Evaluation of genetic diversity and investigation of population structure using SNP markers under late spring cold stress in bread wheat (Triticum aestivum L)

Late spring cold stress in the early reproductive growth of wheat causes damage due to a sudden drop in temperature. The genetic diversity of plants determines their potential to increase efficiency and, as a result, their use in breeding programs. This study was conducted with the aim of evaluating population structure, diversity of wheat genotypes, and selection of superior genotypes under cold and normal stress conditions.

Sixty-seven bread wheat genotypes were evaluated through pot cultivation in the field under two normal conditions and late spring cold stress. The experiment followed a randomized complete block design with two replications. Stress was applied by transferring the pots to a growth room with a temperature of -3ºC at the beginning of the reproductive stage. Phenotypic traits, including performance and performance components, were measured. Genotyping was done using a single nucleotide polymorphism (SNP) array with 9K density. A total of 17,093 SNP markers were used in this study.

The polymorphic information content for SNP markers ranged from 0.03 to 0.38, with an average of 0.26. Population structure analysis grouped the genotypes into five subpopulations. Molecular variance analysis showed that 75% of the observed variance in the population was related to intra-population differences. The studied genotypes were divided into four groups based on SNP markers and five and six groups based on phenotypic traits under normal and stress conditions, respectively. The genotypes in the first group, which exhibited higher average traits than other groups under stress conditions, were identified as tolerant to late spring cold.

The results indicated that main spike weight, seed yield per plant, seed weight in main spike, and weight of 100 seeds were the most important factors for grouping under late spring cold stress conditions. The calculated molecular indices, including marker indices and diversity indices, demonstrated that the SNP markers used performed relatively well in calculating genetic diversity within the studied population. In cluster analysis based on the genotypic matrix, cold-tolerant genotypes formed separate groups, indicating different tolerance mechanisms among these genotypes. These findings provide useful information for wheat breeders regarding the selection of diverse genetic resources to improve cold tolerance.