Detection of epistasis interaction loci for fiber quality-related trait via 3VmrMLM in upland cotton

Zhimin Han; Huifeng Ke; Xiaoyu Li; Ruoxuan Peng; Dongdong Zhai; Yang Xu; Liqiang Wu; Wensheng Wang; Wensheng Wang; Yanru Cui

doi:10.3389/fpls.2023.1250161

Frontiers in Plant Science (Sep 2023)

Detection of epistasis interaction loci for fiber quality-related trait via 3VmrMLM in upland cotton

Zhimin Han,
Huifeng Ke,
Xiaoyu Li,
Ruoxuan Peng,
Dongdong Zhai,
Yang Xu,
Liqiang Wu,
Wensheng Wang,
Wensheng Wang,
Yanru Cui

Affiliations

Zhimin Han: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
Huifeng Ke: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
Xiaoyu Li: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
Ruoxuan Peng: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
Dongdong Zhai: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
Yang Xu: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu, China
Liqiang Wu: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
Wensheng Wang: State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
Wensheng Wang: National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
Yanru Cui: State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China

DOI: https://doi.org/10.3389/fpls.2023.1250161
Journal volume & issue: Vol. 14

Abstract

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Cotton fiber quality-related traits, such as fiber length, fiber strength, and fiber elongation, are affected by complex mechanisms controlled by multiple genes. Determining the QTN-by-QTN interactions (QQIs) associated with fiber quality-related traits is therefore essential for accelerating the genetic enhancement of cotton breeding. In this study, a natural population of 1,245 upland cotton varieties with 1,122,352 SNPs was used for detecting the main-effect QTNs and QQIs using the 3V multi-locus random-SNP-effect mixed linear model (3VmrMLM) method. A total of 171 significant main-effect QTNs and 42 QQIs were detected, of which 22 were both main-effect QTNs and QQIs. Of the detected 42 QQIs, a total of 13 significant loci and 5 candidate genes were reported in previous studies. Among the three interaction types, the AD interaction type has a preference for the trait of FE. Additionally, the QQIs have a substantial impact on the enhancement predictability for fiber quality-related traits. The study of QQIs is crucial for elucidating the genetic mechanism of cotton fiber quality and enhancing breeding efficiency.

Published in Frontiers in Plant Science

ISSN: 1664-462X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: https://www.frontiersin.org/journals/plant-science

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