Construction Of IT-ISJ Genetic Map In Upland Cotton (Gossypium Hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is the major natural fiber crop in the world, so construction of high-density genetic linkage map is important to promote the breeding process. The development of DNA markers prove that the combination of biotechnology and conventional breeding methods will become a new way for the crop improvement. Molecular marker-assisted breeding can select target gene at DNA level and improve the target trait.At present, the maps developed from interspecific population are relatively saturated, but the interspecific maps currently have little use in upland cotton improvement. Because the polymorphism of DNA marker is low in upland cotton, the present upland cotton linkage map has low maker-density and genome coverage and cannot meet the demand of marker-assisted selection. Therefore, a great number of new-type molecular markers, especially which are closely-linked with target genes, are required to be developed and to be used for constructing the whole genome-covered genetic linkage maps in upland cotton. According to the conserved sequences of intron-exon junctions, the present study designed IT-ISJ (intron targeted intron-exon splice junctions) marker primer, and used IT-ISJ and SSR to construct upland cotton genetic map with recombinant inbred line population developed from two upland cotton cultivars, Yumianl and T586. The main results showed as following:Characteristics of IT-ISJ primerIT-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.81 out of 1473 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 5.5% of total primer combinations. The cost of IT-ISJ marker primers is low, the polymorphism is high, and the stability is good. The polymorphism of IT-ISJ marker is close to SSR marker.81 IT-ISJ primer combinations were used to genotype 270 F2:7 recombinant inbred lines developed from (Yumian 1×T586) F2. and 93 IT-ISJ loci were obtained.12 primer combinations produced 2 loci.85 loci represented dominant, accounting for 91.4% Primer pair polymorphism between mapping parents3220 primer pairs/combinations, including 1473 IT-ISJ primer combinations and 1747 SSR primer pairs, were used to detect polymorphisms between T586 and Yumian 1. A total of 143 primer pairs/combinations, including 81 IT-ISJ and 61 SSR, showed polymorphism between parents, and the proportion of polymorphic primers were 4.4%. The polymorphic ratio of IT-ISJ and SSR were 5.5% and 3.6%, respectively.Genotyping recombinant inbred lines143 polymorphic primer pairs/combinations were used to genotype recombinant inbred line population, and 158 loci (93 IT-ISJ,65 SSR) were obtained. One hundred and forty-thee loci, together with 550 loci obtained in our laboratory in the past, were tested with chi-square.178 loci distorted from the 1:1 Mendelian segregation ratio (x2>3.85). accounting for 25.1% of total loci. Fifty-nine loci showed severe deviation (x2>10.83), accounted for 8.3% of total loci. The severe loci include 11 IT-ISJ markers,41 SSR,3 SRAP and 4 morphological markers, accounting for 11.8% of IT-ISJ,7.1% of SSR,10.3% of SRAP and 44.4% of morphological markers, respectively.Linkage mapGenetic linkage analysis was conducted on 708 marker loci, and a genetic linkage map constructed. The map included 690 loci (561 SSR markers.91 IT-ISJ markers,29 SRAP markers and 9 morphological markers) and 63 linkage groups. The genetic map spanned 3340.5cM with 4.84cM of an average length between two markers, accounting for 75.10% of cotton genome.