The genetic control of seed quality traits: effects of allelic variation at the Tri and Vc-2 genetic loci in Pisum sativum L.

Abstract

Genetic variation at the Tri locus, controlling seed trypsin inhibitor activity, is relevant to both food and feed uses of Pisum sativum L. (pea). Near-isogenic lines of Pisum sativum L. (pea) were developed previously to examine the impact on digestibility of variation at Tri on linkage group V. Further studies of these lines have now revealed a significant difference in seed nitrogen concentration between near-isolines having contrasting seed trypsin inhibitor activity. In order to investigate this apparent association, the multiple genes at a closely linked locus, Vc-2, encoding a set of major vicilin polypeptides, were analysed and shown to differ between the near-isolines. Characterisation of Vc-2 cDNAs revealed distinguishing features of the functional genes between the parents of the near-isolines, while analyses of gene structure showed that a disrupted variant Vc-2 gene was present in one, but not the second, parent of the near-isolines. The variant gene appeared to be non-functional, based both on its deduced truncated protein lacking part of one conserved cupin structural domain, and the fact that it did not correspond to any isolated cDNA. Recombinant near-isolines were generated between the closely linked Tri and Vc-2 loci to investigate the genetic association with seed nitrogen concentration. Seeds from near-isolines and recombinant inbred lines where the variant Vc-2 gene was present had lower seed nitrogen concentration than lines lacking the variant gene. Furthermore, the disrupted Vc-2 gene was absent from several pea genotypes with high seed protein content. Expression analyses suggested that gene expression at the Vc-2 locus was higher when the non-functional gene variant was absent. Markers based either on the element which disrupts the coding sequence within the variant gene at the Vc-2 locus, or on the closely linked Tri locus, may be exploited in the selection of haplotypes associated with genetic variation in seed protein composition and concentration. The gene content in the genomic region of Medicago truncatula chromosome 7 that is syntenic with the pea linkage group V has identified further candidates for functional analyses and marker assisted selection.