Detection of Genome Donor Species of Neglected Tetraploid Crop Vigna reflexo-pilosa (Créole Bean), and Genetic Structure of Diploid Species Based on Newly Developed EST-SSR Markers from Azuki Bean (Vigna angularis)

Kenta Shirasawa,Sachiko Isobe,Prakit Somta,Peerasak Srinives,Duncan A Vaughan,Manoj Prasad,Akito Kaga,Norihiko Tomooka,Sompong Chankaew,Takehisa Isemura,Hideki Hirakawa

doi:10.1371/journal.pone.0104990

Abstract

Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

Highlights

The Leguminosae genus Vigna comprises about 100 species
Markers) to other DNA marker systems is the high transferability across species and genera because of primer pairs are designed from conserved transcribed regions, they are generally less polymorphic than genomic SSR markers
Low polymorphism rate of the azuki bean EST-SSRs can be an undesirable character for the use of these markers in comparative genome mapping in the genus Vigna

Summary

Introduction

The Leguminosae genus Vigna comprises about 100 species. These species are morphologically diverse and geographically widespread and mainly found in Africa (African Vigna; subgenus Vigna) and Asia (Asian Vigna; subgenus Ceratotropis) [1]. The Asian Vigna comprises 21 species in which seven are domesticated and/or cultivated in various geographical and climatic regions, and cropping systems in Asia [2]. The seven domesticated/ cultivated species include V. aconitifolia (moth bean), V. angularis (azuki bean), V. mungo (black gram), V. radiata (mungbean), V. reflexo-pilosa (creole bean), V. stipulacea (jungli bean) and V. umbellata (rice bean). Cytogenetic analyses of V. reflexo-pilosa showed that the species formed 22 bivalents without multivalent at meiosis and was, therefor considered to be an amphidiploid [4] [5]

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