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Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090 , GhM_D05G1692 , GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton. • A total of 909 novel fiber and yield loci were detected via WGRS with 10.65× coverage depth in 1,081 cotton accessions. • Three novel stable SNP peaks associated with FL and FS were found. • GhM_D11G2208 can promote cell elongation based up leaf trichome and dark-grown hypocotyls in Arabidopsis. • 14 consistent and stable superior haplotypes were detected based on 915 SNPs in Dt11 region. [ABSTRACT FROM AUTHOR]

With the increasing demands for crop yield and production mechanization, improvement of plant architecture is getting more imperative in cotton. In the present study, we investigated the plant height (PH) and the node of first fruiting branch (NFFB) of 719 upland cotton accessions in six different environments. We used the 10,511 high‐quality single nucleotide polymorphisms (SNPs) to perform single‐locus and multi‐locus genome‐wide association study (GWAS). As many as 278 associated SNPs were identified, 142 by the mixed linear model (MLM) in the single‐locus model and 192 by six multi‐locus models. A total of 42 SNPs were identified in at least four environment‐traits or methods, of which 28 SNPs were significantly associated with PH, 22 were significantly associated with NFFB, and eight were co‐associated with the two traits. Notably, most of loci were novel besides i33922Gh located in the reported QTL for PH. Furthermore, we identified nine promising candidate genes, among which the three genes Gh_D03G0738, Gh_D10G2028, and Gh_D05G3600 contained non‐synonymous SNP mutation. The accessions with alleles of the mutations resulted in significant phenotypic differences. The expression of these genes showed significant differences between short‐PH and high‐PH varieties. Moreover, overexpression of Gh_D03G0738 led to reduction of PH in Arabidopsis. These results provided insights into genetic basis of plant architecture in cotton. Core Ideas: We identified 278 single nucleotide polymorphisms (SNPs) associated plant height (PH) and node of the first fruiting branch with single‐ and multi‐locus genome‐wide association study by using 719 cotton accessions.A total of 42 SNPs were identified in at least four environment‐traits or methods.Overexpression of Gh_D03G0738 led to reduction of PH in Arabidopsis. [ABSTRACT FROM AUTHOR]