Developing Exon-Targeted Intron-Exon Splicing Junction Marker and Establishing Genetic Map of Upland Cotton

The objective of this study was to develop new molecular markers and locate them into the existing genetic map of upland cotton (Gossypium hirsutum L.). Exon-targeted intron-exon splice junction (ET-ISJ) maker primers were designed according to the conserved sequences of intron-exon splicing junction. A total of 1280 ET-ISJ primer combinations were used to screen polymorphism between upland cotton cultivars Yumian 1 and T586. Sixty-nine primer combinations were polymorphic, which accounted for 5.4% of the total primer combinations. A mapping population of F2:7 from Yumian 1 × T586 were tested using the 69 ET-ISJ markers, and 70 ET-ISJ loci were obtained. Linkage analysis was conducted using the 70 ET-ISJ loci as well as 523 simple sequence repeat (SSR), 59 intron-tageted intron-exon splice junction (IT-ISJ), 29 sequence-related amplified polymorphism (SRAP), and 8 morphological loci. The linkage map obtained was composed of 59 linkage groups and 673 loci including 68 ET-ISJ, 510 SSR, 58 IT-ISJ, 29 SRAP, and 8 morphological loci. This linkage map covered 3216.7 cM (72.3%) of cotton genome with an average interval of 4.8 cM between 2 adjacent markers. Sixty-eight ET-ISJ loci were located on 20 chromosomes. The present study showed that ET-ISJ markers are relatively stable, highly polymorphic, and effective in constructing genetic map of upland cotton.

摘 要根据植物结构基因外显子拼接位点的保守序列, 设计扩增外显子的ET-ISJ (exon targeted intron-exon splice junction)标记引物。利用1 280对ET-ISJ引物组合, 对陆地棉品种渝棉1号和T586进行多态性筛选, 获得69对多态性引物组合, 占引物组合的5.4%。用多态性ET-ISJ引物组合检测(渝棉1号×T586)F2:7重组近交系群体, 得到70个位点。以70个ET-ISJ标记位点与523个SSR、59个IT-ISJ、29个SRAP和8个形态标记进行连锁分析, 构建的遗传连锁图谱包括59个连锁群和673个位点(68个ET-ISJ、510个SSR、58个IT-ISJ、29个SRAP和8个形态标记)。连锁图覆盖3 216.7 cM, 约占棉花基因组的72.3%, 标记间平均距离为4.8 cM。68个ET-ISJ标记分布于20条染色体。研究表明, ET-ISJ标记多态性较高、稳定性好, 可有效用于棉花与其他植物遗传连锁图谱构建。