Identification of novel loci for flowering time in mungbean [Vigna radiata (L.) R. Wilczek] using genome-wide association study.

BACKGROUND: Flowering time is an important crop trait. Mungbean flowers do not flower simultaneously, leading to asynchronous pod maturity and laborious multiple harvests per individual plant. The genomic and genetic mechanisms of flowering in mungbean are largely unknown. OBJECTIVE: This study sought to discover new quantitative trait loci (QTLs) for days to first flowering in mungbean using a genome-wide association study (GWAS). METHODS: In total, 206 mungbean accessions collected from 20 countries were sequenced using genotyping by sequencing. A GWAS was conducted using 3,596 single nucleotide polymorphisms (SNPs) using TASSEL v5.2. RESULTS: Seven significant SNPs were associated with first flowering time. Based on the linkage disequilibrium (LD) decay distance, LD block was determined from upstream to downstream of each SNP up to 384 kb. The lead SNP (Chr2_51229568) was located in the DFF2-2 locus. Syntenic analysis between mungbean and soybean revealed the DFF2-2 locus had collinearity with soybean genomic regions containing flowering-related QTLs on Gm13 and Gm20. CONCLUSION: Identification of flowering-related QTLs and SNPs is important for developing synchronous pod maturity and desirable flowering traits in mungbean.

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

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.

Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.

Genome-wide DNA methylation profile in mungbean.

DNA methylation on cytosine residues is known to affect gene expression and is potentially responsible for the phenotypic variations among different crop cultivars. Here, we present the whole-genome DNA methylation profiles and assess the potential effects of single nucleotide polymorphisms (SNPs) for two mungbean cultivars, Sunhwanogdu (VC1973A) and Kyunggijaerae#5 (V2984). By measuring the DNA methylation levels in leaf tissue with the bisulfite sequencing (BSseq) approach, we show both the frequencies of the various types of DNA methylation and the distribution of weighted gene methylation levels. SNPs that cause nucleotide changes from/to CHH - where C is cytosine and H is any other nucleotide - were found to affect DNA methylation status in VC1973A and V2984. In order to better understand the correlation between gene expression and DNA methylation levels, we surveyed gene expression in leaf tissues of VC1973A and V2984 using RNAseq. Transcript expressions of paralogous genes were controlled by DNA methylation within the VC1973A genome. Moreover, genes that were differentially expressed between the two cultivars showed distinct DNA methylation patterns. Our mungbean genome-wide methylation profiles will be valuable resources for understanding the phenotypic variations between different cultivars, as well as for molecular breeding.

Stochastic alternative splicing is prevalent in mungbean (Vigna radiata).

Alternative splicing (AS) can produce multiple mature mRNAs from the same primary transcript, thereby generating diverse proteins and phenotypes from the same gene. To assess the prevalence of AS in mungbean (Vigna radiata), we analysed whole-genome RNA sequencing data from root, leaf, flower and pod tissues and found that at least 37.9% of mungbean genes are subjected to AS. The number of AS transcripts exhibited a strong correlation with exon number and thus resembled a uniform probabilistic event rather than a specific regulatory function. The proportion of frameshift splicing was close to the expected frequency of random splicing. However, alternative donor and acceptor AS events tended to occur at multiples of three nucleotides (i.e. the codon length) from the main splice site. Genes with high exon number and expression level, which should have the most AS if splicing is purely stochastic, exhibited less AS, implying the existence of negative selection against excessive random AS. Functional AS is probably rare: a large proportion of AS isoforms exist at very low copy per cell on average or are expressed at much lower levels than default transcripts. Conserved AS was only detected in 629 genes (2.8% of all genes in the genome) when compared to Vigna angularis, and in 16 genes in more distant species like soya bean. These observations highlight the challenges of finding and cataloguing candidates for experimentally proven AS isoforms in a crop genome.

Translational genomics for plant breeding with the genome sequence explosion.

The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

Draft genome sequence of adzuki bean, Vigna angularis.

Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis, and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.