Climate changes pose challenges to crop production. However, the causes of phenotypic differences across environments remain unclear. Here, heading date (HD), flowering date (FD), and plant height (PH) were measured along with four environmental factors (day length (DL), growing degree days (GDD), precipitation (PRCP), and photothermal ratio (PTR)) to investigate the genetic basis of phenotypic plasticity of these traits in 616 wheat accessions using genome-wide association studies. Regarding quantitative trait locus-by-environment interactions (QEIs), five known and three candidate genes for HD, six known and seven candidate genes for FD, and four known and eighteen candidate genes for PH were identified. For the genes associated with phenotypic plasticity, 10 genes exhibited responsiveness to alterations in diverse environmental conditions according to transcriptome data; haplotype effects of 33 genes were identified as significantly correlated with the changes in environmental factors; six candidate genes were identified as hub genes in the gene network, possibly influencing other genes and causing the phenotypic plasticity. And over-dominant effects can explain over 50% the genetic variance of phenotypic plasticity. More importantly, one FD/HD candidate gene (TraesCS4A01G180700) and two PH candidate genes (TraesCS5B01G054800 and TraesCS2A01G539400) partly explain the phenotypic plasticity for the FD/HD and PH traits, respectively. In addition, the potential utilization of these genes in wheat breeding was discussed. This study elucidated the genetic basis of phenotypic differences caused by environments and provided a foundation for addressing the impact of climate change on crop production.

The Huanghuai winter wheat region, China’s primary wheat-producing area, predominantly cultivates white-grained wheat. Pre-harvest sprouting (PHS) significantly impacts yield and quality, making the breeding of PHS-resistant varieties crucial for ensuring China’s wheat production security. This study evaluated the PHS rate of 344 white-grained wheat varieties over two consecutive growing seasons (2022/2023 and 2023/2024). Furthermore, it analyzed the effects of allelic variations and their combinations in six genes (Tamyb10, TaDFR, TaMKK3-A, TaGASR34, Tasdr, and TaMFT) on PHS resistance. Results revealed average PHS rates of 66.1% and 64.4% for the two growing seasons, with coefficients of variation of 39.1% and 40.2%, respectively, and a narrow-sense heritability of 0.72. These findings indicate substantial genetic variation and relatively high genetic stability within the tested materials. Among the six molecular markers examined, the superior haplotype GS34-7Bb exhibited the lowest average PHS rate (41.9%) over two growing seasons, demonstrating the strongest PHS resistance. Analysis of different haplotype combinations identified two advantageous genotypes for PHS resistance in white-grained wheat: TaMKK3-Ab + GS34-7Bb + Tasdr-2Aa + TaMFT-A1b (average PHS rate: 20.8%) and TaMKK3-Ab + GS34-7Bb + Tasdr-2Ab + TaMFT-A1b (average PHS rate: 34.2%). Notably, the distribution frequency of superior haplotypes of PHS-related genes and these two advantageous haplotype combinations showed varying degrees of decline over time.

Historically, Henan Province has encountered multiple significant incidents of wheat cultivars resistance loss due to the emergence of new species of stripe rust fungus. To identify resistant germplasms exhibiting superior resistance to the emerging CRY34 strain, we employed a wheat 660 K array to genotype 256 Henan cultivars and conducted a genome-wide association study (GWAS) on adult plant resistance (APR) to wheat stripe rust in 2021–2022 and 2022–2023. A total of 48 SNP markers were found to be significantly correlated with APR. Fifteen were consistently detected using multi-locus GWAS methods in both BLUP values and in at least one field season. Among these 15 stable quantitative trait nucleotides (QTNs), 12 were previously reported and three were novel. The major novel QTN QYr.hnk-7DL was located at chr07DL_AX-111,720,006. Twelve associated cultivars possessing this QTN demonstrated high APR to stripe rust, with a 4.69% favorable genotype frequency. The chr07DL_AX-111,720,006 SNP was developed into the KASP marker KASP-YrZM1354 for easier detection. The validity of QYr.hnk-7DL was confirmed using KASP-YrZM1354 in two natural populations and three F2 populations. Through gene expression analysis within the candidate interval region, TraesCS7D01G544100 (designated YrZM1354) was identified as the candidate gene for QYr.hnk-7DL. we identified and verified the major QTN QYr.hnk-7DL associated with APR to stripe rust, elucidated the candidate gene YrZM1354 at this locus, and developed the high-precision marker KASP-YrZM1354. This marker has been successfully used in resistant germplasm screening and wheat breeding.