A panoramic view of cotton resistance to Verticillium dahliae : from genetic architectures to precision genomic selection

Zhang, Xiaojun (author), Liu, Shiming (author), Wu, Peng (author), Lindsey, Keith (author), Štajner, Nataša (author), Zhang, Xianlong (author), Zhu, Longfu (author)

Investigating the genetic regulatory mechanisms underlying complex traits forms the foundation for crop improvement. Verticillium wilt (VW), caused by Verticillium dahliae (V. dahliae), is one of the most devastating diseases affecting crop production worldwide. However, the genetic basis underlying crop resistance to V. dahliae remains largely obscure, hindering progress in the genomic selection for VW resistance breeding. Here, we unraveled the genetic architectures and regulatory landscape of VW resistance in cotton by combining genome‐wide association studies (GWAS) and transcriptome‐wide association studies (TWAS) using 1152 transcriptomes derived from 290 cotton accessions. We identified 10 reliable quantitative trait loci (QTLs) associated with VW resistance across multiple environments. These QTLs showed a pyramiding resistance effect and exhibited promising efficacy in the genomic prediction of cotton's VW resistance supported by an F2:3 population. Moreover, trace analysis of these elite alleles revealed a notably increased utilization of Lsnp1, Lsnp4, Lsnp5, Lsnp8, and Lsnp9, which potentially contribute to the improvement of VW resistance in Chinese cotton breeding since the 1990s. We also identified remarkable gene modules and expression QTL (eQTL) hotspots related to the regulation of reactive oxygen species (ROS) homeostasis and immune response. Furthermore, 15 candidate causal genes were prioritized by TWAS. Knocking down eight genes with a negative effect significantly enhanced cotton resistance to V. dahliae. Among them, GhARM, encoding an armadillo (ARM)‐repeat protein, was verified to modulate cotton resistance to V. dahliae by regulating ROS homeostasis. Overall, this study updates the understanding of the genetic basis and regulatory mechanisms of cotton's VW resistance, providing valuable strategies for VW management through genomic selection in cotton breeding.

• Language: English
• Keywords: armadillo‐repeat protein, cotton, genomic selection, genome‐wide association studies, ROS homeostasis, transcriptome‐wide association studies, Verticillium wilt
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 24 str.
• Numbering: Vol. 4, iss. 3, art. e70029
• PID: 20.500.12556/RUL-169553
• UDC: 577.2
• ISSN on article: 2770-5986
• DOI: 10.1002/imt2.70029
• COBISS.SI-ID: 237448707
• Publication date in RUL: 03.06.2025

Record is a part of a journal

• Title: iMeta
• Publisher: John Wiley & Sons
• ISSN: 2770-5986
• COBISS.SI-ID: 175930627

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: rastlinska genetika, genom, genomske študije, verticilijska uvelost, bolezni rastlin, odpornost rastlin, transkriptomske študije