
Yang C, Zhao T, Yu D, Gai J (2011) Mapping QTLs for tissue culture response in soybean (Glycine max (L.) Merr.) Mol Cells 32:337-342.
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000)Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12(12):2473-2484.
Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145-153.
Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, Xie D, Sun C (2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891-898.
Yu HH, Xie WB, Wang J, Xing YZ, Xu CG, Li XH, Xiao JH, Zhang QF (2011) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE 6(3):e17595.
Yu J, Hu SN, Wang J, Wong GKS, Li WG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Huang XG, Li WJ, Li J, Liu ZW, Li L, Liu JP, Qi QH, Liu JS, Li L, Li T, Wang XG, Lu H, Wu TT, Zhu M, Ni PX, Han H, Dong W, Ren XY, Feng XL, Cui P, Li XR, Wang H, Xu X, Zhai WX, Xu Z, Zhang JS, He SJ. Zhang JG, Xu JC, Zhang KL, Zheng XW, Dong JH, Zeng WY, Tao L, Ye J, Tan J, Ren XD, Chen XW, He J, Liu DF, Tian W, Tian CG, Xia HA, Bao QY, Li G, Gao H, Cao T, Wang J, Zhao WM, Li P, Chen W, Wang XD, Zhang Y, Hu JF, Wang J, Liu S, Yang J, Zhang GY, Xiong YQ, Li XJ, Mao L, Zhou CS, Zhu Z, Chen RS, Hao BL, Zheng WM, Chen SY, Guo W, Li GJ, Liu SQ, Tao M, Wang J, Zhu LH, Yuan LP, Yang HM (2002) A draft sequence of the rice genome (Oryza saliva L. ssp. indica). Science 296 (5565):79-92.
Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17:155-160.
Zaidi MA, Narayanan M, Sardana R, Taga I, Postel S, Johns R, McNulty M, Mottiar Y, Mao J, Loit E, Altosaar I (2006) Optimizing tissue culture media for efficient transformation of different indica rice genotypes. Agronomy Res 4(2): 563-575.
Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci 90:10972-10976.
Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
Zeng ZB, Kao CH, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279-289.
Zhang J, Chiodini R, Badr A, Zhang GF (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38:95-109.
Zhang Z, Ober JA, Kliebenstein DJ (2006) The Gene Controlling the Quantitative Trait Locus EPITHIOSPECIFIER MODIFIER1 Alters Glucosinolate Hydrolysis and Insect Resistance in Arabidopsis. Plant Cell 18:1524-1536.
Zhang J, Xu RJ, Elliott MC, Chen DF (1997) Agrobacterium-mediated transformation of elite indica and japonica rice cultivars. Mol Biotechnol 8:223-231.
Zhao LN, Zhou HJ, Lu LX, Liu L, Li XH, Lin YJ, Yu SB (2009) Identification of quantitative trait loci controlling rice mature seed culturability using chromosomal segment substitution lines. Plant Cell Rep 28:247-256.
Zhao ZY, Cai T, Tagliani L, Miller M, Wang N, Pang H, Rudert M, Schroeder S, Hondred D, Seltzer J, Pierce D (2000) Agrobacterium-mediated sorghum transformation. Plant Mol Biol 44:789-798.
Zhao ZY, Glassman K, Sewalt V, Wang N, Miller M, Chang S, Thompson T, Catron S, Wu E, Bidney D, Kedebe Y, Jung R (2003) Nutritionally improved transgenic sorghum. In:Vasil IK (ed) Plant biotechnology 2002 and beyond. Proceedings of the 10th IAPTC & B Congress. Kluwer Academic Publishers, pp 413-416.
Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Yong ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123-1134.