Association And Genetic Linkage Analysis For Yield And Fiber Quality Traits Of Gossypium Barbadense

1. Development and evaluation of intron and insertion-deletion markers for Gossypium barbadenseA total of588Gossypium barbadense coding sequences (CDSs) from nucleotide database were selected for marker development. After selection,125CDSs were used to design126markers, including39intron polymorphisms (GbIP) and87insertion-deletion polymorphisms (GbIDP). These markers were evaluated by analyzing the genetic diversity of56G. barbadense accessions and10G. hirsutum accessions. The amplification efficiencies of the GbIP and GbIDP were0.56and0.49for polymorphism information content,0.74and0.69for effective multiplex ratio (E),0.65and0.44for qualitative nature of data (QND), and0.27and0.15for effective marker index (EMI). Principal coordinate analysis (PCA) showed profound differences between G. hirsutum and G. barbadense accessions. In addition, most of the G. barbadense accessions of Xinjiang, China were clearly different from foreign and other Chinese G. barbadense accessions. The126markers were also evaluated for their ability to enrich genetic maps, and16polymorphic loci were mapped on nine chromosomes with six loci on A subgenome and10loci on D subgenome. This study well proved that GbIP and GbIDP can be successfully applied to the analysis of genetic diversity and construction of genetic maps.2. Genetic diversity and association analysis of yield and fiber quality in Gossypium barbadenseTwo hundred and thirty-seven commonly mapped SSR markers covering the whole cotton genome and126developed GbIP and GbIDP in this paper were used to constuct genetic diversity, population structure, linkage disequilibrium and association analysis of Gossypium barbadense.Fifty-six G. barbadense accessions were divided into three groups using UPGMA dendrogram and population structure analysis.The first group (Pop1) included accessions from foreign countries and some ones in domestic country, a few fundamental accessions in Xinjiang region also belonged to this group. The second group (Pop2) only consisted of Xinhai5. The third group (Pop3) was made up of Xinjiang accessions bred in recent years.A total of102loci were associated with yield and fiber quality traits in2009, of which36loci were related to yield traits,66to fiber quality traits, and24loci associatied with more than two traits. Explanation rates for trait variation ranged from0.29%-14.19%, with a mean of5.56%. A total of163loci were associated with yield and fiber quality traits in2010, of which91loci were related to yield traits,72to fiber quality traits, and43loci associated with more than two traits. Explanation rates for trait variation ranged from0.07%-18.84%, with a mean of6.81%. In addition,30loci were detected both in2009and2010.3. Construction of intraspecific linkage map and QTL mapping for yield and fiber quality traits in G barbadenseIn this study, a total of15971marker pairs including gSSR, EST-SSR, SRAP and SSCP were used to construct an intraspecific linkage map with124F2individuals derived from G. barbadense cross (Hai7124x3-79). There were412polymorphic loci of which337loci were mapped on52linkage groups, and26groups were assigned to15chromosomes. The full length of linkage map was2108.34cM. The maximum distance between adjacent loci was35.20cM, the minimum distance was0.25cM, and mean distance was6.26cM.According to Chi-square test,52(12.62%) loci showed segregation distortion at0.01level. Among them,34loci (65.38%) deviated towards maternal genotype,15loci (28.85%) towards heterozygous genotype, and3loci (5.78%) towards paternal genotype.A total of51QTLs were detected in2009and2010. In2009, there were18QTLs, with LOD value from2.50to6.47, explanation rates for trait variation were from8.85%to28.26%. In2010, there were33QTLs, with LOD value from2.52to4.63, explanation rates for trait variation from6.93%to34.52%. Moreover, MON-CGR5376-NAU257was linked to SW (Seed cotton weight per boll), LW (Lint weight per boll), HSW (A hundred seeds weight), FE (Fiber elongation) and SI (Seed index). There was only one QTL detected both in2009and2010, namely, MON-CGR5376-NAU2575, linked to FE. Among51QTLs,31were located on chromosomes, while20QTLs were on linkage groups. The main QTL effect was over-dominance (OD), and only4QTLs showed additive effect.