基于海岛棉纤维发育EST的分子标记开发及遗传图谱与基因组序列整合分析
|
摘要
棉花是目前世界上最为重要的天然纤维来源。海岛棉和陆地棉是两大四倍体栽培棉种。与陆地棉相比,海岛棉为开发高档、高附加值的新型纺织品提供了重要的纤维材料,并对优化棉花产业结构起着尤为重要的经济作用。同时,海岛棉又是优质棉纤维基因的重要供体。但是相对陆地棉其广泛的适应性和高产特性,海岛棉则生育期长,成熟较晚,棉铃小且产量低。目前,棉纤维发育的基因组学研究和生物信息学分析将有效用于发掘纤维品质基因并阐明棉纤维发育机制,并用于分子设计育种技术创制优质棉资源材料,对改善纤维品质具有极为重要的意义。本文基于棉纤维发育EST序列进行分子标记开发及棉属不同棉种来源EST序列同源性生物信息学分析研究,主要研究结果如下：
1.简单重复序列SSRs于转录组中大量存在,具有较高的多态性且已广泛的应用于分子标记的开发。本研究基于海岛棉-3-5DPA和6-25DPA纤维发育时期的2个cDNA文库大规模测序所得的ESTs序列数据,鉴定出638个SSRs和13,275个海陆同源EST序列中InDels信息。进而开发出海岛棉380个EST-SSRs及2,160个海陆EST-InDels分子标记。其中随机合成90对EST-InDels标记引物用于海陆多态PCR电泳检测,结果显示,64对引物扩增位点具有海陆种间或种内亚组间多态性,20对引物未检测到多态性,6对引物无扩增产物。随机选择的9对EST-InDel标记产生的多态位点进一步测序证实其InDel的真实性。
2.海陆间EST序列的InDel差异直接与其功能相关。进一步对检测到InDels信息的13,275个海陆同源EST序列进行基因功能注释、基因本体学GO分析和KEGG代谢途径分析。生物信息学分析显示涉及蔗糖代谢以及次生壁合成过程的相关纤维发育基因,如蔗糖合酶、纤维素合酶及糖基转移酶等基因,在海陆间存在InDels差异。这些基因转录产物的序列差异可能与海陆纤维品质表型差异相关。同时也检测到种子脂类代谢和蛋白代谢相关的基因。研究结果为揭示棉纤维及棉籽发育关键基因以及阐明其基因网络作用机理奠定了基础。
3.棉花四倍体棉种大约于1-2百万年前由自然发生的两个二倍体A,D基因组杂交后经过多倍化形成,棉属不同棉种是共同起源,单元进化的。不同棉种来源的EST序列同源分析,也证明棉属不同棉种基因序列的保守性及基因内部位点的变异性。本研究中,基于棉属四个棉种(包括两个四倍体棉种：陆地棉和海岛棉；两个二倍体棉种：亚洲棉和雷蒙德氏棉)来源的ESTs序列聚类组装,分析了不同棉种ESTs重叠群Contigs的物种分布,发现来源于雷蒙德氏棉D基因组ESTs,50.77%的序列可以和四倍体聚类到一个重叠群Contig中,而亚洲棉A基因组仅17.15%的ESTs参与四倍体的聚类,说明雷蒙德氏棉与四倍体Dt基因组间较近的亲缘关系,而亚洲棉与四倍体At基因组亲缘关系则相对较远。
4.通过对包含四倍体和二倍体棉种的四个不同基因组组成的重叠群进行SNPs/InDels挖掘,发现了高可信度的SNP/InDels位点信息,随后通过单体型分析,鉴定了A/At、D/Dt同源基因,发现在A/At与D/Dt差异位点具有高度保守性外,大部分重叠群At和Dt基因组内部均各自产生了许多新的变异位点,说明异源四倍体At、Dt基因组在基因进化中呈现独立进化,且在多倍化过程中产生了更多适应性进化的结构变异。基于海陆同源基因的SNP差异,开发出针对1340个基因的海陆差异SNP标记,用于基因结构及表达水平分析研究。
5.鉴于棉花多倍体基因组进化特征,使得棉花基因组数据中存在大量同源序列,造成了不同来源SSRs分子标记的冗余性。本研究针对CMD收录的棉花SSRs标记以及本实验室新开发的NAU系列标记,共计15,810对引物进行冗余性分析。共获得1,530冗余组,含有4,034对引物。基于获得的冗余引物组,可开发1,530通用性SSRs分子标记,整合余下的非冗余SSRs标记,获得13,306对非冗余SSRs标记。
6.基于美国JGI释放的雷蒙德氏棉基因组测序数据,将已开发的所有SSRs标记进行了物理定位。结果显示,9,697个SSRs标记引物成功锚定在雷蒙德氏棉全基因组,分布在不同的染色体上。其中8,809对引物特异的锚定在单一染色体区间,26对标记引物锚定在同一染色体多个位点,而862对引物则分布在不同染色体上。根据模拟扩增产物大小分析,9,124个SSRs分子标记的产物大小位于500bp阈值内,是高准确性定位位点。产物大小位于500-1000bp内的中度准确性定位的标记有369个SSRs标记,而>=2000bp的物理定位可靠性低的标记有204个。分子标记的物理定位结果将为后续目标基因图位克隆,QTL精细定位等研究提供整合标记资源。
7.基于美国JGI释放的雷蒙德氏棉基因组测序数据,将我室构建的含3,414位点的海陆高密度遗传图谱和雷蒙德氏棉全基因组物理序列进行整合。2,696对(81.10%)标记引物成功被锚定在雷蒙德氏棉13对染色体基因组上。其中,大部分均为特异性锚定(2,236,82.94%)。分析发现D/Dt基因组具有较高的共线性,而在At2/At3, At4/At5染色体间则存在较大区域的染色体易位。图谱整合数据为棉花四倍体棉种全基因组测序,重要性状QTL及候选基因精细定位、图位克隆及比较基因组学等研究奠定了基础。
Cotton is the most important source of natural fiber in the world. Gossypium barbadense and Gossypium hirsutum are two cultivated tetraploid species. G. barbadense provides vital fiber material for top-grade and high value new textile, and plays crucial economic role in optimizing cotton industrial utilization. Meanwhile G. barbadense is the major gene donor for high quality fiber. However, compared with G. hirsutum which is more adaptable and productive, G. barbadense has longer growth period, smaller boll and lower yield. The genomics study and bioinformatics analysis of fiber development will effectively unearth the gene of fiber quality and illustrate the mechanism of fiber development. Further, new elite fiber quality accessions will be enhanced by molecular breeding by design. In this paper, new and nonredundant molecular markers were developed and exploited based on EST sequence of fiber development and bioinformatics analysis among paralogous loci from different cotton species were carried out based on EST sequences. The main results were as following:
1. Larger numbers of SSRs exist in the transcriptome, they have high polymorphism and been widely used in the development and exploitation of molecular marker. Based on Gossypium barbadense fiber ESTs and homology analysis against G. hirsutum ESTs,638SSRs and13,275InDels information were mined. Then380non-redundant EST-SSRs of G. barbadense and2,160EST-InDels molecular markers between G. barbadense and G. hirsutum were exploited.90pairs EST-InDels marker primer pairs selected randomly were synthesized for interspecific or intersubgenome polymorphism confirmation by PCR electrophoresis detection. The results indicated that64primer pairs had certain polymorphism between the two species or between subgroup within species;20pairs primer did not show polymorphism, and6pairs had no amplification product.9polymorphism loci were selected to confirm the efficiency and accuracy of InDel.
2. The InDel difference of EST sequence between two species on the molecular level has correlation with its function. Gene function annotation, Gene Ontology analysis and KEGG metabolic pathway analysis were carried out with those13,275ESTs containing InDel. Bioinformatics analysis indicated that fiber development genes related to sucrose metabolism and secondary wall synthesis process such as sucrose synthase gene, cellulose synthase gene and glycosyl transferase gene had InDels difference between G. barbadense and G. hirsutum. These differences on the transcriptional level may be related to the fiber quality difference between the two species. These results laid the foundation for discovering the key genes of fiber development and elucidating the genes network function mechanism.
3. The tetraploid cotton species in Gossypium were formed about1-2million years ago by naturally happened genomic hybridization of two diploid A and D genome and then polyploidization. Different species in Gossypium have a common descent. EST homology analysis of different cotton species also showed the Higher-level sequence conservation between different cotton species and between the A-and D-subgenomes in tetraploid cotton. The Clustering analysis based on four species ESTs sequence in Gossypium, including two tetraploid cotton species, G. barbadense and G. hirsutum, and two diploid cotton species, G. arboreum and G. raimondii, indicated that50.77%sequence of D genome ESTs from G. raimondii can cluster with one contig of tetraploid, while only17.15%ESTs of A genome from G. arboreum cluster with tetraploid. These results implied that there were a close genetic relationship between G. raimondii and tetraploid Dt genome, whereas remote affinity existed between G. arboreum and tetraploid At genome in transcriptional level.
4. High reliability SNP/InDels site information was detected by SNPs/InDels mining of contig from four genomes of teraploid and diploid. Further haplotype analysis were carried out and identified A/At, D/Dt homologous gene. The results showed that except A/At, D/Dt variation had high conservatism, most of the contig had a lot of new intragenomic variation sites within At or Dt genome. These demonstrated that allotetraploid At and Dt genome evolve separately during the gene evolution and more adaptive evolutional structural variation has emerged. As a result, SNP markers distinguishing1340homologous genes between G. barbadense and G. hirsutum were further developed.
5. Because of polyploidy genome of Gossypium, there were a large number of homologous sequences which caused redundancy of different source SSRs molecular markers. According to Gossypium SSRs markers published by CMD, in addition to NAU series markers newly developed by our laboratory, total15,180SSR primers pairs were used for redundancy analysis. As a result,1,530redundancy groups were obtained and there were4,034primers pairs. Based on the redundancy primer groups we obtained,1,530universe SSRs molecular markers can be developed. Integrated with the rest non-redundant SSRs markers, non-redundant SSRs12,676primer paris were obtained.
6. Based on released G. raimondii genomic sequencing data of JGI, all the developed SSRs were physically mapped. The results indicated that9,697SSRs marker primers were successfully anchored to the G. raimondii scaffolds with scattered in different chromosomes. Among them,8,809pairs anchored within one chromosome,26pairs existed different positions on the same chromosome, while the rest862pairs scattered in different chromosomes. According to amplification products size,9,124SSRs molecular markers were mapped with high accuracy whose product size were smaller than500bp,369SSRs were mapped with moderate accuracy whose product size were between500and1000bp, and204were mapped with low reliability whose product size were larger than2000bp. The physical mapping results of molecular markers will provide integrated genomic resources for further molecular breeding studies such as map-based cloning, QTLfine mapping, and so on.
7. Based on released G. raimondii genomic sequencing data of JGI,3,414marker loci from high density tetraploid cultivated cotton species genetic map constructed by our laboratory were further integrated with G. raimondii whole genome.2,696marker loci (81.10%) were successfully anchored to13chromosomes of G. raimondii. Among them, most were specifically anchored (2,236,82.94%). The results demonstrated that D/Dt genome had high colinearity, while At2/At3, At4/At5had certain chromosomal translocation. Integrated data laid foundation for tetraploid whole genome sequencing, fine mapping and map-based cloning of elite genes and QTL, and comparative genomics in Gossypium.
1.简单重复序列SSRs于转录组中大量存在,具有较高的多态性且已广泛的应用于分子标记的开发。本研究基于海岛棉-3-5DPA和6-25DPA纤维发育时期的2个cDNA文库大规模测序所得的ESTs序列数据,鉴定出638个SSRs和13,275个海陆同源EST序列中InDels信息。进而开发出海岛棉380个EST-SSRs及2,160个海陆EST-InDels分子标记。其中随机合成90对EST-InDels标记引物用于海陆多态PCR电泳检测,结果显示,64对引物扩增位点具有海陆种间或种内亚组间多态性,20对引物未检测到多态性,6对引物无扩增产物。随机选择的9对EST-InDel标记产生的多态位点进一步测序证实其InDel的真实性。
2.海陆间EST序列的InDel差异直接与其功能相关。进一步对检测到InDels信息的13,275个海陆同源EST序列进行基因功能注释、基因本体学GO分析和KEGG代谢途径分析。生物信息学分析显示涉及蔗糖代谢以及次生壁合成过程的相关纤维发育基因,如蔗糖合酶、纤维素合酶及糖基转移酶等基因,在海陆间存在InDels差异。这些基因转录产物的序列差异可能与海陆纤维品质表型差异相关。同时也检测到种子脂类代谢和蛋白代谢相关的基因。研究结果为揭示棉纤维及棉籽发育关键基因以及阐明其基因网络作用机理奠定了基础。
3.棉花四倍体棉种大约于1-2百万年前由自然发生的两个二倍体A,D基因组杂交后经过多倍化形成,棉属不同棉种是共同起源,单元进化的。不同棉种来源的EST序列同源分析,也证明棉属不同棉种基因序列的保守性及基因内部位点的变异性。本研究中,基于棉属四个棉种(包括两个四倍体棉种：陆地棉和海岛棉；两个二倍体棉种：亚洲棉和雷蒙德氏棉)来源的ESTs序列聚类组装,分析了不同棉种ESTs重叠群Contigs的物种分布,发现来源于雷蒙德氏棉D基因组ESTs,50.77%的序列可以和四倍体聚类到一个重叠群Contig中,而亚洲棉A基因组仅17.15%的ESTs参与四倍体的聚类,说明雷蒙德氏棉与四倍体Dt基因组间较近的亲缘关系,而亚洲棉与四倍体At基因组亲缘关系则相对较远。
4.通过对包含四倍体和二倍体棉种的四个不同基因组组成的重叠群进行SNPs/InDels挖掘,发现了高可信度的SNP/InDels位点信息,随后通过单体型分析,鉴定了A/At、D/Dt同源基因,发现在A/At与D/Dt差异位点具有高度保守性外,大部分重叠群At和Dt基因组内部均各自产生了许多新的变异位点,说明异源四倍体At、Dt基因组在基因进化中呈现独立进化,且在多倍化过程中产生了更多适应性进化的结构变异。基于海陆同源基因的SNP差异,开发出针对1340个基因的海陆差异SNP标记,用于基因结构及表达水平分析研究。
5.鉴于棉花多倍体基因组进化特征,使得棉花基因组数据中存在大量同源序列,造成了不同来源SSRs分子标记的冗余性。本研究针对CMD收录的棉花SSRs标记以及本实验室新开发的NAU系列标记,共计15,810对引物进行冗余性分析。共获得1,530冗余组,含有4,034对引物。基于获得的冗余引物组,可开发1,530通用性SSRs分子标记,整合余下的非冗余SSRs标记,获得13,306对非冗余SSRs标记。
6.基于美国JGI释放的雷蒙德氏棉基因组测序数据,将已开发的所有SSRs标记进行了物理定位。结果显示,9,697个SSRs标记引物成功锚定在雷蒙德氏棉全基因组,分布在不同的染色体上。其中8,809对引物特异的锚定在单一染色体区间,26对标记引物锚定在同一染色体多个位点,而862对引物则分布在不同染色体上。根据模拟扩增产物大小分析,9,124个SSRs分子标记的产物大小位于500bp阈值内,是高准确性定位位点。产物大小位于500-1000bp内的中度准确性定位的标记有369个SSRs标记,而>=2000bp的物理定位可靠性低的标记有204个。分子标记的物理定位结果将为后续目标基因图位克隆,QTL精细定位等研究提供整合标记资源。
7.基于美国JGI释放的雷蒙德氏棉基因组测序数据,将我室构建的含3,414位点的海陆高密度遗传图谱和雷蒙德氏棉全基因组物理序列进行整合。2,696对(81.10%)标记引物成功被锚定在雷蒙德氏棉13对染色体基因组上。其中,大部分均为特异性锚定(2,236,82.94%)。分析发现D/Dt基因组具有较高的共线性,而在At2/At3, At4/At5染色体间则存在较大区域的染色体易位。图谱整合数据为棉花四倍体棉种全基因组测序,重要性状QTL及候选基因精细定位、图位克隆及比较基因组学等研究奠定了基础。
Cotton is the most important source of natural fiber in the world. Gossypium barbadense and Gossypium hirsutum are two cultivated tetraploid species. G. barbadense provides vital fiber material for top-grade and high value new textile, and plays crucial economic role in optimizing cotton industrial utilization. Meanwhile G. barbadense is the major gene donor for high quality fiber. However, compared with G. hirsutum which is more adaptable and productive, G. barbadense has longer growth period, smaller boll and lower yield. The genomics study and bioinformatics analysis of fiber development will effectively unearth the gene of fiber quality and illustrate the mechanism of fiber development. Further, new elite fiber quality accessions will be enhanced by molecular breeding by design. In this paper, new and nonredundant molecular markers were developed and exploited based on EST sequence of fiber development and bioinformatics analysis among paralogous loci from different cotton species were carried out based on EST sequences. The main results were as following:
1. Larger numbers of SSRs exist in the transcriptome, they have high polymorphism and been widely used in the development and exploitation of molecular marker. Based on Gossypium barbadense fiber ESTs and homology analysis against G. hirsutum ESTs,638SSRs and13,275InDels information were mined. Then380non-redundant EST-SSRs of G. barbadense and2,160EST-InDels molecular markers between G. barbadense and G. hirsutum were exploited.90pairs EST-InDels marker primer pairs selected randomly were synthesized for interspecific or intersubgenome polymorphism confirmation by PCR electrophoresis detection. The results indicated that64primer pairs had certain polymorphism between the two species or between subgroup within species;20pairs primer did not show polymorphism, and6pairs had no amplification product.9polymorphism loci were selected to confirm the efficiency and accuracy of InDel.
2. The InDel difference of EST sequence between two species on the molecular level has correlation with its function. Gene function annotation, Gene Ontology analysis and KEGG metabolic pathway analysis were carried out with those13,275ESTs containing InDel. Bioinformatics analysis indicated that fiber development genes related to sucrose metabolism and secondary wall synthesis process such as sucrose synthase gene, cellulose synthase gene and glycosyl transferase gene had InDels difference between G. barbadense and G. hirsutum. These differences on the transcriptional level may be related to the fiber quality difference between the two species. These results laid the foundation for discovering the key genes of fiber development and elucidating the genes network function mechanism.
3. The tetraploid cotton species in Gossypium were formed about1-2million years ago by naturally happened genomic hybridization of two diploid A and D genome and then polyploidization. Different species in Gossypium have a common descent. EST homology analysis of different cotton species also showed the Higher-level sequence conservation between different cotton species and between the A-and D-subgenomes in tetraploid cotton. The Clustering analysis based on four species ESTs sequence in Gossypium, including two tetraploid cotton species, G. barbadense and G. hirsutum, and two diploid cotton species, G. arboreum and G. raimondii, indicated that50.77%sequence of D genome ESTs from G. raimondii can cluster with one contig of tetraploid, while only17.15%ESTs of A genome from G. arboreum cluster with tetraploid. These results implied that there were a close genetic relationship between G. raimondii and tetraploid Dt genome, whereas remote affinity existed between G. arboreum and tetraploid At genome in transcriptional level.
4. High reliability SNP/InDels site information was detected by SNPs/InDels mining of contig from four genomes of teraploid and diploid. Further haplotype analysis were carried out and identified A/At, D/Dt homologous gene. The results showed that except A/At, D/Dt variation had high conservatism, most of the contig had a lot of new intragenomic variation sites within At or Dt genome. These demonstrated that allotetraploid At and Dt genome evolve separately during the gene evolution and more adaptive evolutional structural variation has emerged. As a result, SNP markers distinguishing1340homologous genes between G. barbadense and G. hirsutum were further developed.
5. Because of polyploidy genome of Gossypium, there were a large number of homologous sequences which caused redundancy of different source SSRs molecular markers. According to Gossypium SSRs markers published by CMD, in addition to NAU series markers newly developed by our laboratory, total15,180SSR primers pairs were used for redundancy analysis. As a result,1,530redundancy groups were obtained and there were4,034primers pairs. Based on the redundancy primer groups we obtained,1,530universe SSRs molecular markers can be developed. Integrated with the rest non-redundant SSRs markers, non-redundant SSRs12,676primer paris were obtained.
6. Based on released G. raimondii genomic sequencing data of JGI, all the developed SSRs were physically mapped. The results indicated that9,697SSRs marker primers were successfully anchored to the G. raimondii scaffolds with scattered in different chromosomes. Among them,8,809pairs anchored within one chromosome,26pairs existed different positions on the same chromosome, while the rest862pairs scattered in different chromosomes. According to amplification products size,9,124SSRs molecular markers were mapped with high accuracy whose product size were smaller than500bp,369SSRs were mapped with moderate accuracy whose product size were between500and1000bp, and204were mapped with low reliability whose product size were larger than2000bp. The physical mapping results of molecular markers will provide integrated genomic resources for further molecular breeding studies such as map-based cloning, QTLfine mapping, and so on.
7. Based on released G. raimondii genomic sequencing data of JGI,3,414marker loci from high density tetraploid cultivated cotton species genetic map constructed by our laboratory were further integrated with G. raimondii whole genome.2,696marker loci (81.10%) were successfully anchored to13chromosomes of G. raimondii. Among them, most were specifically anchored (2,236,82.94%). The results demonstrated that D/Dt genome had high colinearity, while At2/At3, At4/At5had certain chromosomal translocation. Integrated data laid foundation for tetraploid whole genome sequencing, fine mapping and map-based cloning of elite genes and QTL, and comparative genomics in Gossypium.
引文
1.曹承忠,李洪连,简桂良.棉花抗黄萎病分子标记研究进展[J].中国棉花,2005,32(6)：7-10.
2.曹越.植物遗传研究与分子标记技术[J].青海农林科技,2004(2)：21-24.
3.郭瑞星,刘小红,荣廷昭,孙东发,谭振波.植物SSR标记的发展及其在遗传育种中的应用[J].玉米科学,2005,13(2)：8-11.
4.郭旺珍,张天真,丁业掌,朱一超,沈新莲,朱协飞.分子标记辅助聚合两个棉纤维高强主效QTLs的选择效果[J].遗传学报,2006,32(12)：1275-1285.
5.茎重丝,王天宇.分子标记的种类及其发展[J].生物技术通报,1999(4).
6.梁明山,曾宇,周翔,侯留记,李霞.遗传标记及其在作物品种鉴定中的应用[J].植物学通报,2001,18(3)：257-265.
7.刘春林,官春云.植物RAPD标记的可靠性研究[J].生物技术通报,1999,15(2)：31-34.
8.刘勋甲,郑用琏.遗传标记的发展及分子标记在农作物遗传育种中的运用[J].湖北农业科学,1998(1)：33-35.
9.阮成江,何祯祥,钦佩.我国农作物QTL定位研究的现状和进展[J].植物学通报,2003,20(1)：10-22.
10.孙洪,程静,詹克慧,张相武,杨艳会.ISSR标记技术及其在作物遗传育种中的应用[J].分子植物育种,2005,3(001)：123-127.
11.汪小全,邹喻苹.RAPD应用于遗传多样性和系统学研究中的问题[J].植物学报：英文版,1996,38(12)：954-962.
12.王红梅,张正英.SSR标记技术及其在植物遗传学中的应用[J].西北师范大学学报：自然科学版,2003,39(1)：113-116.
13.周延清.DNA分子标记技术在植物研究中的应用[M].化学工业出版社,2005.
14.周延清.遗传标记的发展[J].生物学通报,2000,35(5)：17-18.
15.祝水金,童旭宏,洪彩霞,季道藩,吴伟,王仁杯.三系杂交棉新组合——浙杂2号[J].中国棉花,2006,33(005)：12-13.
16.庄南生,郑成木.植物AFLP标记转化为特异PCR标记的研究进展木[J].华南热带农业大学学报,2004,10(3)：1.
17.邹喻苹,葛颂,王晓东,植物.系统与进化植物学中的分子标记[M].科学出版社,2001.
18. Adams K L, Cronn R, Percifield R, Wendel J F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing[J]. Proceedings of the National Academy of Sciences,2003,100(8):4649-4654.
19. Adams M D, Celniker S E, Holt R A, Evans C A, Gocayne J D, Amanatides P G, Scherer S E, Li P W, Hoskins R A, Galle R F, Others. The genome sequence of Drosophila melanogaster[Y]. Science, 2000,287(5461):2185-2195.
20. Alba R, Fei Z, Payton P, Liu Y, Moore S L, Debbie P, Conn J, D'Ascenzo M, Gordon J S, Rose J K, Martin G, Tanksley S D, Bouzayen M, Jahn M M, Giovannoni J. ESTs, cDNA microarrays, and gene expression profiling:tools for dissecting plant physiology and development[J]. The Plant Journal,2004,39:697-714.
21. Altschul S F, Madden T L, Schaffer A A, Zhang I, Zhang Z, Miller W, Lipman D J. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J]. Nucleic Acids Res,1997,25:3389-3402.
22. Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci A, Da Silva C, Cascardo J, Allegre M, Kuhn D, Verica J, Courtois B, Loor G, Babin R, Sounigo O, Ducamp M, Guiltinan M, Ruiz M, Alemanno L, Machado R, Phillips W, Schnell R, Gilmour M, Rosenquist E, Butler D, Maximova S, Lanaud C. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions[J]. BMC Genomics,2008,9(1):512.
23. Asamizu E, Nakamura Y, Sato S, Tabata S. A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries[J]. DNA research,2000,7(3):175-180.
24. Atwell S, Huang Y S, Vilhj A Lmsson B J, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone A M, Hu T T, Others. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines[J]. Nature,2010,465(7298):627-631.
25. Bairoch A, Apweiler R, Wu C H, Barker W C, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M. The Universal Protein Resource (UniProt).[J]. Nucleic Acids Res, 2005,33:D154-D159.
26. Balkunde R, Pesch M, Hulskamp M. Trichome patterning in Arabidopsis thaliana from genetic to molecular models[J]. Curr Top Dev Biol,2010,91:299-321.
27. Beasley J O. The production of polyploids in Gossypium[J]. Journal of Heredity,1940,31(1):39-48.
28. Becerra Lopez-Lavalle L A, Matheson B, Brubaker C L, Van Deynze A. A genetic map of an Australian wild Gossypium C genome and assignment of homoeologies with tetraploid cultivated cotton[J]. Genome,2011,54(9):779-794.
29. Benson D A, Karsch-Mizrachi I, Lipman D J, Ostell J, Wheeler D L. GenBank.[J], Nucleic Acids. Res,2005,33:D34-D38.
30. Betancur L, Singh B, Rapp R A, Wendel J F, Marks M D, Roberts A W, Haigler C H. Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber[J]. J Integr Plant Biol,2010,52(2):205-220.
31. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J, Yu J, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D. CMD:a Cotton Microsatellite Database resource for Gossypium genomics[J]. BMC Genomics,2006,7(1):132.
32. Boguski M S, Lowe T M, Tolstoshev C M. dbEST-database for "expressed sequence tags"[J]. Nat Genet,1993,4(4):332-333.
33. Brenner E D, Katari M S, Stevenson D W, Rudd S A, Douglas A W, Moss W N, Twigg R W, Runko S J, Stellari G M, McCombie W R. EST analysis in Ginkgo biloba:an assessment of conserved developmental regulators and gymnosperm specific genes[J]. BMC genomics, 2005,6:143.
34. Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, hize D, Zabeau M. Quantitative cDNA-AFLP analysis for genome-wide expression studies[J]. Mol Genet Genomics,2003,269(2):173-179.
35. Brill E, van Thournout M, White R G, Llewellyn D, Campbell P M, Engelen S, Ruan Y L, Arioli T, Furbank R T. A novel isoform of sucrose synthase is targeted to the cell wall during secondary cell wall synthesis in cotton fiber[J]. Plant Physiol,2011,157(1):40-54.*
36. Brown D M, Zhang Z, Stephens E, Dupree P, Turner S R. Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis[J]. Plant J, 2009,57(4):732-746.
37. Burke J, Davidson D, Hide W. d2_cluster:A Validated Method for Clustering EST and Full-Length cDNA Sequences[J]. Genome Res,1999,9:1135-1142.
38. Cardie L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants[J]. Genetics,2000,156(2):847-854.
39. Chee P W, Rong J, Williams-Coplin D, Schulze S R, Paterson A H. EST derived PCR-based markers for functional gene homologues in cotton.[J]. Genome,2004,47(3):449-462.
40. Chen Z J, Scheffler B E, Dennis E, Triplett B A, Zhang T, Guo W, Chen X, Stelly D M, Rabinowicz P D, Town C D. Toward sequencing cotton (Gossypium) genomes[J]. Plant Physiology, 2007,145(4):1303.
41. Chinwalla A T, Cook L L, Delehaunty K D, Fewell G A, Fulton L A, Fulton R S, Graves T A, Hillier L D W, Mardis E R, McPherson J D, Others. Initial sequencing and comparative analysis of the mouse genome[J]. Nature,2002,420(6915):520-562.
42. Conesa A, Gotz S, Garcia-Gomez J M, Terol J, Talon M, Robles M. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research[J]. Bioinformatics, 2005,21(18):3674-3676.
43. Conesa A, Gotz S. Blast2GO:A comprehensive suite for functional analysis in plant genomics[J]. Intl J Plant Genomics,2008,2008:619832.
44. Cordeiro G V, Casu R, McIntyre C L, Manners J M, Henry R J. Microsatellite markers from sugarcane (Saccharum spp) ESTs cross transferable to erianthus and sorghum[J]. Plant Science, 2001.
45. Cronn R C, Small R L, Haselkorn T, Wendel J F. Rapid diversification of the cotton genus {Gossypium:Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes[J]. American Journal of Botany,2002,89(4):707.
46. DeJoode D R, Wendel J F. Genetic diversity and origin of the Hawaiian Islands cotton, Gossypium tomentosum[Y]. American Journal of Botany,1992:1311-1319.
47. Edwards D, Batley J. Plant bioinformatics:from genome to phenome[J]. Trends in biotechnology, 2004,22(5):232-237.
48. Endrizzi J E, Turcotte E L, Kohel R J. Genetics, Cytology, and Evolution of Gossypium[J]. Advances in Genetics,1985,23:271-375.
49. Ewing B, Green P. Base-calling of automated sequencer traces using phred. Ⅱ. Error probabilities[J]. Genome Res,1998,8:186-194.
50. Ewing B, Hillier L, Wendl M C, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment[J]. Genome Res,1998,8(3):175-185.
51. Fryxell P A. The natural history of the cotton tribe(Malvaceae, tribe Gossypieae)[M]. Texas A & M University Press,1979.
52. Fryxell P A. A revised taxonomic interpretation of Gossypium L. (Malvaceae)[J]. Rheedea, 1992,2:108-165.
53. Galau G A, Wilkins T A. Alloplasmic male sterility in AD allotetraploid Gossypium hirsutum upon replacement of its resident A cytoplasm with that of D species G. harknessii[J]. TAG Theoretical and Applied Genetics,1989,78(1):23-30.
54. Ganal M W, Altmann T, Roder M S. SNP identification in crop plants[J]. Curr Opin Plant Biol, 2009,12(2):211-217.
55. Ge B, Gurd S, Gaudin T, Dore C, Lepage P, Harmsen E, Hudson T J, Pastinen T. Survey of allelic expression using EST mining[J]. Genome Res,2005,15(11):1584-1591.
56. Goff S A, Ricke D, Lan T H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Others. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)[J]. Science, 2002,296(5565):92-100.
57. Grover C E, Kim H R, Wing R A, Paterson A H, Wendel J F. Incongruent patterns of local and global genome size evolution in cotton[J]. Genome Res,2004,14:1474-1482.
58. Grover C E, Kim H R, Wing R A, Paterson A H, Wendel J F. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)[T]. Plant Journal, 2007,50(6):995-1006.
59. Grover C E, Yu Y, Wing R A, Paterson A H, Wendel J F. A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus[J]. Molecular Biology and Evolution,2008,25(7):1415-1428.
60. Guo W Z, Sang Z Q, Zhou B L, Zhang T Z. Genetic relationships of D-genome species based on two types of EST-SSR markers derived from G.arboreum and G.raimondii in Gossypium[J]. Plant Science,2007,172(4):808-814.
61. Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, Shi B, Zhang T. A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium[J]. Genetics,2007,176(1):527-541.
62. Guo W, Cai C, Wang C, Zhao L, Wang L, Zhang T. A preliminary analysis of genome structure and composition in Gossypium hirsutum[J]. BMC Genomics,2008,9(1):314.
63. Guo W, Wang W, Zhou B, Zhang T. Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium[J]. TAG Theoretical and Applied Genetics, 2006,112(8):1573-1581.
64. Guo W, Zhang T, Shen X, Yu J Z, Kohel R J. Development of SCAR marker linked to a major QTL for high fiber strength and its usage in molecular-marker assisted selection in upland cotton[J]. Crop science,2003,43(6):2252-2256.
65. Gupta PK B H S P. Microsatellites in plants:a new class of molecular markers[J]. Current Sci, 1996(70):45-53.
66. Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton[J]. Theor Appl Genet, 2006,112(3):430-439.
67. Han Z G, Guo W Z, Song X L, Zhang T Z. Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton[J]. Molecular Genetics and Genomics, 2004,272(3):308-327.
68. He L, Du C, Covaleda L, Xu Z, Robinson A F, Yu J Z, Kohel R J, Zhang H B. Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.)[J]. Molecular plant-microbe interactions, 2004,17(11):1234-1241.
69. Heesacker A, Kishore V K, Gao W, Tang S, Kolkman J M, Gingle A, Matvienko M, Kozik A, Michelmore R M, Lai Z, Rieseberg L H, Knapp S J. SSRs and INDELs mined from the sunflower EST database:abundance, polymorphisms, and cross-taxa utility[J]. Theor Appl Genet, 2008,117(7):1021-1029.
70. Hendrix B, Stewart J M. Estimation of the nuclear DNA content of Gossypium species[J]. Annals of Botany,2005,95(5):789-797.
71. Hu J, Vick B A. Target region amplification polymorphism:a novel marker technique for plant genotyping[J]. Plant Molecular Biology Reporter,2003,21(3):289-294.
72. Hu Y, Lu Y, Ma D, Guo W, Zhang T. Construction and characterization of a bacterial artificial chromosome library for the A-genome of cotton (G. arboreum L.)[J]. J Biomed Biotechnol, 2010,2010.
73. Huang G Q, Xu W L, Gong S Y, Li B, Wang X L, Xu D, Li X B. Characterization of 19 novel cotton FLA genes and their expression profiling in fiber development and in response to phytohormones and salt stress[J]. Physiol Plant,2008,134(2):348-359.
74. Huang X, Madan A. CAP3:A DNA sequence assembly program[J]. Genome Res,1999,9(9):868.
75. Iandolino A B, Goes Da Silva F, Lim H, Choi H, Williams L E, Cook D R. High-quality RNA, cDNA, and derived EST libraries from grapevine (Vitis vinifera L.)[J]. Plant Molecular Biology Reporter,2004,22(3):269-278.
76. Ji S J, Lu Y C, Feng J X, Wei G, Li J, Shi Y H, Fu Q, Liu D, Luo J C, Zhu Y X. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array[J]. Nucleic Acids Research,2003,31(10):2534-2543.
77. Jiang Y, Guo W, Zhu H, et al. Overexpression of GhSusAl increases plant biomass and improves cotton fiber yield and quality [J]. Plant Biotechnol J,2012,10(3):301-312.
78. John Z Y, Kohel R J, Fang D D, Cho J, Van Deynze A, Ulloa M, Hoffman S M, Pepper A E, Stelly D M, Jenkins J N, Others. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome[J]. G3:Genes| Genomes| Genetics, 2012,2(1):43-58.
79. Jurka J, Kapitonov V V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements[J]. Cytogenet Genome Res,2005,110:462-467.
80. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes.[J]. Nucleic Acids Res, 2000,28:27-30.
81. Kantety R V, La Rota M, Matthews D E, Sorrells M E. Data mining for simple sequence repeats in expressed sequence tags from barely, maize, rice, sorghum and wheat[J]. Plant Mol Biol,2002.
82. Khan B M Y, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S, Others. Identification of micro-RNAs in cotton.[J]. Plant physiology and biochemistry, 2008,46(8-9):739.
83. Kohel R J, Yu J, Park Y H, Lazo G R. Molecular mapping and characterization of traits controlling fiber quality in cotton[J]. Euphytica,2001,121(2):163-172.
84. Kota R, Varshney R K, Thiel T, Dehmer K J, Graner A. Generation and Comparison of EST-Derived SSRs and SNPs in Barley (Hordeum Vulgare L.)[J]. Hereditas, 2001,135(2-3):145-151.
85. Lacape J M, Jacobs J, Arioli T, Derijcker R, Forestier-Chiron N, Llewellyn D, Jean J, Thomas E Viot C. A new interspecific, Gossypium hirsutum×G. barbadense, RIL population:towards a unified consensus linkage map of tetraploid cotton[J]. TAG Theoretical and Applied Genetics, 2009,119(2):281-292.
86. Li G, Gao M, Yang B, Quiros C F. Gene for gene alignment between the Brassica and Arabidopsis genomes by direct transcriptome mapping[J]. TAG Theoretical and Applied Genetics, 2003,107(1):168-180.
87. Li W, Godzik A. cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences[J]. Bioinformatics,2006,22(13):1658-1659.
88. Lin L, Pierce G J, Bowers J E, Estill J C, Compton R O, Rainville L K, Kim C, Lemke C, Rong J, Tang H, Others. A draft physical map of a D-genome cotton species (Gossypium raimondii)[J]. BMC genomics,2010,11(1):395.
89. Lin Z, Zhang Y, Zhang X, Guo X. A high-density integrative linkage map for Gossypium hirsutum[J].Euphytica,2009,166(1):35-45.
90. Liu B, Brubaker C L, Mergeai G, Cronn R C, Wendel J F. Polyploid formation in cotton is not accompanied by rapid genomic changes[J]. Genome,2001,44(3):321-330.
91. Liu D, Tu L, Li Y, Wang L, Zhu L, Zhang X. Genes Encoding Fasciclin-Like Arabinogalactan Proteins are Specifically Expressed During Cotton Fiber Development[J]. Plant Molecular Biology Reporter,2008,26(2):98.
92. Lu B, Cai X, Xin J. Efficient indica and japonica rice identification based on the InDel molecular method:Its implication in rice breeding and evolutionary research[J]. Progress in Natural Science, 2009,19(10):1241.
93. Lv Y, Cai C, Wang L, Lin S, Zhao L, Tian L, Lv J, Zhang T, Guo W. Mining, characterization, and exploitation of EST-derived microsatellites in Gossypium barbadense[J]. Chinese Science Bulletin, 2010,55(18):1889.
94. Lynch M, Milligan B G. Analysis of population genetic structure with RAPD markers[J]. Molecular Ecology,2008,3(2):91-99.
95. Maia LC, Palmieri DA, Souza VQ, Kopp MM, Carvalho FIF, Costa De Oliveira A. SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation[J]. International Journal of Plant Genomics,2008,2008:9
96. Meinke D W, Cherry J M, Dean C, Rounsley S D, Koornneef M. Arabidopsis thaliana:a model plant for genome analysis[J]. Science,1998,282(5389):662-682.
97. Mills R E, Luttig C T, Larkins C E, Beauchamp A, Tsui C, Pittard W S, Devine S E. An initial map of insertion and deletion (INDEL) variation in the human genome[J]. Genome Res, 2006,16(9):1182-1190.
98. Nguyen T B, Giband M, Brottier P, Risterucci A M, Lacape J M. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers[J]. Theor Appl Genet, 2004,109(1):167-175.
99. Ogurtsov A Y, Sunyaev S, Kondrashov A S. Indel-based evolutionary distance and mouse-human divergence[J]. Genome Res,2004,14(8):1610-1616.
100. Pan C, Li A, Dai Z, Zhang H, Liu G, Wang Z, Ma Y, Yin Y, Zhang Y, Zuo S, Chen Z, Pan X. InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes[J]. Rice Science,2008,15(4):251-258.
101. Pang M, Woodward A W, Agarwal V, Guan X, Ha M, Ramachandran V, Chen X, Triplett B A, Stelly D M, Chen Z J, Others. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)[J]. Genome Biol,2009,10(11):R122.
102. Pang Y, Song W Q, Chen F Y, et al. A new cotton SDR family gene encodes a polypeptide possessing aldehyde reductase and 3-ketoacyl-CoA reductase activities [J]. Biochemistry. Biokhimiia,2010,75(3):320-326.
103.Paterson A H, Bowers J E, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Others. The Sorghum bicolor genome and the diversification of grasses[J]. Nature,2009,457(7229):551-556.
104. Paterson A, Brubaker C, Wendel J. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis[J]. Plant Molecular Biology Reporter, 1993,11(2):122-127.
105. Paterson A. DOE Joint Genome Institute:Cotton D V2.0[M]. Phytozome,2012.
106. Paterson A H. Genetics and genomics of cotton[M]. Springer,2009.
107. Pear J R, Kawagoe Y, Schreckengost W E, Delmer D P, Stalker D M. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase[J]. Proc Natl Acad Sci,1996,93(22):12637-12642.
108. Pearson W R. Rapid and sensitive sequence comparison with FASTP and FASTA[J]. Methods Enzymol,1990,183:63-98.
109. Pleasants, Wendel. Genetic diversity in a clonal narrow endemic, Erythronium propullans, and its widespread progenitor, Erythronium albidum.[J]. Am. J. Bot,1989(76):1136-1151.
110. Qin Y M, Hu C Y, Pang Y, et al. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis [J]. Plant Cell,2007,19(11): 3692-3704.
111. Qin Y M, Pujol F M, Shi Y H, et al. Cloning and functional characterization of two cDNAs encoding NADPH-dependent 3-ketoacyl-CoA reductased from developing cotton fibers [J]. Cell Res,2005,15(6):465-473.
112. Qureshi S N, Saha S, Kantety R V, Jenkins J N. EST-SSR:a new class of genetic markers in cotton[J]. J Cotton Sci,2004,8:112-123.
113. Reinisch A J, Dong J M, Brubaker C L, Stelly D M, Wendel J F, Paterson A H. A Detailed RFLP Map of Cotton, Gossypium hirsutum×Gossypium barbadense:Chromosome Organization and Evolution in a Disomic Polyploid Genome[J]. Genetics,1994,138(3):829-847.
114. Rhee S Y, Dickerson J, Xu D. Bioinformatics and its applications in plant biology[J]. Annu. Rev. Plant Biol.,2006,57:335-360.
115. Rong J, Abbey C, Bowers J E, Brubaker C L, Chang C, Chee P W, Delmonte T A, Ding X, Garza J J, Marler B S. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium)[J]. Genetics, 2004(166):389-417.
116. Rong J, Feltus F A, Waghmare V N, Pierce G J, Chee P W, Draye X, Saranga Y, Wright R J, Wilkins T A, May O L. Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development[J]. Genetics,2007,176(4):2577.
117. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers.[J]. Methods Mol Biol,2000,132:365-386.
118. Ruan Y L, Chourey P S. A fiberless seed mutation in cotton is associated with lack of fiber cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds [J]. Plant Physiol,1998,118(2):399-406.
119. Ruan Y L, Jin Y, Huang J. Capping invertase activity by its inhibitor:roles and implications in sugar signaling, carbon allocation, senescence and evolution [J]. Plant Signal Behav,2009,4(10): 983-985.
120. Ruan Y L, Llewellyn D J, Furbank R T. Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development [J]. Plant Cell,2003,15(4):952-964.
121. Ruan Y L, Xu S M, White R, Furbank R T. Genotypic and developmental evidence for the role of plasmodesmatal regulation in cotton fiber elongation mediated by callose turnover[J]. Plant Physiol, 2004,136(4):4104-4113.
122. Ruan Y L. Goldacre paper:Rapid cell expansion and cellulose synthesis regulated by plasmodesmata and sugar:insights from the single-celled cotton fibre [J]. Funct. Plant Biol.,2007, 34(1):1-10.
123. Saeys Y, Inza I, Larra N Aga P. A review of feature selection techniques in bioinformatics[J]. Bioinformatics,2007,23(19):2507-2517.
124. Saha S, Raska D A, Stelly D M. Upland cotton (Gossypium hirsutum L.) x Hawaiian cotton (G. tomentosum Nutt. ex. Seem) Fl hybrid hypoaneuploid chromosome substitution series[J]. J Cotton Sci,2006,10:146-154.
125. Salamov A A, Solovyev V V. Ab initio gene finding in Drosophila genomic DNA[J]. Genome Res, 2000,10(4):516-522.
126. Salmon A, Flagel L, Ying B, Udall J A, Wendel J F. Homoeologous nonreciprocal recombination in polyploid cotton[J]. New Phytol,2010,186(1):123-134.
127. Schnable P S, Ware D, Fulton R S, Stein J C, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves T A, Others. The B73 maize genome:complexity, diversity, and dynamics[J]. science, 2009,326(5956):1112-1115.
128. Seagull R W. A quantitative electron microscopic study of changes in microtubule arrays and wall microfibril orientation during in vitro cotton fiber development[J]. Journal of Cell Science, 1992,101 (3):561-577.
129. Seelanan T, Schnabel A, Wendel J F. Congruence and consensus in the cotton tribe (Malvaceae)[J]. Systematic Botany,1997:259-290.
130. Senchina D S, Alvarez I, Cronn R C, Liu B, Rong J, Noyes R D, Paterson A H, Wing R A, Wilkins T A, Wendel J F. Rate variation among nuclear genes and the age of polyploidy in Gossypium[J]. Molecular biology and evolution,2003,20(4):633-643.
131. Shi Y H, Zhu S W, Mao X Z, Feng J X, Qin Y M, Zhang L, Cheng J, Wei L P, Wang Z Y, Zhu Y X. Transcriptome profiling, molecular biological, and physiological studies reveal a major role(?)for ethylene in cotton fiber cell elongation[J]. The Plant Cell,2006,18(3):651-664.
132. Skovsted A. Cytological studies in cotton[J]. Journal of Genetics,1934,28(3):407-424.
133. Smit A, Hubley R, Green P. RepeatMasker Open-3.0[J]. Computer Program,1996.
134. Song W Q, Qin Y M, Saito M, et al. Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif [J]. J Exp Bot,2009, 60(6):1839-1848.
135. Stam P. Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP.[J]. Plant. J.3 (1993) 739-744.,1993.
136. Stewart J M. Potential for crop improvement with exotic germplasm and genetic engineering, 1995[C].
137. Stewart J, Craven L A, Wendel J F. A new Australian species of Gossypium,2007[C].
138. Taliercio E, Allen R D, Essenberg M, Klueva N, Nguyen H, Patil M A, Payton P, Millena A C M, Phillips A L, Pierce M L, Others. Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs[J]. Genome,2006,49(4):306-319.
139. Tang J, Vosman B, Voorrips R E, Linden C G, Leunissen J. QualitySNP:a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species[J]. BMC Bioinformatics,2006,7:438.
140. Thiel, T T, Michalek, W M, Varshney, R V, Graner, A G. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theor Appl Genet,2003,106(3):411-422.
141.Tomkins J P, Peterson D G, Yang T J, Main D, Wilkins T A, Paterson A H, Wing R A. Development of genomic resources for cotton (Gossypium hirsutum L.):BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development[J]. Molecular Breeding,2001,8(3):255-261.
142. Trainin T, Shmuel M, Delmer D P. In Vitro Prenylation of the Small GTPase Rac13 of Cotton[J]. Plant Physiol,1996,112(4):1491-1497.
143. Udall J A, Swanson J M, Haller K, Rapp R A, Sparks M E, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat A B. A global assembly of cotton ESTs[J]. Genome Res,2006,16:441-450.
144. Udall J A, Wendel J F. Polyploidy and crop improvement[J]. Crop Science,2006,46.
145. Ulloa M, Saha S, Jenkins J N, Meredith W R, McCarty J C, Stelly D M. Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotto(Gossypium hirsutum L.) joinmap[J]. J Hered,2005,96:132-144.
146. Van Deynze A, Stoffel K, Lee M, Wilkins T A, Kozik A, Cantrell R G, Yu J Z, Kohel R J, Stelly D M. Sampling nucleotide diversity in cotton[J]. BMC Plant Biol,2009,9:125.
147. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M. AFLP:a new technique for DNA fingerprinting[J]. Nucleic Acids Res,1995,23(21):4407-4414.
148. Wang CB, Guo WZ, Cai CP, Zhang TZ. Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich[J]. Chin Sci Bull,2006,51:557-561.
149. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel R J, Percy R G, Yu J Z, Zhu Y, Wang J, Yu S. The draft genome of a diploid cotton Gossypium raimondii[J].2012,44(10):1098-1103.
150. Wang L, Li X R, Lian H, et al. Evidence that high activity of vacuolar invertase is required for cotton fiber and Arabidopsis root elongation through osmotic dependent and independent pathways, respectively [J]. Plant Physiol,2010,154(2):744-756.
151. Wang L, Tian L, Zhu Y, Cai C, Zhao L, Zhang T, Guo W. Cloning, Expression and Chromosome Mapping of Arabinogalactan Protein Gene in Cotton[J]. Cotton Science,2010,1:7.
152. Wendel J F, Brubaker C, Alvarez I, Cronn R, Stewart J M D. Evolution and natural history of the cotton genus[J]. Genetics and Genomics of Cotton,2009:1-20.
153. Wendel J F, Cronn R C. Polyploidy and the evolutionary history of cotton[J]. Adv Agron, 2003,78:139-186.
154. Wendel J F, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium)[J]. Proceedings of the National Academy of Sciences,1995,92(1):280-284.
155. Wendel J F. Genome evolution in polyploids[J]. Plant Mol Biol,2000,42:225-249.
156. Wu A M, Hornblad E, Voxeur A, Gerber L, Rihouey C, Lerouge P, Marchant A. Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L pairs of glycosyltransferase genes reveals critical contributions to biosynthesis of the hemicellulose glucuronoxylan[J]. Plant Physiol, 2010,153(2):542-554.
157. Xu Z, Kohel R J, Song G, Cho J, Yu J, Yu S, Tomkins J, Yu J Z. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.)[J]. BMC genomics,2008,9(1):108.
158. Yin J M, Guo W Z, Zhang T Z. Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton[J]. Journal of Integrative Plant Biology, 2006,48(2):219-222.
159. Yin J, Guo W, Yang L, Liu L, Zhang T. Physical mapping of the Rfl fertility-restoring gene to a 100 kb region in cotton[J]. Theor Appl Genet,2006,112(7):1318-1325.
160. Yu J, Yu S, Lu C, Wang W, Fan S, Song M, Lin Z, Zhang X, Zhang J. High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers[J]. Journal of Integrative Plant Biology,2007,49(5):716-724.
161. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X. Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense[J]. BMC Genomics,2011,12:15.
162. Zhang B, Wang Q, Wang K, Pan X, Liu F, Guo T, Cobb G P, Anderson T A, Others. Identification of cotton microRNAs and their targets.[J]. Gene,2007,397(1-2):26.
163. Zhang D, Hrmova M, Wan C H, Wu C, Balzen J, Cai W, Wang J, Densmore L D, Fincher G B, Zhang H, Haigler C H. Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls[J]. Plant Mol Biol,2004,54(3):353-372.
164. Zhang J, Wu Y T, Guo W Z, Zhang T Z. Fast screening of microsatellite markers in cotton with PAGE/silver staining[J]. Acta Gossypii Sinica,2000,12(5):267-269.
165. Zhang M, Zhang Y, Huang J J, Zhang X, Lee M K, Stelly D M, Zhang H B. Genome Physical Mapping of Polyploids:A BIBAC Physical Map of Cultivated Tetraploid Cotton, Gossypium hirsutum L[J]. PloS one,2012,7(3):e33644.
166. Zhang T, Yuan Y, Yu J, Guo W, Kohel R J. Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection[J]. TAG Theoretical and Applied Genetics, 2003,106(2):262-268.
167. Zhong R, Lee C, Ye Z H. Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis[J]. Trends Plant Sci,2010,15(11):625-632.
2.曹越.植物遗传研究与分子标记技术[J].青海农林科技,2004(2)：21-24.
3.郭瑞星,刘小红,荣廷昭,孙东发,谭振波.植物SSR标记的发展及其在遗传育种中的应用[J].玉米科学,2005,13(2)：8-11.
4.郭旺珍,张天真,丁业掌,朱一超,沈新莲,朱协飞.分子标记辅助聚合两个棉纤维高强主效QTLs的选择效果[J].遗传学报,2006,32(12)：1275-1285.
5.茎重丝,王天宇.分子标记的种类及其发展[J].生物技术通报,1999(4).
6.梁明山,曾宇,周翔,侯留记,李霞.遗传标记及其在作物品种鉴定中的应用[J].植物学通报,2001,18(3)：257-265.
7.刘春林,官春云.植物RAPD标记的可靠性研究[J].生物技术通报,1999,15(2)：31-34.
8.刘勋甲,郑用琏.遗传标记的发展及分子标记在农作物遗传育种中的运用[J].湖北农业科学,1998(1)：33-35.
9.阮成江,何祯祥,钦佩.我国农作物QTL定位研究的现状和进展[J].植物学通报,2003,20(1)：10-22.
10.孙洪,程静,詹克慧,张相武,杨艳会.ISSR标记技术及其在作物遗传育种中的应用[J].分子植物育种,2005,3(001)：123-127.
11.汪小全,邹喻苹.RAPD应用于遗传多样性和系统学研究中的问题[J].植物学报：英文版,1996,38(12)：954-962.
12.王红梅,张正英.SSR标记技术及其在植物遗传学中的应用[J].西北师范大学学报：自然科学版,2003,39(1)：113-116.
13.周延清.DNA分子标记技术在植物研究中的应用[M].化学工业出版社,2005.
14.周延清.遗传标记的发展[J].生物学通报,2000,35(5)：17-18.
15.祝水金,童旭宏,洪彩霞,季道藩,吴伟,王仁杯.三系杂交棉新组合——浙杂2号[J].中国棉花,2006,33(005)：12-13.
16.庄南生,郑成木.植物AFLP标记转化为特异PCR标记的研究进展木[J].华南热带农业大学学报,2004,10(3)：1.
17.邹喻苹,葛颂,王晓东,植物.系统与进化植物学中的分子标记[M].科学出版社,2001.
18. Adams K L, Cronn R, Percifield R, Wendel J F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing[J]. Proceedings of the National Academy of Sciences,2003,100(8):4649-4654.
19. Adams M D, Celniker S E, Holt R A, Evans C A, Gocayne J D, Amanatides P G, Scherer S E, Li P W, Hoskins R A, Galle R F, Others. The genome sequence of Drosophila melanogaster[Y]. Science, 2000,287(5461):2185-2195.
20. Alba R, Fei Z, Payton P, Liu Y, Moore S L, Debbie P, Conn J, D'Ascenzo M, Gordon J S, Rose J K, Martin G, Tanksley S D, Bouzayen M, Jahn M M, Giovannoni J. ESTs, cDNA microarrays, and gene expression profiling:tools for dissecting plant physiology and development[J]. The Plant Journal,2004,39:697-714.
21. Altschul S F, Madden T L, Schaffer A A, Zhang I, Zhang Z, Miller W, Lipman D J. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J]. Nucleic Acids Res,1997,25:3389-3402.
22. Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci A, Da Silva C, Cascardo J, Allegre M, Kuhn D, Verica J, Courtois B, Loor G, Babin R, Sounigo O, Ducamp M, Guiltinan M, Ruiz M, Alemanno L, Machado R, Phillips W, Schnell R, Gilmour M, Rosenquist E, Butler D, Maximova S, Lanaud C. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions[J]. BMC Genomics,2008,9(1):512.
23. Asamizu E, Nakamura Y, Sato S, Tabata S. A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries[J]. DNA research,2000,7(3):175-180.
24. Atwell S, Huang Y S, Vilhj A Lmsson B J, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone A M, Hu T T, Others. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines[J]. Nature,2010,465(7298):627-631.
25. Bairoch A, Apweiler R, Wu C H, Barker W C, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M. The Universal Protein Resource (UniProt).[J]. Nucleic Acids Res, 2005,33:D154-D159.
26. Balkunde R, Pesch M, Hulskamp M. Trichome patterning in Arabidopsis thaliana from genetic to molecular models[J]. Curr Top Dev Biol,2010,91:299-321.
27. Beasley J O. The production of polyploids in Gossypium[J]. Journal of Heredity,1940,31(1):39-48.
28. Becerra Lopez-Lavalle L A, Matheson B, Brubaker C L, Van Deynze A. A genetic map of an Australian wild Gossypium C genome and assignment of homoeologies with tetraploid cultivated cotton[J]. Genome,2011,54(9):779-794.
29. Benson D A, Karsch-Mizrachi I, Lipman D J, Ostell J, Wheeler D L. GenBank.[J], Nucleic Acids. Res,2005,33:D34-D38.
30. Betancur L, Singh B, Rapp R A, Wendel J F, Marks M D, Roberts A W, Haigler C H. Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber[J]. J Integr Plant Biol,2010,52(2):205-220.
31. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J, Yu J, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D. CMD:a Cotton Microsatellite Database resource for Gossypium genomics[J]. BMC Genomics,2006,7(1):132.
32. Boguski M S, Lowe T M, Tolstoshev C M. dbEST-database for "expressed sequence tags"[J]. Nat Genet,1993,4(4):332-333.
33. Brenner E D, Katari M S, Stevenson D W, Rudd S A, Douglas A W, Moss W N, Twigg R W, Runko S J, Stellari G M, McCombie W R. EST analysis in Ginkgo biloba:an assessment of conserved developmental regulators and gymnosperm specific genes[J]. BMC genomics, 2005,6:143.
34. Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, hize D, Zabeau M. Quantitative cDNA-AFLP analysis for genome-wide expression studies[J]. Mol Genet Genomics,2003,269(2):173-179.
35. Brill E, van Thournout M, White R G, Llewellyn D, Campbell P M, Engelen S, Ruan Y L, Arioli T, Furbank R T. A novel isoform of sucrose synthase is targeted to the cell wall during secondary cell wall synthesis in cotton fiber[J]. Plant Physiol,2011,157(1):40-54.*
36. Brown D M, Zhang Z, Stephens E, Dupree P, Turner S R. Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis[J]. Plant J, 2009,57(4):732-746.
37. Burke J, Davidson D, Hide W. d2_cluster:A Validated Method for Clustering EST and Full-Length cDNA Sequences[J]. Genome Res,1999,9:1135-1142.
38. Cardie L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants[J]. Genetics,2000,156(2):847-854.
39. Chee P W, Rong J, Williams-Coplin D, Schulze S R, Paterson A H. EST derived PCR-based markers for functional gene homologues in cotton.[J]. Genome,2004,47(3):449-462.
40. Chen Z J, Scheffler B E, Dennis E, Triplett B A, Zhang T, Guo W, Chen X, Stelly D M, Rabinowicz P D, Town C D. Toward sequencing cotton (Gossypium) genomes[J]. Plant Physiology, 2007,145(4):1303.
41. Chinwalla A T, Cook L L, Delehaunty K D, Fewell G A, Fulton L A, Fulton R S, Graves T A, Hillier L D W, Mardis E R, McPherson J D, Others. Initial sequencing and comparative analysis of the mouse genome[J]. Nature,2002,420(6915):520-562.
42. Conesa A, Gotz S, Garcia-Gomez J M, Terol J, Talon M, Robles M. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research[J]. Bioinformatics, 2005,21(18):3674-3676.
43. Conesa A, Gotz S. Blast2GO:A comprehensive suite for functional analysis in plant genomics[J]. Intl J Plant Genomics,2008,2008:619832.
44. Cordeiro G V, Casu R, McIntyre C L, Manners J M, Henry R J. Microsatellite markers from sugarcane (Saccharum spp) ESTs cross transferable to erianthus and sorghum[J]. Plant Science, 2001.
45. Cronn R C, Small R L, Haselkorn T, Wendel J F. Rapid diversification of the cotton genus {Gossypium:Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes[J]. American Journal of Botany,2002,89(4):707.
46. DeJoode D R, Wendel J F. Genetic diversity and origin of the Hawaiian Islands cotton, Gossypium tomentosum[Y]. American Journal of Botany,1992:1311-1319.
47. Edwards D, Batley J. Plant bioinformatics:from genome to phenome[J]. Trends in biotechnology, 2004,22(5):232-237.
48. Endrizzi J E, Turcotte E L, Kohel R J. Genetics, Cytology, and Evolution of Gossypium[J]. Advances in Genetics,1985,23:271-375.
49. Ewing B, Green P. Base-calling of automated sequencer traces using phred. Ⅱ. Error probabilities[J]. Genome Res,1998,8:186-194.
50. Ewing B, Hillier L, Wendl M C, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment[J]. Genome Res,1998,8(3):175-185.
51. Fryxell P A. The natural history of the cotton tribe(Malvaceae, tribe Gossypieae)[M]. Texas A & M University Press,1979.
52. Fryxell P A. A revised taxonomic interpretation of Gossypium L. (Malvaceae)[J]. Rheedea, 1992,2:108-165.
53. Galau G A, Wilkins T A. Alloplasmic male sterility in AD allotetraploid Gossypium hirsutum upon replacement of its resident A cytoplasm with that of D species G. harknessii[J]. TAG Theoretical and Applied Genetics,1989,78(1):23-30.
54. Ganal M W, Altmann T, Roder M S. SNP identification in crop plants[J]. Curr Opin Plant Biol, 2009,12(2):211-217.
55. Ge B, Gurd S, Gaudin T, Dore C, Lepage P, Harmsen E, Hudson T J, Pastinen T. Survey of allelic expression using EST mining[J]. Genome Res,2005,15(11):1584-1591.
56. Goff S A, Ricke D, Lan T H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Others. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)[J]. Science, 2002,296(5565):92-100.
57. Grover C E, Kim H R, Wing R A, Paterson A H, Wendel J F. Incongruent patterns of local and global genome size evolution in cotton[J]. Genome Res,2004,14:1474-1482.
58. Grover C E, Kim H R, Wing R A, Paterson A H, Wendel J F. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)[T]. Plant Journal, 2007,50(6):995-1006.
59. Grover C E, Yu Y, Wing R A, Paterson A H, Wendel J F. A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus[J]. Molecular Biology and Evolution,2008,25(7):1415-1428.
60. Guo W Z, Sang Z Q, Zhou B L, Zhang T Z. Genetic relationships of D-genome species based on two types of EST-SSR markers derived from G.arboreum and G.raimondii in Gossypium[J]. Plant Science,2007,172(4):808-814.
61. Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, Shi B, Zhang T. A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium[J]. Genetics,2007,176(1):527-541.
62. Guo W, Cai C, Wang C, Zhao L, Wang L, Zhang T. A preliminary analysis of genome structure and composition in Gossypium hirsutum[J]. BMC Genomics,2008,9(1):314.
63. Guo W, Wang W, Zhou B, Zhang T. Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium[J]. TAG Theoretical and Applied Genetics, 2006,112(8):1573-1581.
64. Guo W, Zhang T, Shen X, Yu J Z, Kohel R J. Development of SCAR marker linked to a major QTL for high fiber strength and its usage in molecular-marker assisted selection in upland cotton[J]. Crop science,2003,43(6):2252-2256.
65. Gupta PK B H S P. Microsatellites in plants:a new class of molecular markers[J]. Current Sci, 1996(70):45-53.
66. Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton[J]. Theor Appl Genet, 2006,112(3):430-439.
67. Han Z G, Guo W Z, Song X L, Zhang T Z. Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton[J]. Molecular Genetics and Genomics, 2004,272(3):308-327.
68. He L, Du C, Covaleda L, Xu Z, Robinson A F, Yu J Z, Kohel R J, Zhang H B. Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.)[J]. Molecular plant-microbe interactions, 2004,17(11):1234-1241.
69. Heesacker A, Kishore V K, Gao W, Tang S, Kolkman J M, Gingle A, Matvienko M, Kozik A, Michelmore R M, Lai Z, Rieseberg L H, Knapp S J. SSRs and INDELs mined from the sunflower EST database:abundance, polymorphisms, and cross-taxa utility[J]. Theor Appl Genet, 2008,117(7):1021-1029.
70. Hendrix B, Stewart J M. Estimation of the nuclear DNA content of Gossypium species[J]. Annals of Botany,2005,95(5):789-797.
71. Hu J, Vick B A. Target region amplification polymorphism:a novel marker technique for plant genotyping[J]. Plant Molecular Biology Reporter,2003,21(3):289-294.
72. Hu Y, Lu Y, Ma D, Guo W, Zhang T. Construction and characterization of a bacterial artificial chromosome library for the A-genome of cotton (G. arboreum L.)[J]. J Biomed Biotechnol, 2010,2010.
73. Huang G Q, Xu W L, Gong S Y, Li B, Wang X L, Xu D, Li X B. Characterization of 19 novel cotton FLA genes and their expression profiling in fiber development and in response to phytohormones and salt stress[J]. Physiol Plant,2008,134(2):348-359.
74. Huang X, Madan A. CAP3:A DNA sequence assembly program[J]. Genome Res,1999,9(9):868.
75. Iandolino A B, Goes Da Silva F, Lim H, Choi H, Williams L E, Cook D R. High-quality RNA, cDNA, and derived EST libraries from grapevine (Vitis vinifera L.)[J]. Plant Molecular Biology Reporter,2004,22(3):269-278.
76. Ji S J, Lu Y C, Feng J X, Wei G, Li J, Shi Y H, Fu Q, Liu D, Luo J C, Zhu Y X. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array[J]. Nucleic Acids Research,2003,31(10):2534-2543.
77. Jiang Y, Guo W, Zhu H, et al. Overexpression of GhSusAl increases plant biomass and improves cotton fiber yield and quality [J]. Plant Biotechnol J,2012,10(3):301-312.
78. John Z Y, Kohel R J, Fang D D, Cho J, Van Deynze A, Ulloa M, Hoffman S M, Pepper A E, Stelly D M, Jenkins J N, Others. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome[J]. G3:Genes| Genomes| Genetics, 2012,2(1):43-58.
79. Jurka J, Kapitonov V V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements[J]. Cytogenet Genome Res,2005,110:462-467.
80. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes.[J]. Nucleic Acids Res, 2000,28:27-30.
81. Kantety R V, La Rota M, Matthews D E, Sorrells M E. Data mining for simple sequence repeats in expressed sequence tags from barely, maize, rice, sorghum and wheat[J]. Plant Mol Biol,2002.
82. Khan B M Y, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S, Others. Identification of micro-RNAs in cotton.[J]. Plant physiology and biochemistry, 2008,46(8-9):739.
83. Kohel R J, Yu J, Park Y H, Lazo G R. Molecular mapping and characterization of traits controlling fiber quality in cotton[J]. Euphytica,2001,121(2):163-172.
84. Kota R, Varshney R K, Thiel T, Dehmer K J, Graner A. Generation and Comparison of EST-Derived SSRs and SNPs in Barley (Hordeum Vulgare L.)[J]. Hereditas, 2001,135(2-3):145-151.
85. Lacape J M, Jacobs J, Arioli T, Derijcker R, Forestier-Chiron N, Llewellyn D, Jean J, Thomas E Viot C. A new interspecific, Gossypium hirsutum×G. barbadense, RIL population:towards a unified consensus linkage map of tetraploid cotton[J]. TAG Theoretical and Applied Genetics, 2009,119(2):281-292.
86. Li G, Gao M, Yang B, Quiros C F. Gene for gene alignment between the Brassica and Arabidopsis genomes by direct transcriptome mapping[J]. TAG Theoretical and Applied Genetics, 2003,107(1):168-180.
87. Li W, Godzik A. cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences[J]. Bioinformatics,2006,22(13):1658-1659.
88. Lin L, Pierce G J, Bowers J E, Estill J C, Compton R O, Rainville L K, Kim C, Lemke C, Rong J, Tang H, Others. A draft physical map of a D-genome cotton species (Gossypium raimondii)[J]. BMC genomics,2010,11(1):395.
89. Lin Z, Zhang Y, Zhang X, Guo X. A high-density integrative linkage map for Gossypium hirsutum[J].Euphytica,2009,166(1):35-45.
90. Liu B, Brubaker C L, Mergeai G, Cronn R C, Wendel J F. Polyploid formation in cotton is not accompanied by rapid genomic changes[J]. Genome,2001,44(3):321-330.
91. Liu D, Tu L, Li Y, Wang L, Zhu L, Zhang X. Genes Encoding Fasciclin-Like Arabinogalactan Proteins are Specifically Expressed During Cotton Fiber Development[J]. Plant Molecular Biology Reporter,2008,26(2):98.
92. Lu B, Cai X, Xin J. Efficient indica and japonica rice identification based on the InDel molecular method:Its implication in rice breeding and evolutionary research[J]. Progress in Natural Science, 2009,19(10):1241.
93. Lv Y, Cai C, Wang L, Lin S, Zhao L, Tian L, Lv J, Zhang T, Guo W. Mining, characterization, and exploitation of EST-derived microsatellites in Gossypium barbadense[J]. Chinese Science Bulletin, 2010,55(18):1889.
94. Lynch M, Milligan B G. Analysis of population genetic structure with RAPD markers[J]. Molecular Ecology,2008,3(2):91-99.
95. Maia LC, Palmieri DA, Souza VQ, Kopp MM, Carvalho FIF, Costa De Oliveira A. SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation[J]. International Journal of Plant Genomics,2008,2008:9
96. Meinke D W, Cherry J M, Dean C, Rounsley S D, Koornneef M. Arabidopsis thaliana:a model plant for genome analysis[J]. Science,1998,282(5389):662-682.
97. Mills R E, Luttig C T, Larkins C E, Beauchamp A, Tsui C, Pittard W S, Devine S E. An initial map of insertion and deletion (INDEL) variation in the human genome[J]. Genome Res, 2006,16(9):1182-1190.
98. Nguyen T B, Giband M, Brottier P, Risterucci A M, Lacape J M. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers[J]. Theor Appl Genet, 2004,109(1):167-175.
99. Ogurtsov A Y, Sunyaev S, Kondrashov A S. Indel-based evolutionary distance and mouse-human divergence[J]. Genome Res,2004,14(8):1610-1616.
100. Pan C, Li A, Dai Z, Zhang H, Liu G, Wang Z, Ma Y, Yin Y, Zhang Y, Zuo S, Chen Z, Pan X. InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes[J]. Rice Science,2008,15(4):251-258.
101. Pang M, Woodward A W, Agarwal V, Guan X, Ha M, Ramachandran V, Chen X, Triplett B A, Stelly D M, Chen Z J, Others. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)[J]. Genome Biol,2009,10(11):R122.
102. Pang Y, Song W Q, Chen F Y, et al. A new cotton SDR family gene encodes a polypeptide possessing aldehyde reductase and 3-ketoacyl-CoA reductase activities [J]. Biochemistry. Biokhimiia,2010,75(3):320-326.
103.Paterson A H, Bowers J E, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Others. The Sorghum bicolor genome and the diversification of grasses[J]. Nature,2009,457(7229):551-556.
104. Paterson A, Brubaker C, Wendel J. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis[J]. Plant Molecular Biology Reporter, 1993,11(2):122-127.
105. Paterson A. DOE Joint Genome Institute:Cotton D V2.0[M]. Phytozome,2012.
106. Paterson A H. Genetics and genomics of cotton[M]. Springer,2009.
107. Pear J R, Kawagoe Y, Schreckengost W E, Delmer D P, Stalker D M. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase[J]. Proc Natl Acad Sci,1996,93(22):12637-12642.
108. Pearson W R. Rapid and sensitive sequence comparison with FASTP and FASTA[J]. Methods Enzymol,1990,183:63-98.
109. Pleasants, Wendel. Genetic diversity in a clonal narrow endemic, Erythronium propullans, and its widespread progenitor, Erythronium albidum.[J]. Am. J. Bot,1989(76):1136-1151.
110. Qin Y M, Hu C Y, Pang Y, et al. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis [J]. Plant Cell,2007,19(11): 3692-3704.
111. Qin Y M, Pujol F M, Shi Y H, et al. Cloning and functional characterization of two cDNAs encoding NADPH-dependent 3-ketoacyl-CoA reductased from developing cotton fibers [J]. Cell Res,2005,15(6):465-473.
112. Qureshi S N, Saha S, Kantety R V, Jenkins J N. EST-SSR:a new class of genetic markers in cotton[J]. J Cotton Sci,2004,8:112-123.
113. Reinisch A J, Dong J M, Brubaker C L, Stelly D M, Wendel J F, Paterson A H. A Detailed RFLP Map of Cotton, Gossypium hirsutum×Gossypium barbadense:Chromosome Organization and Evolution in a Disomic Polyploid Genome[J]. Genetics,1994,138(3):829-847.
114. Rhee S Y, Dickerson J, Xu D. Bioinformatics and its applications in plant biology[J]. Annu. Rev. Plant Biol.,2006,57:335-360.
115. Rong J, Abbey C, Bowers J E, Brubaker C L, Chang C, Chee P W, Delmonte T A, Ding X, Garza J J, Marler B S. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium)[J]. Genetics, 2004(166):389-417.
116. Rong J, Feltus F A, Waghmare V N, Pierce G J, Chee P W, Draye X, Saranga Y, Wright R J, Wilkins T A, May O L. Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development[J]. Genetics,2007,176(4):2577.
117. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers.[J]. Methods Mol Biol,2000,132:365-386.
118. Ruan Y L, Chourey P S. A fiberless seed mutation in cotton is associated with lack of fiber cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds [J]. Plant Physiol,1998,118(2):399-406.
119. Ruan Y L, Jin Y, Huang J. Capping invertase activity by its inhibitor:roles and implications in sugar signaling, carbon allocation, senescence and evolution [J]. Plant Signal Behav,2009,4(10): 983-985.
120. Ruan Y L, Llewellyn D J, Furbank R T. Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development [J]. Plant Cell,2003,15(4):952-964.
121. Ruan Y L, Xu S M, White R, Furbank R T. Genotypic and developmental evidence for the role of plasmodesmatal regulation in cotton fiber elongation mediated by callose turnover[J]. Plant Physiol, 2004,136(4):4104-4113.
122. Ruan Y L. Goldacre paper:Rapid cell expansion and cellulose synthesis regulated by plasmodesmata and sugar:insights from the single-celled cotton fibre [J]. Funct. Plant Biol.,2007, 34(1):1-10.
123. Saeys Y, Inza I, Larra N Aga P. A review of feature selection techniques in bioinformatics[J]. Bioinformatics,2007,23(19):2507-2517.
124. Saha S, Raska D A, Stelly D M. Upland cotton (Gossypium hirsutum L.) x Hawaiian cotton (G. tomentosum Nutt. ex. Seem) Fl hybrid hypoaneuploid chromosome substitution series[J]. J Cotton Sci,2006,10:146-154.
125. Salamov A A, Solovyev V V. Ab initio gene finding in Drosophila genomic DNA[J]. Genome Res, 2000,10(4):516-522.
126. Salmon A, Flagel L, Ying B, Udall J A, Wendel J F. Homoeologous nonreciprocal recombination in polyploid cotton[J]. New Phytol,2010,186(1):123-134.
127. Schnable P S, Ware D, Fulton R S, Stein J C, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves T A, Others. The B73 maize genome:complexity, diversity, and dynamics[J]. science, 2009,326(5956):1112-1115.
128. Seagull R W. A quantitative electron microscopic study of changes in microtubule arrays and wall microfibril orientation during in vitro cotton fiber development[J]. Journal of Cell Science, 1992,101 (3):561-577.
129. Seelanan T, Schnabel A, Wendel J F. Congruence and consensus in the cotton tribe (Malvaceae)[J]. Systematic Botany,1997:259-290.
130. Senchina D S, Alvarez I, Cronn R C, Liu B, Rong J, Noyes R D, Paterson A H, Wing R A, Wilkins T A, Wendel J F. Rate variation among nuclear genes and the age of polyploidy in Gossypium[J]. Molecular biology and evolution,2003,20(4):633-643.
131. Shi Y H, Zhu S W, Mao X Z, Feng J X, Qin Y M, Zhang L, Cheng J, Wei L P, Wang Z Y, Zhu Y X. Transcriptome profiling, molecular biological, and physiological studies reveal a major role(?)for ethylene in cotton fiber cell elongation[J]. The Plant Cell,2006,18(3):651-664.
132. Skovsted A. Cytological studies in cotton[J]. Journal of Genetics,1934,28(3):407-424.
133. Smit A, Hubley R, Green P. RepeatMasker Open-3.0[J]. Computer Program,1996.
134. Song W Q, Qin Y M, Saito M, et al. Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif [J]. J Exp Bot,2009, 60(6):1839-1848.
135. Stam P. Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP.[J]. Plant. J.3 (1993) 739-744.,1993.
136. Stewart J M. Potential for crop improvement with exotic germplasm and genetic engineering, 1995[C].
137. Stewart J, Craven L A, Wendel J F. A new Australian species of Gossypium,2007[C].
138. Taliercio E, Allen R D, Essenberg M, Klueva N, Nguyen H, Patil M A, Payton P, Millena A C M, Phillips A L, Pierce M L, Others. Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs[J]. Genome,2006,49(4):306-319.
139. Tang J, Vosman B, Voorrips R E, Linden C G, Leunissen J. QualitySNP:a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species[J]. BMC Bioinformatics,2006,7:438.
140. Thiel, T T, Michalek, W M, Varshney, R V, Graner, A G. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theor Appl Genet,2003,106(3):411-422.
141.Tomkins J P, Peterson D G, Yang T J, Main D, Wilkins T A, Paterson A H, Wing R A. Development of genomic resources for cotton (Gossypium hirsutum L.):BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development[J]. Molecular Breeding,2001,8(3):255-261.
142. Trainin T, Shmuel M, Delmer D P. In Vitro Prenylation of the Small GTPase Rac13 of Cotton[J]. Plant Physiol,1996,112(4):1491-1497.
143. Udall J A, Swanson J M, Haller K, Rapp R A, Sparks M E, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat A B. A global assembly of cotton ESTs[J]. Genome Res,2006,16:441-450.
144. Udall J A, Wendel J F. Polyploidy and crop improvement[J]. Crop Science,2006,46.
145. Ulloa M, Saha S, Jenkins J N, Meredith W R, McCarty J C, Stelly D M. Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotto(Gossypium hirsutum L.) joinmap[J]. J Hered,2005,96:132-144.
146. Van Deynze A, Stoffel K, Lee M, Wilkins T A, Kozik A, Cantrell R G, Yu J Z, Kohel R J, Stelly D M. Sampling nucleotide diversity in cotton[J]. BMC Plant Biol,2009,9:125.
147. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M. AFLP:a new technique for DNA fingerprinting[J]. Nucleic Acids Res,1995,23(21):4407-4414.
148. Wang CB, Guo WZ, Cai CP, Zhang TZ. Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich[J]. Chin Sci Bull,2006,51:557-561.
149. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel R J, Percy R G, Yu J Z, Zhu Y, Wang J, Yu S. The draft genome of a diploid cotton Gossypium raimondii[J].2012,44(10):1098-1103.
150. Wang L, Li X R, Lian H, et al. Evidence that high activity of vacuolar invertase is required for cotton fiber and Arabidopsis root elongation through osmotic dependent and independent pathways, respectively [J]. Plant Physiol,2010,154(2):744-756.
151. Wang L, Tian L, Zhu Y, Cai C, Zhao L, Zhang T, Guo W. Cloning, Expression and Chromosome Mapping of Arabinogalactan Protein Gene in Cotton[J]. Cotton Science,2010,1:7.
152. Wendel J F, Brubaker C, Alvarez I, Cronn R, Stewart J M D. Evolution and natural history of the cotton genus[J]. Genetics and Genomics of Cotton,2009:1-20.
153. Wendel J F, Cronn R C. Polyploidy and the evolutionary history of cotton[J]. Adv Agron, 2003,78:139-186.
154. Wendel J F, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium)[J]. Proceedings of the National Academy of Sciences,1995,92(1):280-284.
155. Wendel J F. Genome evolution in polyploids[J]. Plant Mol Biol,2000,42:225-249.
156. Wu A M, Hornblad E, Voxeur A, Gerber L, Rihouey C, Lerouge P, Marchant A. Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L pairs of glycosyltransferase genes reveals critical contributions to biosynthesis of the hemicellulose glucuronoxylan[J]. Plant Physiol, 2010,153(2):542-554.
157. Xu Z, Kohel R J, Song G, Cho J, Yu J, Yu S, Tomkins J, Yu J Z. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.)[J]. BMC genomics,2008,9(1):108.
158. Yin J M, Guo W Z, Zhang T Z. Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton[J]. Journal of Integrative Plant Biology, 2006,48(2):219-222.
159. Yin J, Guo W, Yang L, Liu L, Zhang T. Physical mapping of the Rfl fertility-restoring gene to a 100 kb region in cotton[J]. Theor Appl Genet,2006,112(7):1318-1325.
160. Yu J, Yu S, Lu C, Wang W, Fan S, Song M, Lin Z, Zhang X, Zhang J. High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers[J]. Journal of Integrative Plant Biology,2007,49(5):716-724.
161. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X. Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense[J]. BMC Genomics,2011,12:15.
162. Zhang B, Wang Q, Wang K, Pan X, Liu F, Guo T, Cobb G P, Anderson T A, Others. Identification of cotton microRNAs and their targets.[J]. Gene,2007,397(1-2):26.
163. Zhang D, Hrmova M, Wan C H, Wu C, Balzen J, Cai W, Wang J, Densmore L D, Fincher G B, Zhang H, Haigler C H. Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls[J]. Plant Mol Biol,2004,54(3):353-372.
164. Zhang J, Wu Y T, Guo W Z, Zhang T Z. Fast screening of microsatellite markers in cotton with PAGE/silver staining[J]. Acta Gossypii Sinica,2000,12(5):267-269.
165. Zhang M, Zhang Y, Huang J J, Zhang X, Lee M K, Stelly D M, Zhang H B. Genome Physical Mapping of Polyploids:A BIBAC Physical Map of Cultivated Tetraploid Cotton, Gossypium hirsutum L[J]. PloS one,2012,7(3):e33644.
166. Zhang T, Yuan Y, Yu J, Guo W, Kohel R J. Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection[J]. TAG Theoretical and Applied Genetics, 2003,106(2):262-268.
167. Zhong R, Lee C, Ye Z H. Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis[J]. Trends Plant Sci,2010,15(11):625-632.