Guo Wangzhen, Cai Caiping, Wang Changbiao, Han Zhiguo, Song Xianliang, Wang Kai, Niu Xiaowei, Wang Cheng, Lu Keyu, Shi Ben, Zhang Tianzhen
National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China.
Genetics. 2007 May;176(1):527-41. doi: 10.1534/genetics.107.070375. Epub 2007 Apr 3.
The mapping of functional genes plays an important role in studies of genome structure, function, and evolution, as well as allowing gene cloning and marker-assisted selection to improve agriculturally important traits. Simple sequence repeats (SSRs) developed from expressed sequence tags (ESTs), EST-SSR (eSSR), can be employed as putative functional marker loci to easily tag corresponding functional genes. In this paper, 2218 eSSRs, 1554 from G. raimondii-derived and 754 from G. hirsutum-derived ESTs, were developed and used to screen polymorphisms to enhance our backbone genetic map in allotetraploid cotton. Of the 1554 G. raimondii-derived eSSRs, 744 eSSRs were able to successfully amplify polymorphisms between our two mapping parents, TM-1 and Hai7124, presenting a polymorphic rate of 47.9%. However, only a 23.9% (159/754) polymorphic rate was produced from G. hirsutum-derived eSSRs. No relationship was observed between the level of polymorphism, motif type, and tissue origin, but the polymorphism appeared to be correlated with repeat type. After integrating these new eSSRs, our enhanced genetic map consists of 1790 loci in 26 linkage groups and covers 3425.8 cM with an average intermarker distance of 1.91 cM. This microsatellite-based, gene-rich linkage map contains 71.96% functional marker loci, of which 87.11% are eSSR loci. There were 132 duplicated loci bridging 13 homeologous At/Dt chromosome pairs. Two reciprocal translocations after polyploidization between A2 and A3, and between A4 and A5, chromosomes were further confirmed. A functional analysis of 975 ESTs producing 1122 eSSR loci tagged in the map revealed that 60% had clear BLASTX hits (<1e(-10)) to the Uniprot database and that 475 were associated mainly with genes belonging to the three major gene ontology categories of biological process, cellular component, and molecular function; many of the ESTs were associated with two or more category functions. The results presented here will provide new insights for future investigations of functional and evolutionary genomics, especially those associated with cotton fiber improvement.
功能基因的定位在基因组结构、功能及进化研究中发挥着重要作用，同时也有助于基因克隆和标记辅助选择，以改良具有重要农业价值的性状。从表达序列标签（EST）开发而来的简单序列重复（SSR），即EST-SSR（eSSR），可用作推定的功能标记位点，以便轻松标记相应的功能基因。本文开发了2218个eSSR，其中1554个来自雷蒙德氏棉（G. raimondii）的EST，754个来自陆地棉（G. hirsutum）的EST，并用于筛选多态性，以增强我们在异源四倍体棉花中的骨干遗传图谱。在1554个来自雷蒙德氏棉的eSSR中，有744个eSSR能够成功扩增我们的两个作图亲本TM-1和海7124之间的多态性，多态率为47.9%。然而，来自陆地棉的eSSR仅产生了23.9%（159/754）的多态率。未观察到多态性水平、基序类型和组织来源之间的关系，但多态性似乎与重复类型相关。整合这些新的eSSR后，我们增强后的遗传图谱由26个连锁群中的1790个位点组成，覆盖3425.8 cM，平均标记间距为1.91 cM。这个基于微卫星的、富含基因的连锁图谱包含71.96%的功能标记位点，其中87.11%是eSSR位点。有132个重复位点跨越了13对同源的At/Dt染色体对。进一步证实了多倍体化后A2与A3、A4与A5染色体之间的两次相互易位。对在图谱中标记的产生1122个eSSR位点的975个EST进行功能分析，结果显示60%在Uniprot数据库中有明确的BLASTX比对结果（<1e(-10)），475个主要与属于生物过程、细胞成分和分子功能这三个主要基因本体类别的基因相关；许多EST与两种或更多类别功能相关。本文给出的结果将为未来功能基因组学和进化基因组学的研究，特别是与棉花纤维改良相关的研究，提供新的见解。
