Theoretical and Applied Genetics

, Volume 131, Issue 6, pp 1299–1314 | Cite as

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

  • Junji Su
  • Libei Li
  • Chi Zhang
  • Caixiang Wang
  • Lijiao Gu
  • Hantao Wang
  • Hengling Wei
  • Qibao Liu
  • Long Huang
  • Shuxun Yu
Original Article


Key message

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton.


A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.



Plant height


Fruit branch length


Fruit branch angle


First fruit branch position


Height of the first fruit branch position






Quantitative trait loci


Single nucleotide polymorphisms


Genome-wide association study


Linkage disequilibrium


Specific-locus amplified fragment sequencing


Best linear unbiased predictions


Mixed linear model


Minor allele frequency


Analysis of variance


Virus-induced gene silencing



This research was funded by the Chinese National Natural Science Foundation (31660409, 31601346 and 31621005) and the China Agriculture Research System (CARS-15-06).

Compliance with ethical standards

This research complied with ethical standards.

Conflict of interest

The authors declare no conflicts of interest.

Availability of supporting data

The sequence read data from the SLAF-seq analysis for the 355 sequenced upland cotton lines are available in the Sequence Read Archive ( (SRP071133 under the Accession Number PRJNA314284).

Supplementary material

122_2018_3079_MOESM1_ESM.pdf (881 kb)
Supplementary material 1 (PDF 881 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Junji Su
    • 1
    • 2
  • Libei Li
    • 1
  • Chi Zhang
    • 1
  • Caixiang Wang
    • 1
  • Lijiao Gu
    • 1
  • Hantao Wang
    • 1
  • Hengling Wei
    • 1
  • Qibao Liu
    • 1
  • Long Huang
    • 3
  • Shuxun Yu
    • 1
  1. 1.State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangChina
  2. 2.Cotton Research InstituteXinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Ministry of AgricultureShiheziChina
  3. 3.Shanghai Majorbio Bio-pharm Biotechnology Co. Ltd.ShanghaiChina

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