ARS | Publication request: Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing.

Submitted to: Genetical Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 29, 2008
Publication Date: October 8, 2008
Repository URL: http://hdl.handle.net/10113/44302
Citation: Wang, M.L., Barkley, N.L., Gillaspie, A.G., Pederson, G.A. 2008. Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing.. Genetical Research. 90(6):467-480.

Interpretive Summary: Cultivated Vigna species include five Asian beans: moth bean, azuki bean, black gram, mung bean, and rice bean; and two African beans: bambara groundnut and cowpea. The cultivated Vigna species are an important protein source in countries where the people have limited access to food rich in protein. The phylogenetic relationships in the USDA Vigna germplasm collection were unclear and their genetic diversity had not been measured empirically. To reveal interspecific phylogenetic relationships and assess their genetic diversity, 48 accessions representing 12 Vigna species were selected, and 30 gene-derived markers from legumes were employed. Some high-quality amplicons were sequenced. Insertion/deletions were discovered through the sequence alignments that were specific identifiers for some Vigna species. In regards to revealing polymorphisms, intron-spanning markers were more effective than exon-derived markers. These gene-derived markers were more successful in revealing interspecific polymorphisms than intraspecific polymorphisms at both the DNA fragment and sequence level. Two different dendrograms were generated from DNA fragment data and DNA sequence data, respectively. The results from these two dendrograms supported each other and showed similar phylogenetic relationships among Vigna species investigated. The accessions clustered into four main groups and thirteen subgroups. Each subgroup represents a subgenus or a species. Phylogenetic analysis revealed that some accessions were misidentified in our collection. The misidentified accessions were further confirmed by seed morphological observation. Limited intraspecific genetic diversity was revealed by these gene-derived markers and/or sequences. It was noticed that there were many accessions collected within the same subspecies but very few subspecies collected within the same species in the USDA Vigna collection. Based on our results, more attention should be paid to the subspecies, wild forms and/or botanical varieties for future curation.

Technical Abstract: The phylogenetic relationships in the USDA Vigna germplasm collection were unclear and their genetic diversity had not been measured empirically. To reveal interspecific phylogenetic relationships and assess their genetic diversity, 48 accessions representing 12 Vigna species were selected, and 30 gene-derived markers from legumes were employed. Some high-quality amplicons were sequenced. Indels (insertion/deletions) were discovered through the sequence alignments that were specific identifiers for some Vigna species. In regards to revealing polymorphisms, intron-spanning markers were more effective than exon-derived markers. These gene-derived markers were more successful in revealing interspecific polymorphisms than intraspecific polymorphisms at both the DNA fragment and sequence level. Two different dendrograms were generated from DNA fragment data and DNA sequence data, respectively. The results from these two dendrograms supported each other and showed similar phylogenetic relationships among Vigna species investigated. The accessions clustered into four main groups and thirteen subgroups. Each subgroup represents a subgenus or a species. Phylogenetic analysis revealed that some accessions were misidentified in our collection. The misidentified accessions were further confirmed by seed morphological observation. Limited intraspecific genetic diversity was revealed by these gene-derived markers and/or species. It was noticed that there were many accessions collected within the same subspecies but very few subspecies collected within the same species in the USDA Vigna collection. Based on our results, more attention should be paid to the subspecies, wild forms and/or botanical varieties for future curation in order to expand the genetic diversity of Vigna germplasm in the USDA collection.