Genomics-Enabled Analysis of Genes Identifies New Alleles in Wheat and Related Species.

Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes and ( and ). Genes homologous to , namely , have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci not syntenic to the locus, with locus containing three tandem copies. PINB2 proteins have several features conserved for the / phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new allele specific markers and demonstrated their usefulness by 1) identifying new alleles in species; and 2) performing an association analysis of with kernel hardness. The association result suggests that genes may have no substantial contribution to kernel hardness. Our results provide new insights into evolution and expression and the new allele-specific markers are useful to further explore s contribution to seed traits in wheat.