A SNP and SSR Based Genetic Map of Asparagus Bean (Vigna. unguiculata ssp. sesquipedialis) and Comparison with the Broader Species

Abstract

Asparagus bean (Vigna. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea [Vigna. unguiculata (L.) Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as ‘long beans’ or ‘asparagus beans’. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs), with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs) identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level.

Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies

“…Given the genome size of 630 Mb and the genetic linkage map of 680 cM (Lucas et al, 2011;Xu et al, 2011), this approximately equals 1.84 Mb of physical distance. Such level and extent of LD are comparable to those observed in the European barley collection (Rostoks et al, 2006), and the LD decay distance is even shorter than that in a small population of common bean (Phaseolus vulgaris L.) from America, a close relative of asparagus Linkage disequilibrium patterns in asparagus bean P Xu et al bean, where LD decays to 0.1-0.2 within 6-12 cM (McConnell et al, 2010).…”

“…The latter is also known as asparagus bean or 'yard-long' bean, for it is characterized by its very long (0.5-1 m) pods with less fiber, narrow kidney-shaped seeds and climbing growth habit. Genetic similarity between the two subspecies is high as evidenced by fully fertile hybrids and synteny for most of the shared molecular markers between genetic maps (Muchero et al, 2009;Xu et al, 2011). Cowpea is thought to have undergone a severe bottleneck during domestication (Panella and Gepts, 1992).…”

“…unguiculata were constructed (Muchero et al, 2009;Lucas et al, 2011). A comparable genetic linkage map of asparagus bean also was constructed in the authors' lab using the same system and additional SSR markers (Xu et al, 2011). The main objective of the present study was to analyze the genetic variation and LD patterns in asparagus bean based on a panel of 95 Chinese accessions genotyped using the above SNP markers.…”

SSR and e-PCR Provide a Bridge Between Genetic Map and Genome Sequence of Potato for Marker Development in Target QTL Region

“…In comparative mapping with SSRs, synteny is often determined by BLAST using source sequences of SSR markers as queries (Shirasawa et al 2011;Suwabe et al 2006;Xu et al 2011). In such procedure, related gene family member, pseudogene and especially the microsatellite sequence can lead to false positives.…”

Technical and economic analysis of irrigation of asparagus bean in protected environment

“…sesquipedalis, L.) is an annual climbing plant, and produces long pods (0.5 to 1.0m) harvested still in the immature stage (XU et al, 2011). It is tolerant to high temperatures and acid soils (FLYMAN & AFOLAYAN, 2008).…”