Evaluation of PSII Thermal Stability in Grapevine Germplasm and Identification of Candidate Genes Based on a Genome-Wide Association Study

Heat stress damages the photosynthetic apparatus of grapevine leaves. It also restricts plant growth and reduces fruit yield and quality. However, natural variation in photosystem II (PSII) thermal stability under heat stress in grapevine and its genetic basis remain poorly understood. Here, we evaluated 404 genetically diverse grapevine accessions. We measured the maximum quantum efficiency of photosystem II (Fv/Fm) after treatment at 47 °C. Phenotypic analysis, cluster analysis and genome-wide association analysis were then used to investigate the genetic basis of PSII thermal stability. The coefficient of variation for Fv/Fm increased from 4.52% at 25 °C to 40.60% at 47 °C. Wild accessions generally retained higher Fv/Fm than interspecific hybrids and Vitis vinifera cultivars. We also identified 21 accessions with relatively high PSII thermal stability. A genome-wide association analysis of 5,074,860 high-quality SNPs detected a suggestive association signal on chromosome 4. The lead SNP was Chr4_1743280_G_A. We integrated gene annotations within the associated interval, putatively functional variants and diplotype-phenotype comparisons. This analysis prioritized seven candidate genes potentially associated with variation in PSII thermal stability. The Hap2/Hap2 diplotype of Vitvi005414 was associated with higher Fv/Fm. However, these associations should be regarded as candidate hypotheses for further validation rather than evidence of causal relationships. These findings provide candidate loci, genes and diplotypes for understanding the genetic basis of PSII thermal stability. They also support the use of germplasm with relatively high PSII thermal stability, validation of candidate variants and future breeding for improved heat resilience.