| Xinjiang cotton region plays a hold and balance role in high-quality cotton production areas in China. The major diseases in Xinjiang cotton region are Fusarium and Verticillium wilt .It has become an obstacle which affected high-yield,steady-yield and high-grade in cotton. Selected breeding and planted cultivars of resistance to disease are the only solution to the problem. Breeding a new cultivar through the traditional way need a long period, so it doesn't meet the stringent demand of production .Once the molecular markers which closely linked with the important economy traits of cotton were screened, and combined the MAS, we can breed the cultivars with fertility,high-quality and resistance to disease in order to meet demand in production. This paper constructs the linkage map using cotton cultivars planted and screens the molecular markers which closely linked with the important economy traits of cotton. The conclusions followed:The genetic diversity among 50 Xinjiang Upland Cotton cultivars, which had been popularized during recent 50 years, was investigated by using 50 simple sequence repeats (SSR) marker. 10 pair primer with better polymorphism can be established the hallmark of hybridism. Through identified with the two compoundings of Zms35×Jm1 and Xlz10×Junmian 1, F1 of the two compoundings was proved to the true, which improved the study of the molecular marker and the constructions of the genetic linkage map.A genetic linkage map was constructed using 173 F2 individuals developed by across of Xlz10 with high resistance to Verticillium wilt×Junmian1 with effecting Verticillium wilt The linkage map comprised 47 loci mapped to 14 linkage groups. There are two markers in the eight linkage groups. The rest linkage groups conclude three to ten markers. These molecular markers distributed averagely in the linkage map. The remainder twenty markers are independent. One QTL was detected on eleven linkage groups by composite interval mapping. But this loci must be detected further because of the little LOD peak.A genetic linkage map was constructed using 153 F2 individuals developed by across of upland cotton. Zms35 with high resistance to Fusarium wilt×G. hirsutumcv junmian1 with effecting Fusarium wilt . The linkage map comprised 69 loci mapped to 23 linkage groups with an average distance of 15.31cM between markers, covering 1069.5cM, or approximately 21.3% of the total cotton genome. This map was used to map the character of high resistance disease to Fusarium wilt, by multiple interval methods. Three QTLs were detected on three linkage groups(LG13,LG 15,LG17) with LOD peaks ranging from 5.1 to 7.6, and explained 12.0%, 15.9% and 25.2% of the phenotypic variance ,respectively, which might mean that the resistance of Fusarium wilt is controlled by three major QTLs groups. In the first linkage group, the markers NAU1949,NAU455,NAU740 associated with anti disease were tightly linked with 7.1cM ,9.5cM ,13.0cM interval genetic distance respectively. Zms35 with high resistance to Fusarium wilt×upland cotton Junmian1 with effecting Fusarium wiltwere analyzed about some agronomic traits. One QTL which controlled the boll weight was detected on 17 linkage groups. And dominance effect was explained 18.7% of the phenotypic variance. Dominance effect was the major effect; the other QTL which controlled the losing water ration of leaf were detected on 16 linkage groups. And additive effect was explained 12.2% of the phenotypic variance. Through detecting, one had to detect further because of the low LOD peak. The additive effect was the major effect in the second detection.
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