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Review
. 2022 Oct 18:13:1019347.
doi: 10.3389/fpls.2022.1019347. eCollection 2022.

Status and prospects of genome-wide association studies in cotton

Muhammad Yasir  1 , Hafiza Hamrah Kanwal  2 , Quaid Hussain  3 , Muhammad Waheed Riaz  3 , Muhammad Sajjad  3 , Junkang Rong  1 , Yurong Jiang  1
Affiliations
Review

Status and prospects of genome-wide association studies in cotton

Muhammad Yasir et al. Front Plant Sci. .

Abstract

Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.

Keywords: GWAS; SNP; cotton; fiber; linkage disequilibrium.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Schematic flow of GWAS. Collection of diverse germplasm; (A) Yellow shaded area on the world map depicts key cotton-growing countries; (B) Genotyping platform (C) Phenotypic diversity in cotton crop (D) GWAS analysis to find associated SNPs. (E) Functional validation of genes associated with traits under study.
Figure 2
Figure 2
An increasing number of GWAS publications from 2009-22. Each opened boll represents one publication, specific color depicts publications of a specific year.
Figure 3
Figure 3
(A) This figure illustrates the GWAS conducted for different aspects of cotton, the bottom part shows less studied traits of cotton crop with GWAS tool; (B) This illustration shows total number of GWAS studies in all Gossypium species till now and node ends show total number of studies on a particular trait in different Gossypium species.
See this image and copyright information in PMC

References

    1. Abdelraheem A., Kuraparthy V., Hinze L., Stelly D., Wedegaertner T., Zhang J. (2021. a). Genome-wide association study for tolerance to drought and salt tolerance and resistance to thrips at the seedling growth stage in US upland cotton. Ind. Crops Prod. 169. doi: 10.1016/j.indcrop.2021.113645 - DOI
    1. Abdelraheem A., Thyssen G. N., Fang D. D., Jenkins J. N., Mccarty J. C., Wedegaertner T., et al. . (2021. b). GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 upland cotton (Gossypium hirsutum) parents. Mol. Genet. Genomics 296, 119–129. doi: 10.1007/s00438-020-01733-2 - DOI - PubMed
    1. Atwell S., Huang Y. S., Vilhjalmsson B. J., Willems G., Horton M., Li Y., et al. . (2010). Genome-wide association study of 107 phenotypes in arabidopsis thaliana inbred lines. Nature 465, 627–631. doi: 10.1038/nature08800 - DOI - PMC - PubMed
    1. Cai C., Zhu G., Zhang T., Guo W. (2017). High-density 80 K SNP array is a powerful tool for genotyping g. hirsutum accessions and genome analysis. BMC Genomics 18, 654. doi: 10.1186/s12864-017-4062-2 - DOI - PMC - PubMed
    1. Chen Z. J., Scheffler B. E., Dennis E., Triplett B. A., Zhang T., Guo W., et al. . (2007). Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145, 1303–1310. doi: 10.1104/pp.107.107672 - DOI - PMC - PubMed

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