De novo genome assembly of rice bean (Vigna umbellata) – A nominated nutritionally rich future crop reveals novel insights into flowering potential, habit, and palatability centric – traits for efficient domestication

Abstract

Rice bean is a less-known underutilized legume crop with a high nutritional value among members of the Vigna family. As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimated identification of 31,276 high confidence index genes via 15,521 scaffolds generated from Illumina and PacBio platform 30X coverage data has achieved 96.08% functional coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to Vigna angularis (experimental control/outgroup), Vigna radiata, and Vigna unguiculata, however, Vigna angularis being the closest. The assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete coding sequence (CDS) alignment. In contrast, 17 medically influential genomes from the National Institute of General Medical Sciences-National Institutes of Health NIGMS-NIH, when compared to rice bean assembly for LCB clusters, led to the identification of more than 18,000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Significantly, we found deserving late-flowering genes, palatably indexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Therefore, the findings from this report address the genomic value of rice bean to be escalated via breeding by allied and applied approaches.

An associative transcriptomics study on rice bean (Vigna umbellata) provides new insights into genetic basis and candidate genes governing flowering, maturity and seed weight

“…Engineering and Biotechnology, New Delhi, India at scaffold level (Kaul et al, 2022) have increased the scope of genomic research on rice bean.…”

“…However, now its importance is being understood and several research projects are undertaken for the genetic improvement of this crop. The genomes released by Chinese Academy of Agricultural Sciences, Beijing, China (Guan et al ., 2022) at chromosomal level and International Centre for Genetic Engineering and Biotechnology, New Delhi, India at scaffold level (Kaul et al ., 2022) have increased the scope of genomic research on rice bean.…”

“…Very recently in September 2022, one genome assembly of rice bean at chromosomal level has been released by Chinese Academy of Agricultural Sciences, Beijing, China (Guan et al ., 2022) with the genome size of 475.64LMb that is 90.49% of the estimated genome size. However, another assembly by International Centre for Genetic Engineering and Biotechnology, New Delhi, India is available at scaffold level (Kaul et al ., 2022) having the assembled genome size of 414 Mb. They estimated a total of 31276 highly confidential genes from 15521 scaffolds.…”

Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)

“…Very recently in September 2022, one genome assembly of rice bean at the chromosomal level has been released by Chinese Academy of Agricultural Sciences, Beijing, China [ 13 ] with the genome size of 475.64 Mb that is 90.49% of the estimated genome size. However, another assembly by International Centre for Genetic Engineering and Biotechnology, New Delhi, India is available at scaffold level [ 15 ] having the assembled genome size of 414 Mb. They estimated a total of 31276 highly confidential genes from 15521 scaffolds.…”

Unique Salt-Tolerance-Related QTLs, Evolved in Vigna riukiuensis (Na+ Includer) and V. nakashimae (Na+ Excluder), Shed Light on the Development of Super-Salt-Tolerant Azuki Bean (V. angularis) Cultivars

“…The advancement of next-generation sequencing (NGS) technologies has accelerated whole-genome sequencing and genotyping methods. Whole-genome sequences for 14 Vigna species have been constructed, including azuki bean (V. angularis) [17][18][19][20][21][22][23]. Genotyping using high-throughput NGS technologies reduces the complexity of genome analysis and allows for the development of a large number of SNP markers for any species of interest.…”