Dataset Information

A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.).

ABSTRACT: Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.

SUBMITTER: Breria CM

PROVIDER: S-EPMC7397256 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.).

Breria Caleb Manamik CM Hsieh Ching-Hsiang CH Yen Tsair-Bor TB Yen Jo-Yi JY Noble Thomas J TJ Schafleitner Roland R

Genes 20200707 7

Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association ...[more]

PMID: 32646058

Similar Datasets

Project description:Soil salinity is one of the major limiting factors in plant growth regulation. Salinity-tolerant endophytic bacteria (STEB) can be used to alleviate the negative effects of salinity and promote plant growth. In this study, thirteen endophytic bacteria were isolated from mungbean roots and tested for NaCl salt-tolerance up to 4%. Six bacterial isolates, TMB2, TMB3, TMB5, TMB6, TMB7 and TMB9, demonstrated the ability to tolerate salt. Plant growth-promoting properties such as phosphate solubilization, indole-3-acetic acid (IAA) production, nitrogen fixation, zinc solubilization, biofilm formation and hydrolytic enzyme production were tested in vitro under saline conditions. Eight bacterial isolates indicated phosphate solubilization potential ranging from 5.8-17.7 μg mL-1, wherein TMB6 was found most efficient. Ten bacterial isolates exhibited IAA production ranging from 0.3-2.1 μg mL-1, where TMB7 indicated the highest potential. All the bacterial isolates except TMB13 exhibited nitrogenase activity. Three isolates, TMB6, TMB7 and TMB9, were able to solubilize zinc on tris-minimal media. All isolates were capable of forming biofilm except TMB12 and TMB13. Only TMB2, TMB6 and TMB7 exhibited cellulase activity, while TMB2 and TMB7 exhibited pectinase production. Based on in vitro testing, six efficient STEB were selected and subjected to the further studies. 16S rRNA gene sequencing of efficient STEB revealed the maximum similarity between TMB2 and Rhizobium pusense, TMB3 and Agrobacterium leguminum, TMB5 and Achromobacter denitrificans, TMB6 and Pseudomonas extremorientalis, TMB7 and Bradyrhizobium japonicum and TMB9 and Serratia quinivorans. This is the first international report on the existence of A. leguminum, A. denitrificans, P. extremorientalis and S. quinivorans inside the roots of mungbean. Under controlled-conditions, inoculation of P. extremorientalis TMB6, B. japonicum TMB7 and S. quinivorans TMB9 exhibited maximum potential to increase plant growth parameters; specifically plant dry weight was increased by up to 52%, 61% and 45%, respectively. Inoculation of B. japonicum TMB7 displayed the highest potential to increase plant proline, glycine betaine and total soluble proteins contents by 77%, 78% and 64%, respectively, compared to control under saline conditions. It is suggested that the efficient STEB could be used as biofertilizers for mungbean crop productivity under saline conditions after field-testing.

Project description:BackgroundMungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018.ResultsWe used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105?kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein.ConclusionsThe core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts.

Project description:Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.

Dataset Information

A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.).

Publications

A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (<i>Vigna radiata</i> L.).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets