A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program

Mungbean (Vigna radiata L.), a fast-growing legume species, is an important sourceof carbohydrates and proteins in developing countries of Asia. Here, we constructeda near-complete genome sequence of mungbean with a scaffold N50 value of 5.2Mb and only a 0.4% gap, with a total scaffold size of 475 Mb. We identified severalmisassembled pseudomolecules (Chr03, Chr04, Chr05, and Chr08) in the previousdraft assembly; Chr03, Chr04, and Chr08 were assembled into one chromosome, andChr05 was broken into two chromosomes in the improved reference genome assem-bly, thus providing more accurate linkage information to breeders. Additionally, usingan ultra-high-resolution linkage map constructed based on resequencing data, weidentified several quantitative trait loci (QTLs) and the underlying candidate genesaffecting synchronous pod maturity (SPM). Mungbean homologs of two soybean([Glycine max (L.) Merr.] flowering genes, E3 (phytochrome A) and J (early flower-ing 3), were identified as candidate genes for the QTLs, and the candidate genes forplant height, node number, and SPM showed critical nucleotide substitutions betweenthe reference cultivar and other genotypes (landraces and wild accessions). Based onthe analysis of genetic diversity among 276 accessions collected from 23 countries,we identified 36 selective sweep regions and observed that the overall genetic diver-sity of cultivars decreased to 30% of that in wild accessions postdomestication. Thenear-complete genome sequence of mungbean represents an important resource forgenome-assisted improvement in the mungbean breeding program.