Genomic Insights into Winter Wheat Breeding for Severely Cold Climates

Wheat is one of the world's most important crops, cultivated across diverse ecogeographic zones on more than ~245 million hectares annually. Classified by vernalization requirement into spring, facultative, or winter types, the latter typically achieves higher yields due to its extended growing season, reaching ~18 t ha^-1 and 9-10 t ha^-1 as a national average for Western European countries such as Germany, France, and England, compared with the global average of barely above 3 t ha^-1. Despite this potential, winter wheat is largely confined to regions with relatively mild winters, while vast temperate zones with extremely cold winters rely on spring wheat. Breeding has traditionally targeted the <i>vernalization-C-repeat Binding Factor</i> (<i>VRN-CBF</i>) pathway, which confers tolerance to moderately severe winters but is insufficient for extreme cold, implying the need for additional layers of adaptive mechanisms. Using multiple genotypic datasets, we identified genomic regions underlying low-temperature tolerance. Genome- and chromosome-wide scans revealed strong differentiation on chromosome 5A (526-703 Mb), overlapping the <i>VRN-CBF</i> loci. SNP-level <i>FST</i> analysis between spring and winter cultivars highlighted the <i>VRN-A1</i> (586-588 Mb) region and a locus spanning 549 and 559 Mb on chromosome 6A. Further comparisons between winter accessions adapted to extreme cold (≤-12 °C) and mild winters (>0 °C) revealed a differentiated region on chromosome 3B (561-564 Mb) harbouring two key genes conferring CBF-independent cold tolerance, <i>TRAESCS3B02G351100</i> and <i>TRAESCS3B02G354000</i>, encoding diacylglycerol kinase1 (DGK1) and peroxidase 56 (PRX56), respectively. These findings underscore alternative pathways in shaping cold adaptation, highlighting the need to broaden breeding strategies for extreme environments. We further detected a pronounced haplotype divergence between Chinese and U.S. winter cultivars reflecting distinct breeding trajectories; notably, China, where ~90% of wheat production is of the winter type, achieves national yields >5 t ha^-1, compared with ~3 t ha^-1 in the United States, where over 70% of production is winter wheat. This contrast suggests that the haplotypes enriched in Chinese winter cultivars could represent valuable resources for enhancing winter wheat performance in other regions with comparable environments.