Genetic mapping and haplotype analysis identify novel candidate genes for high night temperature tolerance in winter wheat

A diverse panel of 320 winter wheat (Triticum aestivum L.) genotypes was evaluated for yield-related parameters under control and high night-time temperature (HNT) stress using custom-designed, movable field-based heat tents over 2 years. Genome-wide association mapping identified several significant single nucleotide polymorphisms (SNPs) across environments, with SNPs under HNT conditions, based on absolute trait values and stress tolerance indices, grouped into 19 HNT quantitative trait loci (QTLs). Additionally, significant SNPs identified under both (control and HNT) conditions contributed to seven condition-independent QTLs. Thirteen haplotype blocks, derived from some of these QTLs, significantly influenced traits, with nine specific to HNT stress and four shared across conditions. Candidate gene mining identified 17 high-confidence genes involved in the HNT response, including those encoding ATP-dependent RNA helicase, GCN5-related N-acetyltransferase, oxidoreductase FAD/NAD(P)-binding, RNA recognition motif, and sugar/inositol transporter. Gene-based haplotype analysis identified four haplotypes with significant differences under HNT conditions and one block with differences under both conditions. For instance, Hap1^{TraesCS1A02G305700} exhibited higher biomass and spike number under HNT, Hap1^{TraesCS2B02G599800} showed higher biomass under HNT, and Hap2^{TraesCS4B02G264300} demonstrated higher biomass under both conditions. This study elucidates the genetic control of traits contributing to HNT stress responses in wheat, supporting the selection of lines with favorable alleles for crosses and enabling marker-assisted and genomic selections for HNT stress tolerance. The identified candidate genes and haplotypes provide valuable targets for functional validation, breeding strategies, and gene-editing approaches to enhance HNT resilience in wheat.