Sequence diversity of puroindoline-a, puroindoline-b, and the grain softness protein genes in Aegilops tauschii coss

Aegilops tauschii Coss. constitutes a valuable resource of genetic variability for improving cultivated bread wheat, Triticum aestivum L. Nucleotide sequence diversity was examined at the Hardness (Ha) locus, which bears the Puroindoline-a (Pina-D1) and Puroindoline-b (Pinb-D1) genes, and the closely related Gsp-D1 gene. A distinct signature of polymorphism and selection was evident in each of the three genes across loci for the 50 accessions of Ae. tauschii. Pinb-D1 was characterized by a high level of nucleotide diversity (pi = 0.02966; theta = 0.0166) relative to a low level of variation in the neighboring linked Pina-D1 and Gsp-D1 genes. Despite the close genetic and physical linkage among these three loci, recombination and linkage disequilibrium analyses detected at least two recombination events, most likely at the interlocus level. Tests for neutrality showed that polymorphism at Pina-D1 and Gsp-D1 did not depart from a drift-mutation model. Genetic variation at the Pinb-D1 locus was higher than expected under neutrality suggesting that selection might operate to maintain polymorphism at this locus. The sequence variation resolved here will help elucidate the kind of variation that may be important for the function of these genes as well as to identify novel Ae. tauschii genotypes that may be used to broaden the range in wheat endosperm, texture. Lastly, these results on sequence diversity, linkage disequilibrium, and recombination may help in the development of new Strategies for breeding purposes.