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Improving early maturity in upland cotton (Gossypium hirsutum L.) is an important target in breeding. The node of the first fruiting branch (NFFB) and its height (HNFFB) are two important indexes to measure early maturity in cotton. To facilitate breeding for early maturity traits in upland cotton and reveal the genetic control underlying the two traits, a genome-wide association study was performed using 53,848 high-quality single nucleotide polymorphisms (SNPs) from 77,774 of a recently developed CottonSNP80K array. A total of 55 target trait-associated SNPs were detected, of which 12 SNPs were for NFFB and 43 were for HNFFB. Two SNPs for NFFB and 22 SNPs for HNFFB were repeatedly detected in at least two environments and/or by two models. These 24 SNPs also exhibited high phenotypic contributions of more than 10% and could be used for marker-assisted selection in future breeding programs. Furthermore, 89 candidate genes were identified in the genome sequence of upland cotton. These genes were categorized through Gene Ontology analysis. Gh_A05G1482 might be a potential candidate gene for improving the early maturation of cotton. These findings reveal the genetic control underlying NFFB and HNFFB and provide insight into genetic improvements for early maturity in upland cotton.

Node of first fruiting/sympodial branch (NFFB) and its height (HNFFB) are two important indicators to measure cotton (Gossypium spp.) early maturity. This study performed an association mapping using the mixed linear model (MLM) procedure for NFFB and HNFFB based on 172 Upland cotton (Gossypium hirsutum L.) cultivars and 331 polymorphic SSR markers. The gene diversity index of 331 markers ranged from 0.0387 to 0.7799 with a mean value of 0.4002 and the polymorphism information content ranged from 0.0379 to 0.7473 with a mean value of 0.3375. A total of 18 markers associated with NFFB were detected in at least two environments, and the range of explained phenotypic variation by markers in different environments was 2.28–11.36 % with a mean value of 5.20 %. A total of 19 markers associated with HNFFB were detected in at least two environments, and the range of explained phenotypic variation by markers in different environments was 2.83–16.96 % with a mean value of 7.92 %. These markers detected in multiple environments are of good stability and can be used for marker-assisted selection (MAS) of target traits. In addition, favorable alleles for NFFB and HNFFB were mined. These favorable alleles and their representative cultivars are expected to be used for breeding practices. This study provides theoretical basis for the further analysis of genetic basis of NFFB and HNFFB, as well as the use of MAS for cotton early maturity.

A major breeding target in Upland cotton (Gossypium hirsutum L.) is to improve the fiber quality. To address this issue, 169 diverse accessions, genotyped by 53,848 high-quality single-nucleotide polymorphisms (SNPs) and phenotyped in four environments, were used to conduct genome-wide association studies (GWASs) for fiber quality traits using three single-locus and three multi-locus models. As a result, 342 quantitative trait nucleotides (QTNs) controlling fiber quality traits were detected. Of the 342 QTNs, 84 were simultaneously detected in at least two environments or by at least two models, which include 29 for fiber length, 22 for fiber strength, 11 for fiber micronaire, 12 for fiber uniformity, and 10 for fiber elongation. Meanwhile, nine QTNs with 10% greater sizes (R2) were simultaneously detected in at least two environments and between single- and multi-locus models, which include TM80185 (D13) for fiber length, TM1386 (A1) and TM14462 (A6) for fiber strength, TM18616 (A7), TM54735 (D3), and TM79518 (D12) for fiber micronaire, TM77489 (D12) and TM81448 (D13) for fiber uniformity, and TM47772 (D1) for fiber elongation. This indicates the possibility of marker-assisted selection in future breeding programs. Among 455 genes within the linkage disequilibrium regions of the nine QTNs, 113 are potential candidate genes and four are promising candidate genes. These findings reveal the genetic control underlying fiber quality traits and provide insights into possible genetic improvements in Upland cotton fiber quality.

Plant architecture is important for cotton cultivation and breeding. In this study, two mapping generations/populations F2 and F2:3 in Upland cotton (Gossypium hirsutum L.), derived from ‘Baimian1’ and TM-1, were used to identify quantitative trait loci (QTLs) for 10 plant architecture traits. A total of 55 main-effect QTLs (M-QTLs) were detected. Four common M-QTLs, qTFB-10(F2/F2:3) for total fruit branches, qFBL-26b(F2)/qFBL-26(F2:3) for fruit branch length, qFBA-5(F2/F2:3) for fruit branch angle and qFBN-26b(F2)/qFBN-26(F2:3) for fruit branch nodes, were found. The synergistic alleles and the negative alleles can be utilized in cotton plant architecture breeding programmes according to specific breeding objectives. Altogether 54 pairs of epistatic QTLs (E-QTLs) exhibiting the interactions of additive-by-additive (AA), additive-by-dominant (AD), dominant-by-additive (DA) and dominant-by-dominant (DD) were detected. The epistasis appeared to be an important contributor to genetic variation in cotton plant architecture traits. Therefore, the identified markers associated with E-QTLs as well as M-QTLs will be of importance in future breeding programmes to develop cotton cultivars exhibiting desirable plant architecture.