Development of Exon-Targeted Intron-Exon Splicing Conjunction (ET-ISJ) Marker and Establishment of Upland Cotton Genetic Map

Cotton is the leading fiber crop in the world, and upland cotton contributes over 95% of cotton production. The genetic map of upland cotton is far from saturated, so it is necessary to develop new markers for genetic map construction. ET-ISJ (exon targeted intron-exon splice conjunctions) marker primers were designed according to the conserved intron-exon splicing junction sequences. A total of 1 280 ET-ISJ primer combinations were used to screen polymorphism between upland cotton cultivar Yumian 1 and T586, and 69 of which showed polymorphism, accounting for 5.4% of total primer combinations. The 69 polymorphic ET-ISJ primer combinations were used to genotype 270 F2:7 recombinant inbred line derived from (Yumian 1 × T586), and 70 ET-ISJ loci were obtained. Linkage analysis was conducted on 70 ET-ISJ, 523 SSR, 59 IT-ISJ, 29 SRAP and 8 morphological loci, and a linkage map including 59 linkage groups and 673 loci (68 ET-ISJ, 510 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) was established. The linkage map covered 3 216.7 cM, accounting for 72.3% of cotton genome, with an average interval of 4.8 cM between two markers. Sixty-eight ET-ISJ loci were located on 20 chromosomes. The present study demonstrated that ET-ISJ markers were stable, highly polymorphic, and able to be effectively applied in genetic map construction of cotton and other plant’s.