Genetic Diversity and Population Structure of Wheat Germplasm for Grain Nutritional Quality Using Haplotypes and KASP Markers

Wheat germplasm resources are an important material foundation for genetic improvement. In this study, 170 wheat germplasm resources were used from China, the International Maize and Wheat Improvement Center (CIMMYT), Europe (France, Finland, and Sweden), the United States, Canada, and Australia. Seven nutritional quality traits were evaluated for the 2019–2020 and 2020–2021 cropping seasons. The coefficient of variability for seven nutritional quality traits ranged from 6.99% to 30.65%. The average of genetic diversity (Shannon–Wiener diversity index, H′) was 1.87. The results showed that the average frequency of high-throughput competitive allele-specific PCR (KASP) markers was 69.4% on 17 KASP markers related to seven nutritional quality traits, the average of polymorphic information content (PIC) was 0.308, and the genetic effects were from 0.01% to 18.46%. One hundred and seventy wheat germplasm resources were classified into five groups at ΔK = 5 by genetic structure analysis. The first group comprised 62 germplasm resources (36.47%), the second group included 41 germplasm resources (24.11%), the third group contained 20 germplasm resources (11.76%), the fourth group contained 20 germplasm resources (11.76%), and the fifth group had 29 germplasm resources (17.06%). Germplasm resources from CIMMYT and China were found in the first group and the second group, accounting for 56.45% and 65.85%, respectively, while European germplasm resources constituted 50% of those within the fourth group. Five favorable haplotypes were identified, which were located on chromosomes 4A, 6A, 6B, and 7A: G4A1, G4A2, G6A, G6B, and G7A. Their genetic effects were 8.71%, 8.41%, 1.00%, 18.20%, and 1.16%, respectively. In the meantime, we found 12 significant SNPs of seven nutritional quality traits using haplotype analysis. The frequency of favorable haplotypes in the population ranged from 3.53% to 62.35%. Five haplotypes, G4A1, G4A2, G6A, G6B, and G7A, were beneficial, and their genetic effects were positive. Furthermore, the results offered favorable haplotypes and germplasm resources for enhancing nutritional quality.