Wang Hantao, Jin Xin, Zhang Beibei, Shen Chao, Lin Zhongxu
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
DNA Res. 2015 Apr;22(2):147-60. doi: 10.1093/dnares/dsu047. Epub 2015 Feb 5.
RAD sequencing was performed using DH962 and Jimian5 as upland cotton mapping parents. Sequencing data for DH962 and Jimian5 were assembled into the genome sequences of ≈55.27 and ≈57.06 Mb, respectively. Analysing genome sequences of the two parents, 1,323 SSR, 3,838 insertion/deletion (InDel), and 9,366 single-nucleotide polymorphism (SNP) primer pairs were developed. All of the SSRs, 121 InDels, 441 SNPs, and other 6,747 primer pairs were screened in the two parents, and a total of 535 new polymorphic loci were identified. A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population. Twenty-seven new QTLs for yield and fibre quality were identified, indicating that the efficiency of QTL detection was greatly improved by the increase in map density. Comparative genomics showed there to be considerable homology and collinearity between the AT and A2 genomes and between the DT and D5 genomes, although there were a few exchanges and introgressions among the chromosomes of the A2 genome. Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed. This map can be used for molecular marker-assisted selection in cotton.
以陆地棉作图亲本DH962和冀棉5号进行RAD测序。DH962和冀棉5号的测序数据分别组装成约55.27 Mb和约57.06 Mb的基因组序列。通过分析两个亲本的基因组序列，开发了1323个SSR、3838个插入/缺失（InDel）和9366个单核苷酸多态性（SNP）引物对。在两个亲本中筛选了所有的SSR、121个InDel、441个SNP以及另外6747个引物对，共鉴定出535个新的多态性位点。利用这些结果以及该群体先前发表的506个位点构建了包含1013个位点的遗传图谱。鉴定出27个与产量和纤维品质相关的新QTL，表明图谱密度的增加大大提高了QTL检测的效率。比较基因组学显示，AT和A2基因组之间以及DT和D5基因组之间存在相当程度的同源性和共线性，尽管A2基因组的染色体之间存在一些交换和渗入。在此，利用亲本RAD测序开发标记是有效的，并构建了高密度的种内遗传图谱。该图谱可用于棉花的分子标记辅助选择。
