Intron-Targeted Intron-Exon Splice Conjunction (IT-ISJ) Marker and Its Application in Construction o

To develop a new DNA maker, which could be used in genetic diversity analysis and genetic map construction in plants, IT-ISJ (intron targeted intron-exon splice junction) primer combinations, which were designed according to the intron- exon splice junction conserved sequences, were used to construct cotton genetic linkage map in the present study. 49 out of 704 IT-ISJ primer combinations showed polymorphism between upland cotton high quality cultivar Yumian 1 and multiple dominant gene line T586, and the polymorphic primer combinations accounted for 7.0% of total primer combinations. 49 IT-ISJ primer combinations were used to genotype 270 F2:7 recombinant inbred lines developed from (Yumian 1 × T586) F2, and 58 IT-ISJ loci were obtained. 58 IT-ISJ, together with 150 SSR and 8 morphological loci, were used to conduct linkage analysis, and a linkage map including 22 linkage groups and 113 loci (49 IT-ISJ, 62 SSR, and 2 morphological loci) was constructed. The linkage map covered 714.5 cM with an average interval of 6.3 cM between two markers, accounting for 16.1% of cotton genome. The present study demonstrated that the polymorphism of IT-ISJ marker is high, and it could be effectively applied in plant genetic map construction.