Molecular Markers of Agronomic Traits and Superior Germplasm of Spring Wheat in Northern Kazakhstan and Siberia

Spring bread wheat (Triticum aestivum L.) is the principal crop of the vast rainfed region spanning Northern Kazakhstan, the Urals, and Western Siberia, where productivity is limited by moisture stress, diseases, and the slow adoption of genomic tools in traditional breeding. We performed a genome-wide association study (GWAS) of 142 spring wheat genotypes from the Kazakhstan–Siberia Network for Spring Wheat Improvement (KASIB), evaluated at four sites in Russia and Kazakhstan during 2020–2022. The analysis identified 23 significant marker–trait associations (SNPs), of which 21 were stable across at least two environments, and 11 showed pleiotropic effects on two or more traits. Grain yield was associated with two SNPs (1A_12366171_G_A and 1B_15284504_C_T), each also affecting heading and maturity. Heading and maturity were controlled by a cluster of SNPs on chromosomes 1B, 2B, 5A, and 7B, with effects of up to 5.1 days. Plant height was associated with SNPs on 1A, 5A, and 6B, including one marker (5A_585412831_A_G) that was pleiotropic with 1000-kernel weight. Spike productivity was associated with loci on 1A, 3D, 4A, 4D, 5B, and 7B (grain weight and grains per spike, spikelets per spike, and spike harvest index). Grain size and 1000-kernel weight were linked to SNPs on 1B, 5A, and 6B, and protein and gluten content to two loci on 3A and 4B, which raised protein by up to 0.62% and gluten by up to 1.39%.