IT-ISJ Marker and Its Application in Construction of Upland Cotton Linkage Map
[Objective] To develop a new DNA marker, which could be used in genetic diversity analysis and genetic map construction in plant. [Method] IT-ISJ (intron targeted intron-exon splice junction) marker primers designed according to the intron-exon splice junction conserved sequences were used to construct cotton genetic linkage map. [Result] Fourty-nine out of 704 IT-ISJ primer combinations showed polymorphism between high quality upland cotton cultivar Yumian 1 and multiple dominant gene line T586, and the polymorphic primer combinations accounted for 7.0% of total primer combinations. Fourty-nine 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. Fifty-eight 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, accounting for 16.1% of cotton genome, with an average interval of 6.3 cM between two markers. [Conclusion] The present study demonstrated that IT-ISJ marker is highly polymorphic, and it could be effectively applied in plant genetic map construction.
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