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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.

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Acknowledgments

We acknowledge financial support for this work from the Department for Environment Food and Rural Affairs (Defra) projects AR0105 and AR0711, the Pulse Crop Genetic Improvement Network, UK. The JIC is supported by competitive grants from the Biotechnology and Biological Sciences Research Council (BBSRC), and from Defra. We are very grateful to Dr. Hans Weber, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany), and to Sigurd Boisen, Danish Institute of Agricultural Sciences, Department of Animal Nutrition and Physiology Research, Centre Foulum, P.O. Box 39 DK-8830 Tjele Denmark for carrying out N analyses of seed meals in their laboratories. We thank Jevneet Kular and Dominic Conquest, John Innes Centre, for their assistance with seed harvest, meal preparation and assays.

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Correspondence to C. Domoney.

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Supplementary material 1 (DOC 34 kb)

Supplementary material 2 (PDF 142 kb)

10681_2011_363_MOESM3_ESM.ppt

Fig. S1: Seed phenotypes of near-isolines of pea, compared with those of the parent lines, JI 516 and JI 868. L and H refer to lines within a pair that have different alleles at the Tri locus (PPT 4806 kb)

10681_2011_363_MOESM4_ESM.ppt

Fig. S2: Mean seed weight of near-isolines of pea, based on triplicate measurements, ± SE. L and H refer to lines within a pair that have different alleles at the Tri locus. The mean seed weight of the parent lines, JI 516 and JI 868 were 0.391 and 0.355 g, respectively (PPT 67 kb)

10681_2011_363_MOESM5_ESM.doc

Fig. S3: Protein sequences deduced from a Vc-2 cDNA, vicK (X67429, top), and vicJ gene (X67428, lower) DNA sequences. The sequence shown in red for the deduced vicK protein is missing from that deduced for vicJ, with the latter showing divergence after amino acid 354 and a premature stop codon (*) after a further 14 amino acids (in red, underlined). Additional amino acid differences between the two sequences are coloured blue (DOC 29 kb)

10681_2011_363_MOESM6_ESM.ppt

Fig. S4: Seed nitrogen content determined for a range of Pisum round and wrinkled-seeded lines that are parents of mapping populations, based on triplicate measurements, ± SE. White bars indicate round-seeded lines (R), whereas black bars indicate wrinkled-seeded (r) lines (PPT 117 kb)

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Chinoy, C., Welham, T., Turner, L. et al. The genetic control of seed quality traits: effects of allelic variation at the Tri and Vc-2 genetic loci in Pisum sativum L.. Euphytica 180, 107–122 (2011). https://doi.org/10.1007/s10681-011-0363-8

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Keywords

  • Genetic markers
  • Pisum sativum L.
  • Seed protein
  • Tri locus
  • Vc-2 locus