Genome sequencing of adzuki bean ( Vigna angularis ) provides insight into high starch and low fat accumulation and domestication

Abstract

Adzuki bean (Vigna angularis), an important legume crop, is grown in more than 30 countries of the world. The seed of adzuki bean, as an important source of starch, digestible protein, mineral elements, and vitamins, is widely used foods for at least a billion people. Here, we generated a high-quality draft genome sequence of adzuki bean by whole-genome shotgun sequencing. The assembled contig sequences reached to 450 Mb (83% of the genome) with an N50 of 38 kb, and the total scaffold sequences were 466.7 Mb with an N50 of 1.29 Mb. Of them, 372.9 Mb of scaffold sequences were assigned to the 11 chromosomes of adzuki bean by using a single nucleotide polymorphism genetic map. A total of 34,183 protein-coding genes were predicted. Functional analysis revealed that significant differences in starch and fat content between adzuki bean and soybean were likely due to transcriptional abundance, rather than copy number variations, of the genes related to starch and oil synthesis. We detected strong selection signals in domestication by the population analysis of 50 accessions including 11 wild, 11 semiwild, 17 landraces, and 11 improved varieties. In addition, the semiwild accessions were illuminated to have a closer relationship to the cultigen accessions than the wild type, suggesting that the semiwild adzuki bean might be a preliminary landrace and play some roles in the adzuki bean domestication. The genome sequence of adzuki bean will facilitate the identification of agronomically important genes and accelerate the improvement of adzuki bean.adzuki bean | genome sequence | starch synthesis genes | fat synthesis genes | domestication

Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis)

“…The mapping of LGs to more than one chromosome may be explained by genotyping errors, misassembled scaffolds or reciprocal translocations between chromosomes. We suggest that the mapping of LG05 to chromosomes 3 and 8 on the physical map of Yang et al 30. is due to a reciprocal translocation because it corresponds to an “LG 4 + 6” reciprocal translocation model in some wild adzuki bean accessions39.…”

“…Compared with the two SNP maps constructed by Kang et al 29. and Yang et al 30. to assemble the adzuki bean draft genome, the marker number in this individual map is substantially higher.…”

“…Based on the number of SLAF markers mapped to pseudo-chromosomes and the collinearity between LGs and pseudo-chromosomes, we determined that the assembly of the adzuki bean draft genome reported by Yang et al 30. is more accurate than that reported by Kang et al 29…”

“…Colinearity between the high-density linkage map and the adzuki bean genome was determined by comparing the assigned SLAF sequences to two adzuki bean draft genomes2930 with BLASTN (version 2.2.30) and a cut-off value of e −30 . SLAF markers with query sequence lengths ≥80 and sequence identity >98% were selected to calculate the Spearman rank correlation according to their order on LGs and physical position on chromosomes using R (version 3.1.2) software.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Genome sequences for most of the grain legumes are now available, for instance soybean (Schmutz et al, 2010), groundnut progenitors (Bertioli et al, 2016;Chen et al, 2016), chickpea (Varshney et al, 2013d;Parween et al, 2015), pigeonpea (Varshney et al, 2012a), common bean (Schmutz et al, 2014;Yang et al, 2015), and adzuki bean (Kang et al, 2015;Yang et al, 2015) (Table 1). Efforts are underway to sequence the remaining legume genomes.…”