Journal Article

The genetics of domestication of rice bean, <i>Vigna umbellata</i>

Takehisa Isemura, Akito Kaga, Norihiko Tomooka, Takehiko Shimizu and Duncan Alexander Vaughan

in Annals of Botany

Published on behalf of The Annals of Botany Company

Volume 106, issue 6, pages 927-944
Published in print December 2010 | ISSN: 0305-7364
Published online September 2010 | e-ISSN: 1095-8290 | DOI:

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  • Ecology and Conservation
  • Evolutionary Biology
  • Plant Sciences and Forestry


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Background and Aims

The Asian genus Vigna, to which four cultivated species (rice bean, azuki bean, mung bean and black gram) belong, is suitable for comparative genomics. The aims were to construct a genetic linkage map of rice bean, to identify the genomic regions associated with domestication in rice bean, and to compare these regions with those in azuki bean.


A genetic linkage map was constructed by using simple sequence repeat and amplified fragment length polymorphism markers in the BC1F1 population derived from a cross between cultivated and wild rice bean. Using this map, 31 domestication-related traits were dissected into quantitative trait loci (QTLs). The genetic linkage map and QTLs of rice bean were compared with those of azuki bean.

Key Results

A total of 326 markers converged into 11 linkage groups (LGs), corresponding to the haploid number of rice bean chromosomes. The domestication-related traits in rice bean associated with a few major QTLs distributed as clusters on LGs 2, 4 and 7. A high level of co-linearity in marker order between the rice bean and azuki bean linkage maps was observed. Major QTLs in rice bean were found on LG4, whereas major QTLs in azuki bean were found on LG9.


This is the first report of a genetic linkage map and QTLs for domestication-related traits in rice bean. The inheritance of domestication-related traits was so simple that a few major QTLs explained the phenotypic variation between cultivated and wild rice bean. The high level of genomic synteny between rice bean and azuki bean facilitates QTL comparison between species. These results provide a genetic foundation for improvement of rice bean; interchange of major QTLs between rice bean and azuki bean might be useful for broadening the genetic variation of both species.

Keywords: Rice bean; Vigna umbellata; azuki bean; comparative genomics; SSR; domestication; wild species; QTL

Journal Article.  10160 words.  Illustrated.

Subjects: Ecology and Conservation ; Evolutionary Biology ; Plant Sciences and Forestry

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