Frost, a critical stress factor for wheat, can significantly impact yield and quality. Understanding the genetic basis of frost tolerance is essential for developing resilient wheat varieties. This study presents a comprehensive genomic analysis integrating genome-wide association studies and genomic prediction to illustrate the genetic architecture of frost tolerance in wheat.

A diverse panel of 238 wheat varieties was genotyped with the wheat 660K SNP chip, and their frost damage scores were taken in two environments across two growing seasons. GWAS identified 52 key candidate QTL regions which contained at least two significant marker-trait associations (MTAs), revealing the fifth homologous group of chromosomes as pivotal for cold resistance.

Further analysis identified 26 key candidate genes, including MADS box transcription factors, CRT-binding factors, Glutathione S-transferase and cyclic nucleotide-gated ion channel, potentially integral to the frost stress response.

Utilizing Bayesian Ridge Regression for genomic prediction, a prediction accuracy of 79% was achieved with a subset of 102 SNP markers, underscoring the potential of genomic prediction with a limited number of markers in practical breeding applications.

Additionally, two pairs of KASP primers for MTAs AX-110387252 and AX-109056556 were developed and validated in a natural population, marking a step towards marker-assisted selection. Collectively, these results offered valuable insights for uncovering the genes and regulatory networks conferring frost resistance, facilitating the selection of genotypes with enhanced frost resistance.