The genetics of domestication of rice bean, Vigna umbellata

Abstract

Background and AimsThe 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.MethodsA 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 ResultsA 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.ConclusionsThis 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.

QTLs CONTROLLING SEED WEIGHT AND DAYS TO FLOWERING IN MUNGBEAN [Vigna radiata (L.) Wilczek], THEIR CONSERVATION IN AZUKI BEAN [V. angularis (Ohwi) Ohwi & Ohashi] AND RICE BEAN [V. umbellata (Thunb.) Ohwi & Ohashi]

“…Mungbean, azuki bean and rice bean belong to the subgenus Ceratotropis which are known as Asian Vigna because they are all originated in Asia. QTLs for seed weight and flowering time have been reported in azuki bean (Isemura et al, 2007;Kaga et al, 2008) and rice bean (Isemura et al, 2010). Comparison of QTL locations for seed weight and flowering time of mungbean in the present study with those of azuki bean and/or rice bean (Figure 3) further supports previous findings.…”

“…High genome conservation among species in the genus Vigna has been demonstrated (Fatokun et al, 1992;Somta et al, 2006;Isemura et al, 2007Isemura et al, , 2010Kongjaimun et al, 2012). Mungbean, azuki bean and rice bean belong to the subgenus Ceratotropis which are known as Asian Vigna because they are all originated in Asia.…”

QTL analysis reveals the genetic architecture of domestication traits in Crisphead lettuce

“…Quantitative Trait Locus (QTL) studies of domestication-related traits using crosses between crops and their wild relatives have given insights into the origin of crops and speed of domestication (Gross and Olsen 2010). Furthermore, crop-wild crosses provide potential source material for crop improvement (Isemura et al 2010;Vaughan et al 2007), insight on hybridization and introgression between crops and their wild relatives (Hancock 2005;Hooftman et al 2009), and show genomic regions under selection in crop-wild hybrids (Baack et al 2008;Dechaine et al 2009). …”

“…Such regions contain very low variation among cultivars, indicating a rapid and uniform fixation caused by continuous artificial selection over many years ). In maize (Doebley and Stec 1993), rice bean (Isemura et al 2010), eggplant (Doganlar et al 2002), tomato (Frary et al 2000), and rice (Cai and Morishima 2002), a small number of QTL cause large phenotypic changes in seed shattering, seed and fruit size, and branching patterns. In contrast, the crop genetic architecture of sunflower domestication is characterized by a relative high number of QTL, many with minor or intermediate effect .…”

“…Second, domestication-related QTL are not uniformly distributed over the genome, but are often clustered (Burger et al 2008;Ross-Ibarra 2005). For example, clustering has been found in sunflower Dechaine et al 2009), azuki bean (Kaga et al 2008), rice bean (Isemura et al 2010), rice (Cai and Morishima 2002), eggplant (Doganlar et al 2002), pearl millet (Poncet et al 2000), and tomato (Prudent et al 2009). Third, the majority of QTL usually show phenotypic effects in the expected direction; i.e.…”