| Cotton is an important fiber and oil crop in the world. Molecular biology and systematic evolution of cotton have attached great importance all the time. Microsatellite or SSR belongs to molecular markers of the second generation, and it has many advantages such as PCR-based, codominent, hypervariable, infomative and extensive in genome. At present, SSR had been used for the construction of cotton molecular linkage map, the screening of QTL of important agronomic traits, the evaluation of diversity of variaties and characterization of seeds purity. To date, there was not any research on SSR variation and its evolution in cotton. In this study, variaties and accessions of upland cotton, wild races of diploid and allotetraploid were used to characterize of SSR variation and evaluate SNP frequency of cotton variaty in Yangtse and Yellow Rivers and accessions with high fiber quality. The main results were listed as follows:1. The results reveal that the frequency of polymorphism at GENOME-SSR loci is as 2.24 times many as that at EST-SSR loci, electrophoretic patterns of PCR products are identical. There are a variety of motifs at EST-SSR locus, three nucleotide mtoif is predominent among them, 84% PCR products contain perfect motifs. However, there are fewer motifs at GENOME-SSR loci, two nucleotide motif is abundant among them, 40.4% PCR products contain perfect motifs. Microsatellites from Genome library often have more motifs numbers than those from EST. There are six products with micosatellite motif variation at EST-SSR loci, while there are 55 at GENOME-SSR loci, which is 9 times as many as those at EST-SSR loci. There is higher variation frequency of either microsatellite motif variation or motif numbers at GENOME-SSR locus than EST-SSR locus. Hai7124 is one of cotton accessions with high fiber quality, its microsatellites sequence is prone to contract at either EST-SSR or GENOME-SSR locus. With comparison to 8 cultivars, microsatellite sequence of Zhongmiansuol2 is inclined to shorten. Among 4 wild races, microsatellite sequence of G.Darwinii shows high inclination to contract. Size homoplasy is prone to occur at EST-SSR locus because there was higher base substitution at flanking sequence ofEST microsatellite .The distribution of phylogenetic tree is similar at EST-SSR and Genome-SSR locus. The putative diploid ancestor of alloteraploid amplicon was hard to determine at EST-SSR and Genome-SSR loucus with single product, but it was easy to identify at EST-SSR and Genome-SSR locus with double products. The results demonstrated that it was feasible to determine the putative diploid ancestors of alloteraploid amplicon accoring to the pattern of electrophoresis band. D subgenome of alloteraploid was more divergent at EST-SSR locus, A subgenome of alloteraploid was more divergent at Genome-SSR locus instead.2. SNP frequency of Simian3 and Sumianl2 was 0.0027 and SNP frequency of Yumianl and Simian2 was 0.0029 among 4 upland cotton cultivars from Yangtse River. SNP frequency of Xuzhou 142 was 0.0035. The frequency of Zhongmiansuol2 was 0.0048, and the value of Lumianl and Zhongmiansuo 19 was 0.0037. Among 4 accessions with high fiber quality, SNP frequency of Maxxa was 0.0053,and that of Hai7124 and 7235 was 0.0042 and 0.004 respectively. The results demonstrate SNP frequency of flanking sequence at EST-SSR locus was higher than that at GENOME-SSR locus according to flanking sequence from EST-SSR products with comparison to that from GENOME-SSR products.3. The frequency of polymorphism of 26 diploid cottons was 48% at 4 EST-SSR loci. The maximum of polymorphic MWs at single locus was 15, the minimum was 8. Thirty-nine percent of amplicons contain perfect motif, and 59% of amplicons contain indel and substitution at microsatellite motifs. With comparision to alloteraploid cotton, microsatellite motif of diploid has more variation. Size homoplasy causes 41 unique sequences, occupying 46% of the sum of the unique sequences. The phylogenetic results of different chromsome groups were consistent with Fry... |
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