摘要
棉花(Gossypium spp.)是世界上最重要的天然纤维作物。棉属包括约45个二倍体种和5个异源四倍体种,其中栽培种4个,分别是亚洲棉(G. arboreum),草棉(G. herbaceum),陆地棉(G. hirsutum)和海岛棉(G. barbadense).陆地棉(G. hirsutum)提供了世界棉花总产量的95%以上。
但是,作为纺织工业的主要原材料,陆地棉(G. hirsutum)的纤维长度、比强度和细度等纤维品质性状,均比海岛棉(G. barbadense)差。尽管我国自主育成棉种的纤维品质能基本满足当前纺织工业生产的要求,但由于其长度过于单一、纤维比强度较低并且纤维较粗,不能达到高档纺织品的原料要求。随着人们生活水平的提高及棉纺织技术的革新,对棉花纤维品质的要求日益增高。在兼顾产量的同时,大幅、快速的改良纤维品质成为了棉花遗传改良的新焦点。
传统的遗传改良已经为我们育成了一批高产、优质的陆地棉品种。但是由于其选育周期长、效率低、并且棉花纤维品质和产量性状受数量性状基因控制且呈负相关关系,所以传统的遗传改良已经不能满足我们的需要。DNA分子标记技术的出现,为棉花的遗传改良提供了一种快速、准确的选择方法。通过对棉花高品质纤维QTL的分子标记筛选,利用与纤维品质QTL紧密连锁的分子标记进行辅助选择,能够有效的提高选择效率,有助于我国棉花品种的纤维品质水平的提高。目前,陆地棉种间(interspecific)图谱虽然较为饱和,但不能直接用于陆地棉栽培种的改良。而陆地棉种内(intraspecific)图谱的覆盖度及标记密度远达不到分子标记辅助选择和图位克隆的要求。现在以SSR标记为主的陆地棉种内图谱的最大覆盖度约为70%。
复合杂交群体是由三个或三个以上亲本杂交产生的群体,这类群体经常用于作物栽培品种的选育,通过表型选择累积有利的加性效应等位基因来达到对目的性状的改良。然而,目前大多数陆地棉遗传连锁分析和QTL定位都基于两亲本衍生出的群体,如：F2,BC和RIL等。利用两亲本群体进行连锁分析和QTL定位具有很大的局限性,因为早期陆地棉品种选育多通过种内品种间杂交选育品种,使得陆地棉的遗传背景变得十分狭窄,两亲本间的遗传差异较小,获得多态性标记较为困难,所以两亲本的陆地棉种内遗传连锁图谱都表现出较低的标记密度和覆盖度。并且使用两亲本群体进行QTL定位,所检测的到的QTL仅仅是该性状的部分遗传结构,大量的QTL信息都没有被检测到。同时,最多只有两个等位基因的效应能够被检测到,这也大大限制了两亲本遗传连锁图谱定位的QTL在分子标记辅助选择中的应用。而利用复合杂交群体进行连锁分析和QTL定位不仅可以增加遗传连锁图谱的密度,还可以检测到更多的QTL信息,从而定位的QTL在分子标记辅助育种有较好的应用。
目前,利用多亲本构建遗传连锁图谱和QTL定位的报道还较少,本研究旨在利用分子标记技术和多亲本分离群体,构建陆地棉种内高密度遗传连锁图谱,并分析陆地棉纤维品质相关性状的QTL位点。为达到这一目的,本研究用陆地棉丰产品种中棉所35、高纤维强度品种渝棉1号、以及异常棉(G. anomalum)渐渗系7235建立[(渝棉1号×中棉所35)×(渝棉1号×7235)]复合杂交群体及F1 2/3家系,利用多态性稳定的SSR标记构建复合杂交群体遗传连锁图谱,并结合F1(2007)群体和F12/3(2008、2009)家系表型数据对纤维长度、马克隆值、比强度、整齐度、伸长度5个纤维品质性状进行QTL检测,主要研究结果如下：
1.SSR标记多态性与群体基因型检测
利用本实验室的16052对SSR引物,对亲本渝棉1号、中棉所35和7235进行多态性引物筛选,共获得有效多态性引物1057对,多态性比例为6.6%。用1057对多态性SSR引物对陆地棉三亲本复合杂交群体[(渝棉1号×中棉所35)×(渝棉1号×7235)]172个单株进行基因型检测,共获得1067个位点。卡方测验结果显示,1067个标记位点中有375个偏离孟德尔分离比例(P<0.05),偏分离比例35.19﹪。
2.三亲本复合杂交群体遗传连锁图谱
利用Joinmap4.0软件对1067个多态性位点进行遗传连锁分析,构建的遗传连锁图谱包含978个位点,标记间的平均距离为4.3 cM,遗传连锁图覆盖4184.4 cM,约占异源四倍体棉花基因组重组总长的94.1%。该图谱含69个连锁群,4个连锁群未定到染色体上,其余的65个连锁群被定位到26个染色体上,每个染色体含1-6个连锁群。A染色体亚组由32个连锁群组成,总长1954.3 cM,含366个多态性位点,标记间平均距离为5.3 cM；D染色体亚组由33个连锁群组成,总长2122.1 cM,含599个多态性位点,标记间平均距离为3.5 cM。
3.亲本与F,群体和F1:2/3家系的性状表现
2007、2008、2009年重庆三个环境下,亲本7235纤维长度分别为31.9、34.5、34.1 mm,高于渝棉1号的29.9、30.3、30.6 mm和中棉所35的29.3、30.2、31.4 mm。亲本7235和渝棉1号纤维比强度三年分别为38.1、34.2、41.3 cN/tex和38.6、36.2、41.3 cN/tex,高于中棉所35的33.5、30.7、34.9 cN/tex,其它纤维品质性状三亲本都比较接近。
F1群体纤维长度平均为31.2 mm,分布范围为28.2-34.4 mmm；整齐度平均为85.3%,分布范围为80.9-88.1%；马克隆值平均为4.2,分布范围为3.5-5.0；伸长度平均值为6.5%,分布范围为6.2-6.7%；比强度平均值为33.9 cN/tex,分布范围为29.2-39.7 cN/tex。F1：2家系纤维长度平均为31.9 mm,分布范围为28.4-34.8 mm；整齐度平均为85.4%,分布在81.6-87.5%之间；马克隆值平均为4.1,分布范围为3.1-5.2；伸长度平均值为6.6%,分布在6.3-6.8%之间；比强度平均值为34.0 cN/tex,分布在29.8-39.3 cN/tex之间。F13家系纤维长度分布在29.4-36.2 mm,平均32.0 mm；整齐度分布在82.3-87.4%,平均85.3%；马克隆值平均值为4.1,分布范围为3.1-5.1；比强度平均值为37.3 cN/tex,分布范围为31.6-43.9 cN/tex。除纤维伸长度外,其余各纤维品质性状在三个环境中都表现出超亲分离。
CP群体纤维品质性状的相关性分析结果显示,除纤维马克隆值与长度和比强度呈极显著负相关。其他性状间均成极显著正相关,相关系数从0.276-0.687。
方差分析结果显示,纤维马克隆值受基因型和环境影响均达到极显著；纤维整齐度和纤维伸长度受环境和基因型影响均不显著；纤维长度受环境影响显著,受基因型影响不显著；纤维比强度受环境影响极显著,受基因型影响显著。
4.纤维品质QTL定位
以三亲本复合杂交群体[(渝棉1号×中棉所35)×(渝棉1号×7235)]构建的遗传连锁图谱,结合2007-2009年重庆3个环境纤维品质表型数据,利用QTL作图软件MapQTL5.0,采用多QTL模型(multiple-QTL model)进行分析,共检测到63个纤维品质性状QTL,包括27个显著性QTL(1000次排列测,全基因组5%显著水平作为显著QTL的阀值),36个可能性QTL(LOD大于3.0小于5%显著水平阀值),解释性状表型变异8.1-55.8%。其中9个纤维伸长度显著性QTL,2个纤维伸长度可能性QTL,共计11个QTL,解释性状表型变异10.5-47.1%；2个纤维长度显著性QTL,14个纤维长度可能性QTL,共计16个QTL,解释性状表型变异8.6-55.8%；6个马克隆值显著性QTL,3个马克隆值可能性QTL,共计9个QTL,解释性状表型变异9.6-34.7%；6个纤维比强度显著性QTL,4个纤维比强度可能性QTL,共计10个QTL,解释性状表型变异8.1-32.6%；4个纤维整齐度显著性QTL,13个纤维比强度可能性QTL,共计17个QTL,解释性状表型变异12.1-50.5%。在所有QTL中,有11个QTL与前人研究结果一致,6个QTL可在两个环境中检测到,这些共同QTL和环境稳定QTL可用于分子标记辅助选择。
在检测到的63个纤维品质QTL中,渝棉1号等位基因在中棉所35遗传背景下增加纤维品质性状表型值的有36个,在7235遗传背景下增加纤维品质表型值的有28个。中棉所35贡献23个增加纤维品质的等位基因,7235贡献33个增加纤维品质的等位基因。
Cotton (Gossypium spp.), one of the most economically important crops worldwide, is a renewable source of natural fiber and secondary products such as oil, livestock feed and cellulose. The genus Gossypium comprises approximately 45 diploid and 5 tetraploid species, including 4 cultivated species, G. arboreum, G. herbaceum, G. hirsutum and G. barbadense. Of the cultivated species, G. hirsutum supplies over 95% of the world's total fiber production.
During the past decades, cotton breeders have placed more emphasis on increasing yield. As the basic raw materials for textile industry, fiber quality is highly correlated with spinning performance and end product quality. Technological advance in the textile industry requires high fiber quality. This requirement has attracted more efforts toward improving fiber properties, especially those of upland cotton.
Conventional cultivar breeding programs, primarily relying on intermating adapted upland cotton genotypes and selecting novel allele combinations based on phenotypic selection, have certainly improved fiber quality while also increasing fiber yields in upland cotton. However, the quantitative inheritance and unfavorable correlations between lint yield and fiber quality greatly limited the efficiency of conventional breeding efforts in upland cotton improvement. Therefore, it needs to develop more effective strategies in the future cotton breeding programs.
Great advances in DNA maker technologies have provided new insights on genetic improvement of cotton fiber quality. Based on the detailed molecular linkage maps, quantitative trait locus (QTL) affecting fiber quality traits could be mapped, genetically evaluated and selected through linked markers (marker-assisted selection, MAS), and even cloned (map-based cloning). Combining the powerful molecular tools and conventional breeding will provide effective approaches to select and develop cotton cultivars with improved fiber quality. Since the first molecular linkage map was constructed in cotton, genetic maps derived from interspecific populations are relatively saturated. However, so far the interspecific maps have little use in upland cotton breeding programs. The most extensive coverage map of upland cotton spanned 3,140.9 cM, accounting for 70.6% of the whole tetraploid cotton genome. Because the level of intrapecific polymorphism revealed by DNA markers is low in upland cotton, the resolution available in the existing intraspecific maps is satisfactory neither for MAS nor for map-based cloning. To obtain high-density intraspecific map, which can be used in MAS and map-based cloning in upland cotton, it needs to develop new type of markers, use upland cotton cultivars/lines with high polymorphism as mapping parents, or employ new type of mapping populations.
Composite cross populations (CP), developed from three/more cultivars/parental lines, are frequently applied in crop cultivar development programs to improve agronomic and economic traits through gradually accumulating the additive effects of novel allele combinations based on phenotypic selection. However, historically linkage analysis and QTL mapping in cotton routinely capitalize on the populations derived from simple crosses (e.g., F2 and backcross). Upland cotton genetic maps in simple crosses showed limited resolution, most likely as a result of low polymorphism between two mapping parents. QTL detected in a simple cross merely represent the paucity of genetic architecture in traits, whereas a large amount of QTL information could not be exploited. Furthermore, at most two allelic effects are able to be characterized in crosses involving two inbred lines, which is a limitation to feasible options for designing optimum breeding strategies grounded on MAS. Employing CP into linkage analysis and QTL mapping may increase the marker density of upland genetic maps, exploit more adequate gene resources and facilitate MAS.
In the present study, molecular markers and segregating population derived from three parents were used to develop genetic linkage map and to exploit QTL concerned with fiber quality traits. Three upland cultivars/lines, Yumianl, CRI 35 and 7235 were used to obtain the segregating population, Yumianl/CRI 35//Yumianl/7235, and its F1:2/3 inbreed lines. A linkage map developed from CP was constructed by JoinMap4.0. Based on 3 years of phenotypic data, QTL for five fiber quality traits, fiber elongation (FE), fiber length (FL), fiber micronaire reading (FM), fiber strength (FS), and fiber length uniformity ratio (FU) were analysed by MapQTL5.0. The results are followed:
1. Polymorphism of SSR markers and genotyping
In total,16,052 SSR primer pairs were used to screen the polymorphism among Yumian 1, CRI 35 and 7235, and 1,057, acconting for 6.6% of the tatal primer pairs, showed effective polymorphism. The effective polymorphic primer pairs (1,057) produced 1,067 loci when they were used to genotype the CP individuals. Chi-square test showed that 375 loci significantly distorted from the expected segregation ratio (P＜0.05), accounting for 35.1% of the total loci.
2. Genetic mapconstruction
When 1,067 loci were used to construct the linkage groups, a map with 978 loci and 69 groups was obtained, remaining 89 loci unlinked.The map spanned 4,184.4 cM with an average distance of 4.3 cM between two markers, accounting for about 94.1% of the whole tetraploid cotton genome. Sixty-five of sixty-nine linkage groups were assigned to 26 chromosomes of tetraploid cotton. The remaining 4 linkage groups could not be associated with any chromosome and were tentatively named as "Un" following a number. Thirty-two linkage groups were assigned to A-subgenome, containing 366 loci, and spanning 1,954.3 cM with an average distance of 5.3 cM between two markers. Thirty-three linkage groups were assigned to D-subgenome, containing 599 loci, and spanning 2,122.1 cM with an average distance of 3.5 cM between two markers.
3. Fiber quality phenotypes of mapping parents, F1 and F1:2/3families
In year 2007,2008 and 2009, the fiber length of 7235 were 31.9,34.5 and 34.1 mm, respectively, which was higher than that of Yumian 1 (29.9,30.3 and 30.6 mm) and CRI 35 (29.3, 30.2 and 31.4 mm). In year 2007,2008 and 2009, the parental lines, Yumian 1 and 7235, exhibited relatively higher fiber strength (38.1,34.2 and 41.3 cN/tex and 38.6,36.2 and 41.3 cN/tex) than CRI 35 (33.5,30.7 and 34.9 cN/tex). The other fiber quality traits of three parental lines were close to each other.
In year 2007, fiber length ranged from 28.2 to 34.4 mm, and averaged 31.2 mm; Fiber length uniformity ranged from 80.9 to 88.1% and averaged 85.3%; Fiber strength ranged between 29.2 and 39.7 cN/tex, averaged 34.0 cN/tex; Fiber elongation was 6.5% on average and ranged from 6.2 to 6.7%; Fiber micronare reading ranged between 3.5-5.0, and averaged 4.2. In year 2008, fiber length ranged from 28.4 to 34.8 mm, and averaged 31.9 mm; Fiber length uniformity ranged from 81.6 to 87.5% and averaged 85.4%; Fiber strength ranged between 29.8 and 39.3 cN/tex, averaged 34.0 cN/tex; Fiber elongation was 6.6% on average and ranged from 6.3 to 6.8%; Fiber micronare reading ranged between 3.1-5.2 and averaged 4.1. In year 2009, fiber length ranged from 29.4 to 36.2 mm, and averaged 32.0 mm; Fiber length uniformity ranged from 82.3 to 87.4% and averaged 85.3%; Fiber strength ranged between 31.6 and 43.9 cN/tex, averaged 37.3 cN/tex; Fiber elongation was 6.6% on average and ranged from 6.3 and 6.9%; Fiber micronare reading ranged between 3.1-5.1, and averaged 4.1. Among all five fiber traits, transgressive segregation was oberserved except for fiber elongation.
Singnificantly positive correlations were observered between different fiber traits except for fiber micronare reading and length, fiber micronare reading and strength, with correlation coefficients ranged from 0.276-0.687. Singnificantly negative correlations were observered between micronare reading and length, fiber micronare reading and strength, with correlation coefficients-0.472 and-0.321, respectively.
The variance analysis indicated that fiber micronare reading was significantly influenced by both genotype (P＜0.01) and environment (P＜0.01); fiber length uniformity and elongation were influenced by neither genotype nor environment; fiber length was significantly influenced by environment (P＜0.05), but not by genotype; fiber strength was significantly influenced by both genotype (P＜0.05) and environment (P＜0.01).
4. QTL mapping of fiber quality traits
All the five fiber quality traits segregated continuously and transgressive segregations were observed for fiber length, length uniformity, micronaire reading and strength. Totally,63 QTL were identified for five fiber quality traits, and mapped on 18 chromosomes and 2 Un linkage groups, including 27 significant QTL with the LOD thresholds more than the permutation-based LOD thresholds and 36 putative QTL with the LOD thresholds between 3.0 and the permutation-based LOD thresholds.
For fiber elongation, nine significant QTL and two putative QTL were identified, and explained phenotypic variation between 10.5 and 47.1%. Only significant QTL qFE24.2 was detected in two environments (in year 2007 and 2008).
For fiber length, sixteen QTL were identified, and explained phenotypic variation between 8.6 and 55.8%. Two significant QTL and fourteen putative QTL were detected in one environment except for putative QTL qFLunO2.1, which was detected in year 2007 and 2008.
For fiber micronaire reading, six significant QTL and three putative QTL were identified, and explained phenotypic variation between 9.6 and 34.7%. Four significant QTL were detectedin two environments, and one of the four QTL. qFM03.1, was detected in year 2007 and 2008, and three others, qFM24.2, qFM24.3 and qFM24.4, were detected in year 2007 and 2009.
For fiber strength, six significant QTL and four putative QTL were identified, and explained phenotypic variation between 8.1 and 32.6%. All the QTL for fiber strength were detected only in one environment.
For fiber length uniformity, four significant QTL and thirteen putative QTL were identified, and explained phenotypic variation between 12.1 and 50.5%. All the QTL for fiber length uniformity were detected only in one environment.
Among the QTL detected, six QTL were detected in two environments, which showed stablity in different environments. According to the sharing common markers, eleven QTL identified in the present study were also found in the same chromosome region in other populations, and these QTL included qFE24.2, qFL23.2, qFL24.2, qFM23.1, qFM24.2, qFM24.3, qFS07.1, qFS23.1, qFE24.2, qFS24.2 and qFS24.3. The QTL identified in the two environments and across different populations are of great value for MAS programs in cotton.
Among the 63 QTL detected,36 and 28 alleles leading to an increase in all 5 fiber quality traits were conferred by Yumian 1 in CRI 35 and 7235 genetic background, respectively. CRI 35 contributed 23 alleles to increase five fiber quality traits.7235 contributed 33 alleles to increase fiber quality traits
引文
[I]Alpert KB, Tanksley SD (1996) High resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2:A major fruit weight quantitative trait locus in tomato. Proc. Natl Acad Sci USA 93:15503-15507
[2]Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407:513-516
[3]Anderson CG (1999) Cotton marketing. In:Smith CW, Cothren JT (eds) Cotton:origin, history, technology, and production. Wiley, New York, pp659-679
[4]Andru S, Pan YB, Thongthawee S, Burner DM, Kimbeng CA (2011) Genetic analysis of the sugarcane (Saccharum spp.) cultivar'LCP 85-384'. I. Linkage mapping using AFLP, SSR, and TRAP markers. Theor Appl Genet
[5]Applequist WL, Cronn R, Wendel JF (2001) Comparative development of fiber in wild and cultivated. Evol Dev 3:3-17
[6]Bernatzky R, Tanksley SD (1986) Towards a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887-898
[7]Bolek Y, El-Zik KM, Pepper AE (2005) Mapping of verticillium wilt resistance genes in cotton. Plant Science 168:1581-1590
[8]Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-331
[9]Bridge RR, Meredith WR (1983) Comparative performance of obsolete and current cotton cultivars. Crop Sci 23:949-952
[10]Brubaker CL, Paterson AH, Wendel JF (1999) Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42:184-203
[11]Brubaker CL, Wendel JF (1994) Reevaluating the origin of domesticated cotton{Gossypium hirsutum:Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). American Journal of Botany 81:1309-1326
[12]Brubaker CL, Brown AHD (2003) The use of multiple alien chromosome addition aneuploids facilitates genetic linkage mapping of the Gossypium G genome. Genome 46:774-791
[13]Burgess-Herbert SL, Cox A, Tsaih SW, Paigen B (2008) Practical applications of the bioinformatics toolbox for narrowing quantitative trait loci. Genetics 180:2227-2235
[14]Cedroni ML, Cronn RC, Adams KL, Wilkins TA, Wendel JF (2003) Evolution and expression of MYB genes in diploid and polyploid cotton. Plant Mol Biol 51:313-325
[15]Chabane K, Ablett GA, Cordeiro GM et al. (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genetic Resources and Crop Evolution 52: 903-909
[16]Chang YL, Tao QZ, Scheming C, Ding KJ, Meksem K, Zhang HB (2001) An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics 159:1231-1242
[17]Chee P, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypiwn barbadense (cotton) by a backcross-self approach:I. Fiber elongation. Theor Appl Genet 111:757-763
[18]Chee PW, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach:III. Fiber length. Theor Appl Genet 111:772-781
[19]Chen CX, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum TG, Gmitter FG (2008) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genet Genomes 4:1-10
[20]Chen H, Qian N, Guo WZ, Song QP, Li BC, Deng FJ, Dong CG, Zhang TZ (2009) Using three overlapped RILs to dissect genetically clustered QTL for fiber strength on Chro.D8 in Upland cotton. Theor Appl Genet 119:605-612
[21]Chen J, Hu J, Vick BA, Jan CC (2006) Molecular mapping of a nuclear male-sterility gene in sunflower (Helianthus annuus L.) using TRAP and SSR markers. Theor Appl Genet 113: 122-127
[22]Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang TZ, Guo WZ, Chen XY, Stelly DM, Rabinowicz PD, Town CD, Arioli T, Brubaker C, Cantrell RG, Lacape JM, Ulloa M, Chee P, Gingle AR, Haigler CH, Percy R, Saha S, Wilkins T, Wright RJ, Deynze AV, Zhu YX, Yu SX, Abdurakhmonov I, Katageri I, Kumar PA, Rahman M, Zafar Y, Yu JZ, Kohel RJ, Wendel JF, Paterson AH (2007) Toward sequencing cotton{Gossypium) genomes. Plant Physiol 145: 1303-1310
[23]Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. Bmc Genet 3:19
[24]Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics 100:713-722
[25]Cong B, Uu J, Tanksley SD (2002) Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatorymutations. Proc Natl Acad Sci USA 99:13606-13611
[26]Cronn RC, Adams KL (2003) Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP. Biotechniques 34:726-730
[27]Cronn RC, Small RL, Wendel JF (1999) Duplicated genes evolve independently after polyploid formation in cotton. Proceedings of the National Academy of Sciences USA 96: 144406-114411
[28]Culp TW (1982) The present state of the art and science of cotton breeding for fiber quality. Proc Beltwide Cotton Prod Res Conf 1982:99-110
[29]Culp TW, Harrell DC (1974) Breeding quality cotton at the Pee Dee Experiment Station, Florence, SC, USDA Publ, ARS-S-30
[30]Culp TW, Harrell DC, Kerr T (1979) Some genetic implication in the transfer of high fiber strength genes to upland cotton. Crop Sci 19:481^184
[31]Darvasi A, Soller M (1992) Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus. Theor Appl Genet 85:353-359
[32]Darvasi A, Soller M (1994) Optimum spacing of genetic markers for determining linkage between marker loci and quantitative trait loci. Theor Appl Genet 89:351-357
[33]Desai A, Chee PW, Rong JK, May OL, Paterson AH (2006) Chromosome structural changes in diploid and tetraploid A genomes of Gossypium. Genome 49:336-345
[34]Dol K, Izawa T, Fuse T, Yemanouchl U, Kubo T, Shimatanl Z, Yano M, Yoshimura A (2004) Ehdl, a B-type response regulator in rice, confers shot-day promotion of flowering and controls FT-hke gene expression independently of Hdl. Genes Dev 18:926-936
[35]Draye X, Chee P, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach:II. Fiber fineness. Theor Appl Genet 111: 764-771
[36]Dyrskjot L, Zieger K, Orntoft TF (2007) Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers. Front Biosci 12:2063-2073
[37]Edwards GA, Endrizzi JE, Stein R (1974) Genome DNA content and chromosome organization in Gossypium. Chromosoma 47:309-326
[38]Edwards GA, Mirza MA. Genomes of the Australian wild species of cotton. II (1979) The designation of a new G genome for Gossypium bickii. Can. J Genet Cytol 21:367-372
[39]Edwards MD, Stuber CW, Wendel JF (1987) Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113-125
[40]Endrizzi J, Turcotte EL, Kohel RJ (1985) Genetics, cytology, and evolution of Gossypium. Adv Genet 23:272-375
[41]Flavell AJ, Bolshakov VN, Booth A, Jing R, Russell J, Ellis TH, Isaac P (2003) A microarray-based high throughput molecular marker genotyping method:the tagged microarray marker (TAM) approach. Nucleic Acids Res 31:el 15
[42]Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14:1812-1819
[43]Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357-574
[44]Frelichowski JE, Palmer MB, Dorrie M, Tomkins JP, Cantrell RG, Stelly DM, John Y, Kohel RJ, Ulloa M (2006) Cotton genome mapping with new microsatellites from Acala'Maxxa' BAC-ends. Mol Genet Genomics 275:479-491
[45]Fridman E, Pleban T, Zamlr D (2000) A recombination hotspot delimits a wild species quantitative trait locus for tomato sugar content to 484 bp within an invedase gene. Proc Natl Acad Sci USA 97:4718^723
[46]Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225-2229
[47]Galau GA, Wilkins TA (1989) Alloplasmic male-sterility in AD allotetraploid Gossypuun hirsutum upon replacement of its resident cytoplasm with that of D-species Gossypium harkness. Theor Appl Genet 78:23-30
[48]Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ (2004) One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet 108:1392-1400
[49]Gardiner J, Schroeder S, Polacco ML, Sanchez-Villeda H, Fang ZW, Morgante M, Landewe T, Fengler K, Useche F, Hanafey M, Tingey S, Chou H, Wing R, Soderlund C, Coe EH (2004) Anchoring 9371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiol 134: 1317-1326
[50]Geever RF, Katterman F, Endrizzi JE (1989) DNA hybridization analyses of a Gossypium allotetraploid and two closely related diploid species. Theor Appl Genet 77:553-559
[51]Gonzalo MJ, Oliver M, Garcia-Mas J, Monfort A, Dolcet-Sanjuan R, Katzir N, Arus P, Monforte AJ (2005) Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theor Appl Genet 110:802-811
[52]Green CC, Culp TW (1990) Simultaneous improvement of yield, fiber quality, and yarn strength in Upland cotton. Crop Sci 30:66-69
[53]Gregory SR, Hernandez E, Savoy BR (1999) Cottonseed processing. In:Smith CW, Cothren JT (eds) Cotton; origin, history, technology, and production. Wiley, New York, pp793-823
[54]Guo WZ, Cai CP, Wang CB, Zhao L, Wang L, Zhang TZ (2008) A preliminary analysis of genome structure and composition in Gossypium hirsutum BMC Genomics 9:314
[55]Guo WZ, Ma GJ, Zhu YC, Yi CX, Zhang TZ (2006) Molecular tagging and mapping of quantitative trait loci for lint percentage and morphological marker genes in upland cotton. Journal of Integrative Plant Biology 48:320-326
[56]Guo YF, McCarty JC, Jenkins JN, Saha S (2008) QTLs for node of first fruiting branch in a cross of an upland cotton, Gossypium hirsutum L., cultivar with primitive accession Texas 701. Euphytica 163:113-122
[57]Gutierrez OA, Basu S, Saha S, Jenkins JN, Shoemaker DB, Cheatham C, McCarty JC (2002) Genetic distance of cottoncultivars and germplasm lines based on SSR markers and itsassociation with agronomic and fiber traits of their F2 hybrids. CropSci.42:1841-1847
[58]Gutierrez OA, Jenkins JN, McCarty JC, Wubben MJ, Hayes RW, Callahan FE (2010) SSR markers closely associated with genes for resistance to root-knot nematode on chromosomes 11 and 14 of Upland cotton.TheorAppl Genet 121:1323-1337
[59]Gutierrez OA, Robinson AF, Jenkins JN, McCarty JC, Wubben MJ, Callahan FE, Nichols RL (2011) Identification of QTL regions and SSR markers associated with resistance to reniform nematode in Gossypium barbadense L. accession GB713. Theor Appl Genet 122:271-280
[60]Haldane (1919) J.B.S. J Genet 8:299-309
[61]Han Z, Guo W, Song X, Zhang T (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol Gen Genomics 272:308-327
[62]He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Feng CD, Stewart JM (2005) Mapping QTLs of traits contributing to yield and analysis of genetic effects in tetraploid cotton. Euphytica 144: 141-149
[63]He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W (2007) QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153:181—197
[64]Hoskins RA, Phan AC, Naeemuddin M, Mapa FA, Ruddy DA, Ryan JJ, Young LM, Wells T, Kopczynski C, Ellis MC (2001) Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res 11:1100-1113
[65]Hu J, Vick BA (2003) Target regeion amplification polymorphism:A novel marker technique for plant genotyping plant. Molecular Biology Reporter 21:289-294
[66]Hu KM, Qiu DY, Shen XL, Li XH, Wang SP (2008) Isolation and manipulation of quantitative trait loci for disease resistance in rice using a candidate gene approach. Mol Plant 1:786-793
[67]Iqbal MJ, Aziz N, Saeed NA, Zafar Y, Malik KA (1997) Genetic diversity evaluation of some elite cotton varieties RAPD analysis. Theor Appl Genet 94:139-144
[68]Jenkins JN, McCarty JC, Wu JX, Saha S, Gutierrez O, Hayes R, Stelly DM (2007) Genetic effects of thirteen Gossypium barbadense L. chromosome substitution lines in topcrosses with Upland cotton cultivars:Ⅱ. fiber quality traits. Crop Sci 47:561-571
[69]Jiang C, Wright RJ, Woo SS, DelMonte TA, Paterson AH (2000) QTL analysis of leaf morphology in tetraploid Gossypium (cotton). Theoretical and Applied Genetics 100:409-418
[70]Jiang C, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140:1111-1127
[71]Jiang CX, Wright RJ, El-Zik KM, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proceedings of the National Academy of Sciences of the United States of America 95:4419-4424
[72]Kantartzi SK, Stewart JM (2008) Association analysis of fibre traits in Gossypium arboreum accessions. Plant Breeding 127:173-179
[73]Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics.152:1203-1216
[74]Kohel RJ, Yu J, Park YH, Lazo GR (2001)Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121:163-172
[75]Kollma S, Takahsshl Y, Kobayashi Y, Monna L, Sssakl T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering down stream of Hdl under short-day conditions. Plant Cell Physiol 43:1096-1105
[76]Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172-175
[77]Krishnaswai R, Kothandaraman R (1975) Favorable influence of Gossypium raimondii genes on fibre properties of cultivated cotton. Genetica Agraria 29:277-281
[78]Lacape JM and Nguyen TB (2005) Mapping quantitative trait loci associated with leaf and stem pubescence in cotton. Journal of Heredity 96:441-144
[79]Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum x Gossypium barbadense backcross generations. Crop Sci 45:123-140
[80]Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population. Genome 46:612-626
[81]Lefebvre V, Pflieger S, Thabuis A, Caranta C, Blattes A, Chauvet JC, Daubeze AM, and Palloix A (2002) Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes. Genome 45:839-854
[82]Li G, Quiros C F (2001) Sequence-related am plified polymorphism (SRAP).a new marker system based on a simple PCR reaction:its application to m apping and gene tagging in Brassica. Theor Appl Genet 103:455^61
[83]Li L, Wang JJ, Guo Y, Jiang FS, Xu YF, Wang YY, Pan HT, Han GZ, Li RJ, Li SS (2008) Development of SSR markers from ESTs of gramineous species and their chromosome location on wheat. Prog Nat Sci 18:1485-1490
[84]Li YN, Uhm T, Ren CW, Wu CC, Santos TS, Lee MK, Yan B, Santos F, Zhang AM, Scheuring C, Sanchez A, Millena AC, Nguyen HT, Kou HD, Liu DQ, Zhang HB (2007) A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence. Genome 50:278-288
[85]Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterizetion and detection of epistatic interactions of 3 QTLs, Hdl, Hd2 and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021-1028
[86]Lin LF, Pierce GJ, Bowers JE, Estill JC, Compton RO, Rainville LK, Kim C, Lemke C, Rong JK, Tang HB, Wang XY, Braidotti M, Chen AH, Chicola K, Collura K, Epps E, Golser W, Grover C, Ingles J, Karunakaran S, Kudrna D, Olive J, Tabassum N, Um E, Wissotski M, Yu Y, Zuccolo A, Rahman MU, Peterson DG, Wing RA, Wendel JF, Paterson AH (2010) A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics 11:359
[87]Lin ZX, Zhang XL, Nie YC, He DH, Wu MQ (2003) Construction of a genetic linkage map for cotton based on SRAP. Chinese Science Bulletin 48 (19):2063-2067
[88]Lin Z, He D, Zhang X, Nie Y, Guo X, Feng C, Stewart J McD (2005) Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD. Plant Breeding 124:180-187
[89]Lin ZX, Zhang YX, Zhang XL, Guo XP (2009) A high-density integrative linkage map for Gossypium hirsutum. Euphytica 166:35—45
[90]Liu L, Guo W, Zhu X, Zhang T (2003) Inheritance and fine mapping of fertility restoration for cytoplasmic male sterility in Gossypium hirsutum L. Theoretical and Applied Genetics 106: 461-469
[91]Liu RZ, Wang BH, Guo WZ, Qin YS Wang LG, Zhang YM, Zhang TZ (2011) Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Mol Breeding online first
[92]Liu S, Saha S, Stelly D, Burr B, Cantrell RG (2000) Chromosomal assignment of microsatellite loci in cotton. J Hered 91:326-332
[93]McCouch SR, Cho YG, Yano PE, Blinstrub M, Morishima H, Kinoshita T (1997) Report on QTL nomenclature. Rice Gene Newslett 14:11-13
[94]Mei M, Syed NH, Gao W, Thaxton PM, Smith CW, Stelly DM, Chen ZJ (2004) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280-291
[95]Moore SS, Sargeant LL, King TJ, Mattick JS, Georges M, Hetzel DJS (1991) Genomics 10: 654-660
[96]Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet 22:271-275
[97]Multanid S, Lyon BR (1995) Genetic finger pringting of Australian cotton cultivars with RAPD markers. Genome 38:1005-1008.
[98]Muramoto H (1973) Hexaploid cotton:some fiber and spinning properties. Crop Sci 13: 396-397
[99]Ndungo V, Demol J, Marechal R (1988) L'amelioration du cotonnierGossypium hirsutum L. par hybridation interspecifique.Bulletin des Recherches Agronomiques de Gembloux 23:1-92
[100]Nguyen TB, Giband M, Brottier P, Risterucci AM, Lacape JM (2004) Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor Appl Genet 109: 167-175
[101]Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800-805
[102]Niu C, Lister HE, Nguyen B, Wheeler TA, Wright RJ (2008) Resistance to Thielaviopsis basicola in the cultivated A genome cotton. Theor Appl Genet 117:1313-1323
[103]Norton GJ, Aitkenhead MJ, Khowaja FS, Whalley WR, Price AH (2008) A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping:an example using rice root-growth QTLs. Genomics 92:344-352
[104]Park YH, Alabady Magdy S, Ulloa M, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274:428-441
[105]Paterson A H, Brubaker C L, Wendel J F (1993) A rapid method for extraction of cotton (Gossypium ssp.) genomic DNA suitable for RFLP and PCR analysis. Plant Mol Biol Rep 11: 112-117
[106]Paterson AH, Estill J, Rong JK, Williams F, Marler B (2002) Toward a genetically-anchored physical map of the cotton genomes. Cotton Sci 14:31
[107]Paterson AH, Jiang CX, Collette A, Rana D, Welch J, Menz M, Chee P, Wright R (1999) Progress in understanding structure, function andevolution of the cotton genome. Plant &Animal Genome VII Conference Abstract 17-21
[108]Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ (2003) QTL analysis of genotype x environment interactions affecting cotton fiber quality. Theoretical and Applied Genetics 106: 384-396
[109]Percival AE, Wendel JF, Stewart JM (1999) Taxonomy and germplasm resources. In:Smith CW, Cothren JT (eds) Cotton origin, history, technology, and production. John Wiley& Sons Inc., New York, pp33-63
[110]Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220-228
[111]Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945-959
[112]Qin HD, Guo WZ, Zhang YM, Zhang TZ (2008) QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theor Appl Genet 117:883-894
[113]Qureshi SN, Saha S, Kantety RV, Jenkins JN (2004) EST-SSR:a new class of genetic markers in cotton. J Cotton Sci 8:112-123
[114]Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94-100
[115]Reddy A, Haisler RM, Weller JW Yu ZH, Kohel RL (1996) Development of amplified fragment length polymorphic makers in cotton. Plant Genome IV Conference. San Diego. CA.
[116]Reinisch AJ, Dong JM, Brubaker CL, Stelly DM, Wendel JF, Paterson AH (1994) A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense:chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829-847
[117]Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ESt (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479-11484
[118]Ren LH, Guo WZ, Zhang TZ (2002) Identification of quantitative trait loci (QTLs) affecting yield and fiber properties in chromosome 16 in cotton using substitution line, Acta Botanica Sinica 44:815-820
[119]Romano GB, Sacks EJ, Stetina SR, Robinson AF, Fang DD, Gutierrez OA, Scheffler JA (2009) Identification and genomic location of a reniform nematode{Rotylenchulus reniformis) resistance locus (Renan) introgressed from Gossypium aridum into upland cotton{G. hirsutum). Theor Appl Genet 120:139-150
[120]Rong J, Pierce GJ, Waghmare VN, Rogers CJ, Desai A, Chee PW, May OL, Gannaway JR, Wendel JF, Wilkins TA, Paterson AH (2005) Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor Appl Genet 111:1137-1146
[121]Rong JK, Abbey C, Bowers JE, Brubaker CL, Chang CL, Chee PW, Delmonte TA, Ding XL, Garza JJ, Marler BS, Park CH, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao XP, Zhu LH, Paterson AH (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton{Gossypium). Genetics 166:389^117
[122]Rostoks N, Mudie S, Cardie L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 274:515-527
[123]Rungis D, Llewellyn D, Dennis ES, Lyon BR (2002) Investigation of the chromosomal location of the bacterial blight resistance gene present in an Australian cotton{Gossypium hirsutum L.) cultivar. Australian Journal of Agricultural Research 53:551-560
[124]Sachidanandam R, Weissman D, Schmidt SC et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933
[125]Saha MC, Mian R, Zwonitzer JC, Chekhovskiy K, Hopkins AA (2005) An SSR-and AFLP-based genetic linkage map of tall fescue{Festuca arundinacea Schreb.) Theor Appl Genet 110:323-336
[126]Saha S, Jenkins JN, Wu J, McCarty JC, Gutierrez OA, Percy RG, Cantrell RG, Stelly DM (2006) Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits. Genetics 172:1927-1938
[127]Saha S, Karaca M, Jenkins JN, Zipf AE, Reddy UK, Kantety RV (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130:355-364
[128]Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs:present and future challenges. Trends Plant Sci 10:297-304
[129]Saranga Y, Jiang CX, Wright RJ, Yakir D, Paterson AH (2004) Genetic dissection of cotton physiological responses to arid conditions and their inter-relationships with productivity. Plant, Cell and Environment 27:263-277
[130]Saranga Y, Menz M, Jiang CX, Wright RJ, Yakir D, Paterson AH (2001) Genomic dissection of genotype x environment interactions conferring adaptation of cotton to arid conditions. Genome Research 11:1988-1995
[131]Shappley ZW (1994) Restriction fragment length polymorphisms in cotton (Gossypium hirsutum L.):feasability of use, diversity among plants within a line, and establishment of molecular markers and linkage groups among two F2 populations. MS thesis, Mississippi State University, Mississippi State, Mississippi
[132]Shappley ZW (1996) Construction of RFLP linkage groups and mapping of quantitative trait loci in Upland cotton (Gossypium hirsutum L.). PhD dissertation, Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi
[133]Shappley ZW, Jenkins JN, Meredith WR, McCarty JC (1998) An RFLP linkage map of upland cotton, Gossypium hirsutum L. Theor Appl Genet 97:756-761
[134]Shappley ZW, Jenkins JN, Zhu J, McCarty JC (1998) Quantitative trait loci associated with agronomic and fiber traits of upland cotton. Journal of Cotton Science 2:153-163
[135]Schlotterer C, Amos B, Tautz D (1991) Conservation of polymorphic simple sequence loci in cetacean species. Nature 354:63-65
[136]Shen X, Becelaere GV, Kumar P, Davis RF, May OL, Chee P (2006) QTL mapping for resistance to root-knot nematodes in the M-120 RNR Upland cotton line{Gossypium hirsutum L.) of the Auburn 623 RNR source. Theoretical and Applied Genetics 113:1539-1549
[137]Shen X, Guo W, Lu Q, Zhu X, Yuan Y, Zhang T (2007) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155:371-380
[138]Shen XL, Guo WZ, Zhu XF, Yuan YL, Yu JZ, Kohel RJ, Zhang TZ (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breeding 15:169-181
[139]Shen X, Zhang T, Guo W, Zhu X, Zhang X (2006) Mapping fiber and yield QTLs with main, epistatic, and QTL x environment interaction effects in recombinant inbred lines of Upland cotton. Crop Science 46:61-66
[140]Shen XL, Guo WZ, Lu QX, Zhu XF, Yuan YL, Zhang TZ (2007) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155:371-380
[141]Shen XL, Guo WZ, Zhu XF, Yuan YL, Yu JZ, Kohel RJ, Zhang TZ (2005) Molecular mapping of QTL for fiber qualities in three diverse lines in upland cotton using SSR markers. Mol Breeding 15:169-181
[142]Sket L, Humphreys MO, Armstead I, Hey wood S, Skot KP, Sanderson R, Thomas ID, Chorlton KH, Sackville NR (2005) An association mapping approach to identify flowering time genes in natural populations of Loliumperenne (L.). Mol Breed 15:233-245
[143]Skovsted A (1937) Cytological studies in cotton IV:chromosome configuration in interspecific hybrids. Genetics 34:97-134
[144]Song XL, Wang K, Guo WZ, Zhang J, Zhang TZ (2005) A comparison of genetic maps constructed from haploid and BC1 mapping populations from the same crossing between Gossypium hirsutum L. and Gossypium barbadense L. Genome 48:378—390
[145]Song XL, Guo WZ, Han ZG, Zhang TZ (2005) Quantitative trait loci mapping of leaf morphological traits and chlorophyll content in cultivated tetraploid cotton. Journal of Integrative Plant Biology 47:1382-1390
[146]Stewart JM (1994) Potential for crop improvement with nues for evolution. Genetics 149: 1987-1996
[147]Takahashi Y, Shomura A, Sasaki T, Yano M (2001). Hd6, a rice quantitive trait locus involved in photoperiod sensitivity, encodes the-subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922-7927
[148]Tang QY, Feng MG (2005) DPS Data processing system. Science Press, Beijing
[149]Tanksley SD, Hewitt J (1988) Use of molecular markers in breeding for soluble solids content in tomato-a re-examination. Theor Appl Genet 75:811-823
[150]Tao Q, Chang YL, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang HB (2001) Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711-1724
[151]Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422
[152]Thornsberry JM, Goodman MM, Doebley JI Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286-289
[153]Uauy C, Distelfeld A, Fehima T, Blechl A, Oubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc and iron content in wheat. Science 314:1298-1301.
[154]Ulloa M, Meredith WR Jr (2000) Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J Cotton Sci 4:161-170
[155]Ulloa M, Meredith WR, Shappley ZW, Kahler AL (2002) RFLP genetic linkage maps from four F23 populations and a joinmap of Gossypium hirsutum L. Theor Appl Genet 104:200-208
[156]Ulloa M, Saha S, Jenkins JN, Meredith WR, McCarty JC, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) joinmap. Journal of Heredity 96:132-144
[157]Valderrama C (2004) Fifth year of record consumption. Cotton:review of the world situation (ICAC) 58:10-12
[158]Van Ooijen JW (2004) MapQTL5.0:Software for the mapping quantitative trait loci in experimental populations. Plant Research International, Wageningen
[159]Van Ooijen JW, Voorrips RE (2006) Joinmap4.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen
[160]Vigouroux Y, Mcmullen M, Hittinger CT (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proceeding of National Academy of Science 99:9650-9655
[161]Voorrips RE (2006) MapChart 2.2:Software for the graphical presentation of linkage maps and QTL. Plant Research International, Wageningen
[162]Waghmare VN, Rong JK, Roger CJ, Pierce GJ, Wendel JF, Paterson AH (2005) Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum. Theoretical and Applied Genetics 111:665-676
[163]Wang B, Guo W. Zhu X, Wu Y, Huang N, Zhang T (2006) QTL mapping of fiber quality in an elite hybrid derived-RIL population of upland cotton. Euphytica 152:367-378
[164]Wang B, Guo W, Zhu X, Wu Y, Huang N, Zhang T, (2007) QTL mapping of yield and yield components for elite hybrid derived-RILs in Upland cotton. Journal of Genetics and Genomics 34:35-45
[165]Wang BH, Wu YT, Huang NT, Zhu XF, Guo WZ, Zhang TZ (2006) QTL mapping for plant architecture traits in upland cotton using RILs and SSR markers. Acta Genetica Sinica 33: 161-170
[166]Wang C, Roberts PA (2006) Development of AFLP and derived CAPS markers for root-knot nematode resistance in cotton. Euphytica 152:185-196
[167]Wang C, Ulloa M, Roberts PA (2006) Identification and mapping of microsatellite markers linked to a root-knot nematode resistance gene (rknl) in Acala NemX cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics 112:770-777
[168]Wang DL, Zhu J, Li KL, Paterson AH (1999) Mapping QTLs with epistatic effects and QTL x environment interactions by mixed linear model approaches. Theor Appl Genet 99:1255-1264
[169]Wang K, Song XL, Han ZG, Guo WZ, Yu JZ, Sun J, Pan JJ, Kohel RJ, Zhang TZ (2006) Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping. Theor Appl Genet 113:73-80
[170]Weining S, Langridge P (1991) Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction. Theor Appl Gene 82:209-216
[171]Wendel JF (2000) Genome evolution in polyploids. Plant Molecular Biology 42:225-249
[172]Wendel JF, Albert FA (1992) Phylogenetics of Cotton genus{Gossypium):character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst Bot 17:115-143
[173]Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Advances Agronomy,78:139-186
[174]Wendel JF, Cronn RC, Johnston JS, Price HJ (2002) Feast and famine in plant genomes. Genetica 115:37-47
[175]Wendel JF, Olson PD, Stewart JM (1989) Genetic diversity,introgression and independent domestication of Old WorldCultivated cottons. Am J Bot 76:1795-1806
[176]Wilkins TA, Wan CY, Liu CC (1994) Ancient origin of the vacuolar H+-ATPase 69-kilodalton catalytic subunit superfamily. Theor Appl Gene 89:514-524
[177]Wright RJ, Thaxton PM, El-Zik KM, Paterson AH (1998) D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues foreution. Genetics 149:1987-1996
[178]Wright RJ, Thaxton PM, El-Zik KM, Paterson AH (1999) Molecular mapping of genes affecting pubescence of cotton. Journal of Heredity 90:215-219
[179]Wu C, Sun S, Nimmakayala P, Santos FA, Meksem K, Springman R, Ding K, Lightfoot DA, Zhang HB (2004) A BAC-and BIBAC-based physical map of the soybean genome. Genome Res 14:319-326
[180]Wu JX, Jenkins JN, McCarty JC, Zhong M, Swindle M (2007) AFLP marker associations with agronomic and fiber traits in cotton. Euphytica 153:153-163
[181]Xiao JH, Fang DD, Bhatti M, Hendrix B, Cantrell R (2010) A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. Malvacearum in upland cotton (Gossypium hirsutum L.). Mol Breeding 25:593-602
[182]Xu S (1996) Mapping quantitative trait loci using four-way crosses. Genet Res 68:175-181
[183]Xu ZY, Kohel RJ, Song GL (2008) An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.). BMC Genomics 9:108
[184]Yanagisawa T, Kiribuchi-Otobe C, Hirano H, Suzuki Y, Fujita M (2003) Detection of single nucleotide polymorphism (SNP) controlling the waxy character in wheat by using a derived cleaved amplified polymorphic sequence (dCAPS) marker. Theor Appl Genet 107:84-88
[185]Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hdl, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473-2484
[186]Yi G, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet 114:113-130
[187]Yin J, Guo W, Yang L, Liu L, Zhang T (2006) Physical mapping of the Rfl fertility-restoring gene to a 100 kb region in cotton. Theoretical and Applied Genetics 112:1318-1325
[188]Ynturi P, Jenkins JN, McCarty JC, Gutierrez OA, Saha S. Association of root-knot nematode resistance genes with simple sequence repeat markers on two chromosomes in cotton. Crop Science 46:2670-2674
[189]Young ND, Tanksley SD (1989) RFLP analysis of the size of chromosomal segments retained around the Tm-2 locus of tomato during backross breeding. Theor Appl Genet 77:353-359
[190]Yu J, Kohel, RJ (1999) Update of the cotton genome mapping. Beltwide cotton conf:pp485
[191]Yu Y, Yuan DJ, Liang SG, Li XM, Wang XQ, Lin ZX, Zhang XL (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC] population between gossypium hirsutum and G. barbadense. BMC Genomics 12:15
[192]Zabean M, P Vos (1993) Selective restriction fragment amplication:a general method for DNA fingerprinting. European Patent Application no.92402629, Publication No. Ep0534858Al
[193]Zeng LH, Meredith WR, Gutierrez OA, Boykin DL (2009) Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple crosses among Gossypium tetraploid speciesTheor Appl Genet 119:93-103
[194]Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972-10976
[195]Zhang HB, Li YN, Wang BH, Chee PW (2008) Recent Advances in Cotton Genomics. Int J Plant Genomics (published online)
[196]Zhang T, Yuan Y, Yu J, Guo W, Kohel RJ (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theoretical and Applied Genetics 106:262-268
[197]Zhang ZS, Hu MC, Zhang J, Liu DJ, Zheng J, Zhang K, Wang W, Wan Q (2009) Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.). Mol Breeding 24:49-61
[198]Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L, Li DM, Pei Y (2005) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica 144:91-99
[199]Zhao XP, Si Y, Hanson RE, Crane CF, Price HJ, Stelly DM, Wendel JF, Paterson AH (1998) Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res 8:479-492
[200]Zheng J, Zhang ZS, Chen L, Wan Q, Hu MC, Wang W, Zhang K, Liu DJ, Chen X, Wei XQ (2008) Intron-targeted intron-exon splice conjunction (IT-ISJ) marker and its application in construction of upland cotton linkage map. Agric Sci China 7:1172-1180
[201]陈利,张正圣,胡美纯,王威,张建,刘大军,郑靓,郑风敏,马靖.陆地棉遗传图谱构建及产量和纤维品质性状QTL定位.作物学报,2008,34(6)：1-7
[202]方宜钧,吴为人,唐纪良.作物DNA标记辅助育种.北京：科学出版社,2002
[203]房卫平,许守明,孙玉堂,唐中杰,王家典.棉花抗黄萎病的RAPD标记.河南农业科学,2001,11-13
[2041高燕会.四个栽培棉种间的种间杂交及其遗传与系统发育研究.浙江大学博士学位论文2004
[2051郭旺珍,张天真,潘家驹,Kohel RJ.棉花胞质雄性不育育性恢复基因的RAPD-PCR标记的筛选.科学通报,1997,42(24)：2645-26470
[206]郭旺珍,周兆华,张天真,潘家驹.RAPD鉴定棉花抗(耐)黄萎病品种(系)的遗传变异研究.江苏农业学报,1999,15(1)：1-60
[207]郭香墨,刘金生.棉花良种引种指南.北京：金盾出版社,2003,p15-17
[208]李宏伟,高丽锋,刘曙东等.用EST-SSR研究小麦遗传多样性.中国农业科学,2005,38(1)：7-12
[209]李首成,江先炎.利用陆中杂种后代选育棉花高强度优质材料.中国棉花,1997,24(11)：9-11
[210]林刚,张轲,张建,藤中华,张正圣.ET-ISJ标记的开发及陆地棉遗传图谱构建.作物学报,2011,37(1)：87-94
[211]刘三宏.四倍体棉种起源与演化的FISH研究田.中国农业科学院硕士学位论文,2004
[212]柳李旺,朱协飞,郭旺珍等.分子标记辅助选择聚合棉花Rf1育性恢复基因和抗虫Bt基因.分子植物育种,2003,1：48-52
[213]齐俊生,马存,赵良忠.海岛棉品种抗黄萎病遗传规律初步研究.棉花学报,2000,12(4)：169-171
[214]钱思颖,黄骏麒,彭跃进,周宝良,应苗成,沈端庄,刘桂玲,胡廷馨,徐英俊,顾立美,倪万潮,陈松.1992.陆地棉(G. hirsutum)与异常棉(G. anomalum Wawr.& Peyr.)种间杂种的研究及其在育种上的应用.中国农业科学杂志,25(06)：44-51
[215]易成新,张天真,郭旺珍.陆地棉衣分QTL的形态和RAPD分子标记筛选.作物学报,2001,27(6)：781-7860
[216]袁有禄.棉花优质纤维特性的遗传及分子标记研究.博士学位论文,南京农业大学,1999
[217]张军,武耀廷,郭旺珍,张天真.棉花微卫星标记的PAGE/银染快速检测.棉花学报,2000,12(5)：267-2690
[218]甄瑞,王省芬,马峙英,张桂寅,王雪.海岛棉抗黄萎病基因SSR标记研究.棉花学报,2006,18(5)：149-152
[219]张正圣,张凤鑫.陆地棉高产量和高品质的同步改良.西南农业学报(增刊),1998,11：230-234
[220]朱云国,王学德,李悦有.用AFLP技术构建棉花雄性不育三系及其杂种F1的DNA指纹图谱.棉花学报,2001,13(3)：158-1600
[221]左开井,孙济中,张献龙,聂以春,刘金兰,冯纯大.利用RAPD, SSR, RFLP标记构建陆地棉分子标记连锁图谱.华中农业大学学报2000,19(3)：190-193