The genetics of domestication of rice bean, Vigna umbellata

Abstract

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.

Methods: A genetic linkage map was constructed by using simple sequence repeat and amplified fragment length polymorphism markers in the BC(1)F(1) 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.

Conclusions: 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.

Fig. 1.

A genetic linkage map of rice bean based on SSR and AFLP markers. This map was constructed from 198 BC₁F₁ individuals of (cultivated rice bean × wild rice bean) × cultivated rice bean. Map distances are shown to the left of the linkage groups and marker names are shown on the right. SSR markers with the prefix ‘CED’ are from azuki bean; those with ‘cp’ and ‘VM’ are from cowpea. SSR markers with the prefix ‘BM’ or ‘PV’ and the SSR markers AY1 (LG4) and GATS11 (LG9) are from common bean. Lower-case letters in SSR markers are suffixed to markers with multiple loci. SSR markers in italics indicate dominant loci. AFLP markers, with the prefix ‘E‘, are named according to the primer combination followed by the estimated fragment size. Markers showing significant deviation from the expected segregation ratios at P levels of 0·05, 0·01 and 0·001 are indicated with *, ** and ***, respectively.

Fig. 2.

Summary of domestication-related QTLs with large effect detected on each linkage group in a population derived from a cross between cultivated and wild rice bean. The signs ‘ + ’ and ‘–’ after trait names indicate positive and negative effects of the allele from cultivated rice bean on the trait. Seed size, SD100WT, SDL, SDW and SDT; pod size, PDL and PDW; leaf size, LFML and LFMW; lower internode length, ST1I and ST2I; upper internode length, ST6I to ST10I.

Fig. 3.

Comparative genetic linkage map of rice bean (left) and azuki bean (right), based on common azuki bean SSR markers. Linkage groups of the rice bean map were aligned with the corresponding LGs of the azuki linkage map (Han et al., 2005). The number of each LG corresponds to that used for the azuki linkage map. Lines between LGs connect the positions of common marker loci. Markers followed by a number in parenthesis indicate the positions of loci on other LGs. In the comparison of the rice bean and azuki bean maps, internal inversions were found between adjacent marker loci in italics.

Fig. 4.

Comparative QTL map of domestication-related traits in rice bean (upper) and azuki bean (lower; after Isemura et al., 2007). QTLs enclosed by rectangles are common to azuki bean and rice bean. QTLs in bold italics explain over 20 % of the phenotypic variation of the trait.