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; Yanru Cui

doi:10.3389/fpls.2023.1250161

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

Front Plant Sci. 2023 Sep 28:14:1250161. doi: 10.3389/fpls.2023.1250161. eCollection 2023.

Authors

Zhimin Han¹, Huifeng Ke¹, Xiaoyu Li¹, Ruoxuan Peng¹, Dongdong Zhai¹, Yang Xu², Liqiang Wu¹, Wensheng Wang^{3

4}, Yanru Cui¹

Affiliations

¹ State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China.
² 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.
³ State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
⁴ National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China.

Abstract

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.

Keywords: 3VmrMLM; GWAS; cotton; epistasis interaction; fiber quality-related trait.

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (32100496); Scientific foundation for the returned overseas Chinese scholars, Hebei provincial department of human resources and social security (C20200328); China Agriculture Research System (CARS-15-03); the CAAS Innovative Team Award, the HainanYazhou Bay Seed Lab Project (B23CJ0208); the National High-level Personnel of Special Support Program, and Nanfan special project, CAAS (YBXM2322) and Alibaba Foundation.