Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton

  • Chengxiang Song
  • Wei Li
  • Xiaoyu Pei
  • Yangai Liu
  • Zhongying Ren
  • Kunlun He
  • Fei Zhang
  • Kuan Sun
  • Xiaojian Zhou
  • Xiongfeng MaEmail author
  • Daigang YangEmail author
Original Article


Key message

A genome-wide associated study identified six novel QTLs for lint percentage. Two candidate genes underlying this trait were also detected.


Increasing lint percentage (LP) is a core goal of cotton breeding. To better understand the genetic basis of LP, a genome-wide association study (GWAS) was conducted using 276 upland cotton accessions planted in multiple environments and genotyped with a CottonSNP63K array. After filtering, 10,660 high-quality single-nucleotide polymorphisms (SNPs) were retained. Population structure, principal component and neighbor-joining phylogenetic tree analyses divided the accessions into two subpopulations. These results along with linkage disequilibrium decay indicated accessions were not highly structured and exhibited weak relatedness. GWAS uncovered 23 polymorphic SNPs and 15 QTLs significantly associated with LP, with six new QTLs identified. Two candidate genes, Gh_D05G0313 and Gh_D05G1124, both contained one significant SNP, highly expressed during ovule and fiber development stages, implying that the two genes may act as the most promising regulators of LP. Furthermore, the phenotypic value of LP was found to be positively correlated with the number of favorable SNP alleles. These favorable alleles for LP identified in the study may be useful for improving lint yield.



This work was supported by the National Key R&D Program for Crop Breeding (2016YFD0100306), the Key Project of Science and Technology of Henan Province of China (182102110306), and the Natural Science Foundation of Henan Province of China (152300410010).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2019_3333_MOESM1_ESM.docx (2 mb)
Figure S1 Frequency distribution of phenotypic variation of LP across multiple environments and correlation coefficients among different locations in 276 accessions. ** indicates a significant difference at a threshold of p = 0.01. Figure S2 Results of relative kinship analysis of 276 upland cotton accessions. Figure S3 Distribution of kinship coefficient (K) values in 276 upland cotton accessions. Figure S4 Manhattan plots of the results of a genome-wide association study for lint percentage (LP) in multiple environments using the mixed linear model (MLM). Figure S5 Heatmap of expressions of genes situated in all QTL regions identified by this study. Gene expression levels were calculated from log2 (FPKM) values, and the color bar denotes gene transcript abundances: red for high and green for low. R, S, L and DPA represent root, stem, leaf and days post-anthesis, respectively. Figure S6 GWAS results for lint percentage and identification of a candidate gene on chromosome Dt05. (a) Local Manhattan plot for the candidate region on Dt05. The purple dot represents the peak SNP i08888Gh. Red dotted lines indicate the candidate region. (b) LD block analysis of SNPs in this region. The degree of linkage is represented by the value of r2. (c) Gene structure of Gh_D05G0313 and a non-synonymous SNP within it. Purple rectangles and black lines indicate exons and introns, respectively. Ref and Alt stand for reference and alternate, respectively. (d) Box plots of LP based on the allele of SNP i08888Gh. The significance of differences was analyzed by a two-sided Wilcoxon test. (e) Tissue-specific expression profiles of Gh_D05G0313. Expression of Gh_D05G0313 was investigated in ovule (0, 10, 20 and 30 DPA) and fiber (10, 20 and 30 DPA) developmental stages by qRT-PCR. GhHis3 was used as an internal control. Error bars indicate the standard deviation of three technical replicates (DOCX 2014 kb)
122_2019_3333_MOESM2_ESM.xlsx (63 kb)
Table S1 Detailed information on 276 upland cotton accessions. Table S2 Variance analysis of lint percentage (LP) across multiple environments in the association population. Table S3 Genome-wide association loci of lint percentage (LP) in all environments. Table S4 Information on QTLs detected in this study and those co-localized with QTLs identified in previous studies. Table S5 Information on candidate genes located in QTL regions. Table S6 Primer sequences for qRT-PCR (XLSX 62 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Chengxiang Song
    • 1
    • 2
  • Wei Li
    • 1
  • Xiaoyu Pei
    • 1
  • Yangai Liu
    • 1
  • Zhongying Ren
    • 1
  • Kunlun He
    • 1
  • Fei Zhang
    • 1
  • Kuan Sun
    • 1
  • Xiaojian Zhou
    • 1
  • Xiongfeng Ma
    • 1
    Email author
  • Daigang Yang
    • 1
    Email author
  1. 1.State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
  2. 2.College of AgricultureYangtze UniversityJingzhouChina

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