Association Mapping of Heat Tolerance SNPs in Upland Cotton During Vegetative Growth

Year 2025, Volume: 30 Issue: 2, 339 - 351, 28.12.2025

Yusuf Güzel Demiray , Remzi Ekinci , Adem Bardak

https://doi.org/10.17557/tjfc.1719539

Abstract

This study aimed to identify genomic regions associated with high-temperature stress tolerance in upland cotton, particularly during the vegetative period of this crop, which is increasingly affected by climate change. Understanding the genetic basis of thermotolerance is essential for improving resilience and sustaining yield under heat stress conditions. A total of 94 upland cotton genotypes were subjected to high-temperature stress in a low tunnel environment for four consecutive days during peak flowering. Physiological parameters, including relative cell injury (RCI), leaf temperature (LT), and SPAD chlorophyll values, were measured before and after the stress treatment to assess the genotypic response. Genotyping by sequencing (GBS) was used to detect single nucleotide polymorphisms (SNPs), and 6670 high-quality markers (MAF < 0.05) were retained for association mapping. Association analyses were conducted using general and mixed linear model (GLM-MLM) approaches. SNP markers associated with heat tolerance were identified using GLM and MLM models at significance levels of p < 0.0001– 0.001 with a –Log10(P) threshold ≥ 2.5, and MLM results were validated using false discovery rate (FDR) correction. Four SNPs on chromosomes A07, A10, D03, and D09 (SNP1680, SNP2537, SNP4374, SNP6415) were linked to RCI; four SNPs on D05, D07, A10, and D08 (SNP5029, SNP5643, SNP2616, SNP5915) were associated with LT; and two SNPs on D12 and A08 (SNP7428, SNP1910) were related to SPAD chlorophyll content. These markers correspond to genomic regions encoding enzymes, proteins, and genes implicated in high-temperature stress responses in cotton (Gossypium hirsutum L.).

Keywords

Cotton (G. hirsutum L.) , Genotyping by sequencing (GBS) , High-temperature stress , QTL , SNP markers

Ethical Statement

The authors have no conflicts of interest to declare.

Supporting Institution

GAP International Agricultural Research and Training Center and Dicle University

Project Number

TAGEM/TBAD/B/22/A7/P5/5139

Thanks

This study presented here was derived from Yusuf Güzel DEMİRAY's PhD, " Determination of DNA markers associated with tolerance/resistance to high temperature stress in cotton (Gossypium hirsutum L.)" at the Department of Field Crops, Institute of Science and Technology, Dicle University. The study was funded by the General Directorate of Agricultural Research and Policies (project number TAGEM/TBAD/A/20/A7/P5/1536) and Dicle University Scientific Research Projects Coordination Unit (project number ZİRAAT.20.007). I would like to express my gratitude to the project financing institutions and my valuable advisors, Assoc. Prof. Dr. Remzi Ekinci and Assoc. Prof. Dr. Adem Bardak.

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