| The germplasm resources of cotton have abundant genetic diversity. And genetic diversities are the basis of breeding excellent varieties. The research of genetic diversity about upland cotton and its offspring lines can reveal the genetic base of cotton in China on breeding origin, and help us to know the background and diversity of germplasm nowadays in use. And the research also can help breeders to mine important traits and use these good germplasm in high efficiency, and have great meaning of creating new germplasm. The goal of genetic research is to know the relationship between phonotype and genotype. Association mapping use natural population with unfixed population structure for research target, with the phonotype and genotype data obtained, we test the association between genetic diversity and heritable variation of traits use statistic method.In this research, on the base of analyzing the genetic diversity of 81 upland cottons, we used software TASSEL analyzed the LD level in cotton genome. And then combined with the traits and the markers data, we detected the quantity traits loci. We also constructed a four-way cross population to detect the QTLs concerned with yield and quality traits.In this paper, we compared the difference of traits between varieties domestic and introduced. We found that the domestic varieties have better representation in agronomic traits, such as the increase of NB (number of bolls per plant), LP (lint percentage), and the decrease of SI (seed index). And also, the variation coefficients increased in NB, LP, and SI. Domestic varieties also have better representation in many aspects of fiber quality, and the variation coefficients increased in FS (fiber strength), FM (fiber micronaire reading), and FE (fiber elongation). It shows that, for more than half a century, cotton breeding in China has developed quickly. When use molecular marker technique to analyze the difference between domestic and overseas varieties, we found that, domestic varieties have more alleles and big span of gene diversity, but the mean value is still low, indicate that though domestic varieties have many variation in genome level, but the variation is less applied to production, it's still difficult to broaden the genetic basis of cotton.When analyzing the phenotypic difference of varieties between Yangtze River and Yellow River Basin, two main producing areas of cotton in our country. We found, varieties from Yangtze River is better if solely on the traits performance, such as more bolls per plant, big bolls, small seed index, high lint percentage and lint index. But the variation coefficients are lower. When analyze with molecular marker technique, the number of alleles, genetic diversity index and PIC value have no significant difference.When analysis the difference between varieties based on the pedigree, we see that the Kings have high mean value in plant branch, plant high, boll weight, fiber length, fiber strength and fiber uniformity ratio, and biggest variation coefficients in number of bolls per plant, boll weight and fiber micronaire reading. The Fosters have the biggest mean value and variation coefficients in lint index and lint percentage. The DPLs and Stonevilles had been used as parents in breeding wildly, and have bred many varieties. So the two pedigree sources have more alleles than others, but low in gene diversity and PIC value.In our research, in order to use association mapping to test association sites and alleles of several traits, we need to know the LD in cotton genome. With the help of software TASSEL, we see low level of LD in cotton genome, cross-pollination and frequent hybridization and selection in breeding is the main reason. We detected numerous associations between marker sites and agronomic or quality traits. After that, we tried to find out alleles with good variation of different markers, and the typical variety with these alleles. It will provide useful messages for cotton breeding, and for further research.Stoneville 2B, Foster 6, DPL 15 and CRI7 are core parents in cotton breeding in China. We constructed a four-way cross segregated population and its F2:3 inbreed lines with these varieties. A linkage map was developed for the four-way cross with SSR markers and JoinMap V3.0 software. The map covered 1129.1cM, and with 102 mapped loci, which was approximately 22.6% of the total recombination length of the cotton genome. The average distance between loci was 11.1cM. The map comprised 31 linkage groups, and these groups were assigned to 15 chromosomes. In the four-way cross population,19 QTLs concerned with agronomic traits and 5 QTLs with fiber quality were detected with MapQTL V5.0. And a QTL concerned with LP (lint percentage,%) was detected both in F2 and F2:3 generations, and is of value for MAS (Marker-assisted selection).In this paper, we used the G. barbadense genetic standard,3-79, and the good cytogenetics material, Sub.18. Combined with cotton genetic map constructed by our lab, we achieved to fine mapping the ob2 gene in chromosome 13 (A13) of tetraploid cotton, located this gene between two loci, BNL2449b and TMP01, the genetic distance is 1.1 cM and 1.7cM, separately. Former research in our lab had finished the mapping of the ob1 gene with the standard Upland stock, TM-1 and Sub.18. It locates in chromosome 18 (D13). Consider the result of two experiments together, we confirmed the result of former research about the hereditary feature of ob gene, and in the same time, laid a solid foundation of further researching and using this gene. BNL2571, BNL2652, NAU817, and NAU1141 also produced duplicate loci bridging of the homoeologous A13/D13 (At/Dt) chromosome pairs. Therefore, the expression of the ob gene in tetraploid cotton is a typical phenomenon of genome duplication.
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