基因组研究中已被广泛挖掘与利用。异源四倍体棉花由于.PDFVIP

Wang Sen, Chen Jiedan, Zhang Wenpan, Hu Yan, Chang Lijing, Fang Lei, Wang Qiong, Lv Fenni, Wu Huaitong, Si Zhanfeng, Chen Shuqi, Cai Caiping, Zhu Xiefei, Zhou Baoliang, Guo Wangzhen*, Zhang Tianzhen*. Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes. Genome Biol, 2015,16: 108 (IF: 10.81 ；他引次数： 0) 摘要： 单核苷酸多态性（SNP ）是一种广泛存在的基因组多态类型，在许多作 物（包括水稻和玉米）基因组研究中已被广泛挖掘与利用。异源四倍体棉花由于 其基因组序列的复杂性和多倍性，SNP 的挖掘与利用相对滞后。本研究基于二代 测序和有效的 SNP 基因分型方法，构建了一张全基因组覆盖的异源四倍体棉花 高密度 SNP 遗传图谱，进而发现了多倍体棉花基因组的结构变异。本研究构建 了一张含4,999,048 个种间SNP 位点的超高密度遗传图谱，覆盖基因组4,042 cM 。 利用该图谱对陆地棉TM-1 基因组scaffold 进行纠错和排序。通过比较遗传图和 物理图，鉴定了棉花基因组的重组率及重组热点。与已公布的雷蒙德氏棉基因组 序列比较，精细分析了多倍体作物进化过程中的基因组结构变异，并且鉴定了着 丝粒区域。通过对二倍体和四倍体棉花基因组结构的比较，发现了亚基因组在进 化过程中的结构变异，D 亚组的功能着丝粒向 A 亚组入侵的现象。本研究为开 发棉花SNP 芯片，为棉花的遗传分子设计育种提供了有用的基因组资源。 Wang et al. Genome Biology (2015) 16:108 DOI 10.1186/s13059-015-0678-1 RESEARCH Open Access Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes † † Sen Wang , Jiedan Chen , Wenpan Zhang, Yan Hu, Lijing Chang, Lei Fang, Qiong Wang, Fenni Lv, Huaitong Wu, * * Zhanfeng Si, Shuqi Chen, Caiping Cai, Xiefei Zhu, Baoliang Zhou, Wangzhen Guo and Tianzhen Zhang Abstract Background: SNPs are the most abundant polymorphism type, and have been explored in many crop genomic studies, including rice and maize. SNP discovery in allotetraploid cotton genomes has lagged behind that of other crops due to their complexity and polyploidy. In this study, genome-wide SNPs are detected systematically using next-generation sequencing and efficient SNP g