Open Access

ARTICLE

Genetic Diversity, Population Structure, and Genome-Wide Association Study of Seven Agronomic Traits in 273 Diverse Upload Cotton Accessions

by Yajun Liang^1,2,#, Juyun Zheng^1,#, Junduo Wang^1,#, Zhaolong Gong¹, Zhiqiang Li³, Ling Min⁴, Zeliang Zhang², Zhiwei Sang², Yanying Qu², Xueyuan Li^1,*, Quanjia Chen^2,*

1 Cash Crops Research Institute of Xinjiang Academy of Agricultural Science (XAAS), Urumqi, China
2 Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China
3 R&D Department, Adsen Biotechnology Corporation, Urumqi, China
4 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

* Corresponding Authors: Xueyuan Li. Email: ; Quanjia Chen. Email:
# These authors contributed equally to this work

Phyton-International Journal of Experimental Botany 2023, 92(12), 3345-3357. https://doi.org/10.32604/phyton.2023.028755

Received 10 January 2023; Accepted 18 April 2023; Issue published 28 December 2023

Abstract

Upland cotton (Gossypium hirsutum) is the most important plant producing natural fibers for the textile industry. In this study, we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018, which were from 18 geographical regions. We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution. We then genotyped the collection with 81,612 high quality SNPs. Phylogenetic tree and population structure revealed a diverse genetic structure of the core collection, and geographical diversification was an important factor, but account for part of the variances of genetic diversification. We then performed genome-wide association study for the seven traits in the years 2017 and 2018, and the average values of each trait in the two years, respectively. We identified a total of 19 significant marker-trait associations and found that Pollen Ole e 1 allergen/extension could be the candidate gene associated with the fall-off cotton bolls from the last three branches. In addition, large variations were observed for the heritability of traits in the years 2017 and 2018. These results provide new potential candidate genes for further functional validation, which could be useful for genetic improvement and breeding of new cotton cultivars with better agronomic performances.

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Keywords

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