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Transcriptomic Profiling Reveals Metabolic and Regulatory Pathways in the Desiccation Tolerance of Mungbean (Vigna radiata [L.] R. Wilczek).

ABSTRACT: Mungbean (Vigna radiate L. Wilczek) is an important legume crop for its valuable nutritional and health benefits. Desiccation tolerance (DT) is a capacity of seeds to survive and maintain physiological activities during storage and under stress conditions. Many studies of DT have been reported in other legume crop, such as soybean and Medicago truncatula with little studies in the mungbean. In this study, the transcript profiles of mungbean seeds under different imbibition times were investigated for DT using RNA-sequencing (RNA-seq). A total of 3210 differentially expressed genes (DEGs) were found at the key period of DT (3-18 h of imbibition). Gene ontology (GO) and KEGG analysis showed that the terms of "response to stimulus," "transcription regulator," "methylation," and "starch and sucrose metabolism" were enriched for DT. Clustering analysis also showed that many transcription factors (MYB, AP2, and NAC), HSPs, embryogenesis abundant (LEA) proteins, and genes encoding methyltransferase and histone were differentially expressed. Nine of these DEGs were further validated by quantitative RT-PCR (qRT-PCR). Our study extends our knowledge of mungbean transcriptomes and further provides insight into the molecular mechanism of DT as well as new strategies for developing drought-tolerant crops.

SUBMITTER: Tian X

PROVIDER: S-EPMC5174128 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Transcriptomic Profiling Reveals Metabolic and Regulatory Pathways in the Desiccation Tolerance of Mungbean (Vigna radiata [L.] R. Wilczek).

Tian Xiangrong X Li Sidi S Liu Yisong Y Liu Xuanming X

Frontiers in plant science 20161221

Mungbean (Vigna radiate L. Wilczek) is an important legume crop for its valuable nutritional and health benefits. Desiccation tolerance (DT) is a capacity of seeds to survive and maintain physiological activities during storage and under stress conditions. Many studies of DT have been reported in other legume crop, such as soybean and Medicago truncatula with little studies in the mungbean. In this study, the transcript profiles of mungbean seeds under different imbibition times we ...[more]

PMID: 28066476

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Project description:BackgroundMungbean (Vigna radiata [L.] R. Wilczek) is an important legume crop with high nutritional value in South and Southeast Asia. The crop plant is susceptible to a storage pest caused by bruchids (Callosobruchus spp.). Some wild and cultivated mungbean accessions show resistance to bruchids. Genomic and transcriptomic comparison of bruchid-resistant and -susceptible mungbean could reveal bruchid-resistant genes (Br) for this pest and give insights into the bruchid resistance of mungbean.ResultsFlow cytometry showed that the genome size varied by 61 Mb (mega base pairs) among the tested mungbean accessions. Next generation sequencing followed by de novo assembly of the genome of the bruchid-resistant recombinant inbred line 59 (RIL59) revealed more than 42,000 genes. Transcriptomic comparison of bruchid-resistant and -susceptible parental lines and their offspring identified 91 differentially expressed genes (DEGs) classified into 17 major and 74 minor bruchid-resistance-associated genes. We found 408 nucleotide variations (NVs) between bruchid-resistant and -susceptible lines in regions spanning 2 kb (kilo base pairs) of the promoters of 68 DEGs. Furthermore, 282 NVs were identified on exons of 148 sequence-changed-protein genes (SCPs). DEGs and SCPs comprised genes involved in resistant-related, transposable elements (TEs) and conserved metabolic pathways. A large number of these genes were mapped to a region on chromosome 5. Molecular markers designed for variants of putative bruchid-resistance-associated genes were highly diagnostic for the bruchid-resistant genotype.ConclusionsIn addition to identifying bruchid-resistance-associated genes, we found that conserved metabolism and TEs may be modifier factors for bruchid resistance of mungbean. The genome sequence of a bruchid-resistant inbred line, candidate genes and sequence variations in promoter regions and exons putatively conditioning resistance as well as markers detecting these variants could be used for development of bruchid-resistant mungbean varieties.

Project description:Mungbean (Vigna radiata L. Wilczek) is one of the important warm-season food legumes, contributing substantially to nutritional security and environmental sustainability. The genetic complexity of yield-associated agronomic traits in mungbean is not well understood. To dissect the genetic basis of phenological and agronomic traits, we evaluated 153 diverse mungbean genotypes for two phenological (days to heading and days to maturity) and eight agronomic traits (leaf nitrogen status using SPAD, plant height, number of primary branches, pod length, number of pods per plant, seeds per pod, 100-seed weight, and yield per plant) under two environmental conditions. A wide array of phenotypic variability was apparent among the studied genotypes for all the studied traits. The broad sense of heritability of traits ranged from 0.31 to 0.95 and 0.21 to 0.94 at the Delhi and Ludhiana locations, respectively. A total of 55,634 genome-wide single nucleotide polymorphisms (SNPs) were obtained by the genotyping-by-sequencing method, of which 15,926 SNPs were retained for genome-wide association studies (GWAS). GWAS with Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK) model identified 50 SNPs significantly associated with phenological and agronomic traits. In total, 12 SNPs were found to be significantly associated with phenological traits across environments, explaining 7%-18.5% of phenotypic variability, and 38 SNPs were significantly associated with agronomic traits, explaining 4.7%-27.6% of the phenotypic variability. The maximum number of SNPs (15) were located on chromosome 1, followed by seven SNPs each on chromosomes 2 and 8. The BLAST search identified 19 putative candidate genes that were involved in light signaling, nitrogen responses, phosphorus (P) transport and remobilization, photosynthesis, respiration, metabolic pathways, and regulating growth and development. Digital expression analysis of 19 genes revealed significantly higher expression of 12 genes, viz. VRADI01G08170, VRADI11G09170, VRADI02G00450, VRADI01G00700, VRADI07G14240, VRADI03G06030, VRADI02G14230, VRADI08G01540, VRADI09G02590, VRADI08G00110, VRADI02G14240, and VRADI02G00430 in the roots, cotyledons, seeds, leaves, shoot apical meristems, and flowers. The identified SNPs and putative candidate genes provide valuable genetic information for fostering genomic studies and marker-assisted breeding programs that improve yield and agronomic traits in mungbean.

Dataset Information

Transcriptomic Profiling Reveals Metabolic and Regulatory Pathways in the Desiccation Tolerance of Mungbean (Vigna radiata [L.] R. Wilczek).

Publications

Transcriptomic Profiling Reveals Metabolic and Regulatory Pathways in the Desiccation Tolerance of Mungbean (<i>Vigna radiata</i> [L.] R. Wilczek).

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