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

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Abstract

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.

Abstract

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.

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Abbreviations

PH:

Plant height

FBL:

Fruit branch length

FBA:

Fruit branch angle

FFBP:

First fruit branch position

HFFBP:

Height of the first fruit branch position

AY:

Anyang

SHZ:

Shihezi

QTL:

Quantitative trait loci

SNPs:

Single nucleotide polymorphisms

GWAS:

Genome-wide association study

LD:

Linkage disequilibrium

SLAF-seq:

Specific-locus amplified fragment sequencing

BLUPs:

Best linear unbiased predictions

MLM:

Mixed linear model

MAF:

Minor allele frequency

ANOVA:

Analysis of variance

VIGS:

Virus-induced gene silencing

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Acknowledgements

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

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  1. Junji Su and Libei Li contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China

    Junji Su, Libei Li, Chi Zhang, Caixiang Wang, Lijiao Gu, Hantao Wang, Hengling Wei, Qibao Liu & Shuxun Yu

  2. Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Ministry of Agriculture, Shihezi, China

    Junji Su

  3. Shanghai Majorbio Bio-pharm Biotechnology Co. Ltd., Shanghai, China

    Long Huang

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The sequence read data from the SLAF-seq analysis for the 355 sequenced upland cotton lines are available in the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA314284/) (SRP071133 under the Accession Number PRJNA314284).

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Su, J., Li, L., Zhang, C. et al. Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton. Theor Appl Genet 131, 1299–1314 (2018). https://doi.org/10.1007/s00122-018-3079-5

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