Genome-wide association study of grain hardness and novel Puroindoline alleles in common wheat.

Grain hardness (HI) is a key trait for wheat milling and end-use quality. Puroindoline genes (PINs) are the major genes responsible for grain hardness, but other QTLs also contribute to the trait. Therefore, it is essential to identify loci associated with the HI and allelic variations of PINs in wheat. In the present study, 287 accessions from Shanxi province representing 70 years of wheat breeding were grown in one rainfed and two irrigated conditions to study grain hardness. Genome-wide association analysis (GWAS) was performed using the 15 K array, and the variability of PIN alleles was investigated. Among the accessions, hard wheat was most common. The broad-sense heritability (H2) among the three environments was 99.5%, suggesting HI was mainly affected by heredity. GWAS identified nine significant marker-trait associations (MTAs), including that PINs, which explained 7.03% to 17.70% of phenotypic variation. Four MTAs on chromosome 2A, 2B, 5A, and 7A were novel loci. As for diversity of PINs, a total of 11 PINs haplotypes were detected, composed of 12 allelic variations of the PIN gene. The most frequent haplotypes were Pina-D1a/Pinb-D1b (43.9%) and Pina-Dla/Pinb-D1p (18.8%), and both the frequency of Pina-D1a/Pinb-D1b and the HI value increased with breeding years were related to local dietary habits probably. A novel double deletion allele of the PINs haplotype was found in Donghei1206. These results will be useful not only in understanding of the genetics of the HI but also in breeding for improved grain texture. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01303-x.