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The most important goal in cotton breeding is to increase the fiber yield which can be increased by improving a key trait, lint percentage (LP). However, narrow genetic background of upland cotton resulting in stagnant yield. In order to effectively dissect the genetic mechanism and enrich the gene loci of LP in cotton, the genetic diversity and population structure and a genome-wide association study (GWAS) was conducted using 204 upland cotton accessions based on 191 pairs of polymorphic microsatellite markers. The results were as follows: (1) The agronomic traits of the materials especially LP varied widely. (2) The SSRs revealed relatively high degree level of genetic diversity at DNA level. (3) Similarity coefficient cluster analysis of SSR markers indicated the influence of male parent on female parents was different after cross, the variation sites of agronomic traits could be further excavate in F 1 . (4) The GWAS revealed that 3 SSR markers were associated with LP: BNL3649-2, GH0132-2, CIR0246-3. There were two genes,  Gh_D02G0125  and  Gh _ D11G2610 , near the three SSR loci. These results provided a theoretical basis for improving fiber yield.

Genetic Diversity and Association Analysis of Lint Percentage Variation Population in Gossypium Hirsutum L. Based on Microsatellite Markers