Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis

Abstract

Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

QTL Analysis of Domestication Syndrome in Zombi Pea (Vigna vexillata), an Underutilized Legume Crop

“…In addition to environmental factors, genetic relatedness of the parents appeared to affect the successful hybridization of between different forms of zombi pea. In our study, the wild zombi pea (JP235863 from India) and the Bali cultivated zombi pea were genetically closely related [4], while in the study of Damayanti et al [8] the wild zombi pea used were from Africa and Australia in which they were genetically highly differentiated from the Bali cultivated zombi pea [4].…”

“…The low polymorphism of SSR markers was also observed in the mapping parents of V. vexillata used by Marubodee et al [33] in which only 6.2% of 1,336 SSR markers were polymorphic. In addition, Dachapak et al [4] reported that only 21.2% of 1,024 SSR markers screened in 6 accessions of V. vexillata from Asia, Africa, Australia and America were polymorphic. However, the percentage of amplifiable SSR markers in Marubodee et al [33] and Dachapak et al [4] (65.4% and 58.1%, respectively) was higher than in our study (36.6%).…”

“…In addition, Dachapak et al [4] reported that only 21.2% of 1,024 SSR markers screened in 6 accessions of V. vexillata from Asia, Africa, Australia and America were polymorphic. However, the percentage of amplifiable SSR markers in Marubodee et al [33] and Dachapak et al [4] (65.4% and 58.1%, respectively) was higher than in our study (36.6%). It is worth noting that almost all of the markers used by Marubodee et al [33] and Dachapak et al [4] were used in our study.…”

“…Two forms of zombi pea exists; seed type and tuber (storage root) types. The seed type is believed to be domesticated in Sudan (Africa) [3;4], while the tuber type is believed to be domesticated in Bali and Timor, Indonesia (Asia) [5] and India [6,7]. Genetic diversity analysis in a large set of V. vexillata germplasm using simple sequence repeat (SSR; also known as microsatellite) markers revealed clear difference between the two types and suggested that these two types were domesticated from different wild gene pools of V. vexillata [4].…”

“…The tuber type zombi pea has not yet been classified as a variety of V. vexillata . This type is likely to be domesticated from wild zombi pea of Asia [4]. It has viny growth habit and large seed size, and is sensitive to day length and no seed dormancy with some degree of pod shattering.…”