TY - JOUR
T1 - Genome-Wide SNP Identification and Characterization in Two Soybean Cultivars with Contrasting Mungbean Yellow Mosaic India Virus Disease Resistance Traits
AU - Yadav, Chandra
AU - Bhareti, Priyanka
AU - Muthamilarasana, Mehanathan
AU - Mukherjee, Minakshi
AU - Khan, Yusuf
AU - Rathi, Pushpendra
AU - Prasad, Manoj
N1 - This work was financially supported by the Department of Biotechnology, Ministry of Science and Technology, Government of India, India (Grant no. BT/PR14302/AGR/02/736/2010) and core grant of National Institute of Plant Genome Research, Government of India, India. MuM is the recipient of research fellowship from University Grants Commission, New Delhi, India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
PY - 2015/4/13
Y1 - 2015/4/13
N2 - Mungbean yellow mosaic India virus (MYMIV) is a bipartite Geminivirus, which causes severe yield loss in soybean (Glycine max). Considering this, the present study was conducted to develop large-scale genome-wide single nucleotide polymorphism (SNP) markers and identify potential markers linked with known disease resistance loci for their effective use in genomics-assisted breeding to impart durable MYMIV tolerance. The whole-genome resequencing of MYMIV resistant cultivar 'UPSM-534 ' and susceptible Indian cultivar 'JS-335' was performed to identify high-quality SNPs and InDels (insertion and deletions). Approximately 234 and 255 million of 100-bp paired-end reads were generated from UPSM-534 and JS-335, respectively, which provided ∼98%coverage of reference soybean genome. A total of 3083987 SNPs (1559556 in UPSM-534 and 1524431 in JS-335) and 562858 InDels (281958 in UPSM-534 and 280900 in JS-335) were identified. Of these, 1514 SNPs were found to be present in 564 candidate disease resistance genes. Among these, 829 non-synonymous and 671 synonymous SNPs were detected in 266 and 286 defence-related genes, respectively. Noteworthy, a non-synonymous SNP (in chromosome 18, named 18-1861613) at the 149th base-pair of LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE gene responsible for a G/C transversion [proline (CCC) to alanine (GCC)] was identified and validated in a set of 12 soybean cultivars. Taken together, the present study generated a large-scale genomic resource such as, SNPs and InDels at a genome-wide scale that will facilitate the dissection of various complex traits through construction of high-density linkage maps and fine mapping. In the present scenario, these markers can be effectively used to design high-density SNP arrays for their large-scale validation and high-throughput genotyping in diverse natural and mapping populations, which could accelerate genomics-assisted MYMIV disease resistance breeding in soybean.
AB - Mungbean yellow mosaic India virus (MYMIV) is a bipartite Geminivirus, which causes severe yield loss in soybean (Glycine max). Considering this, the present study was conducted to develop large-scale genome-wide single nucleotide polymorphism (SNP) markers and identify potential markers linked with known disease resistance loci for their effective use in genomics-assisted breeding to impart durable MYMIV tolerance. The whole-genome resequencing of MYMIV resistant cultivar 'UPSM-534 ' and susceptible Indian cultivar 'JS-335' was performed to identify high-quality SNPs and InDels (insertion and deletions). Approximately 234 and 255 million of 100-bp paired-end reads were generated from UPSM-534 and JS-335, respectively, which provided ∼98%coverage of reference soybean genome. A total of 3083987 SNPs (1559556 in UPSM-534 and 1524431 in JS-335) and 562858 InDels (281958 in UPSM-534 and 280900 in JS-335) were identified. Of these, 1514 SNPs were found to be present in 564 candidate disease resistance genes. Among these, 829 non-synonymous and 671 synonymous SNPs were detected in 266 and 286 defence-related genes, respectively. Noteworthy, a non-synonymous SNP (in chromosome 18, named 18-1861613) at the 149th base-pair of LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE gene responsible for a G/C transversion [proline (CCC) to alanine (GCC)] was identified and validated in a set of 12 soybean cultivars. Taken together, the present study generated a large-scale genomic resource such as, SNPs and InDels at a genome-wide scale that will facilitate the dissection of various complex traits through construction of high-density linkage maps and fine mapping. In the present scenario, these markers can be effectively used to design high-density SNP arrays for their large-scale validation and high-throughput genotyping in diverse natural and mapping populations, which could accelerate genomics-assisted MYMIV disease resistance breeding in soybean.
KW - Amino Acid Substitution/genetics
KW - Base Sequence
KW - Begomovirus/physiology
KW - Chromosomes, Plant/genetics
KW - Disease Resistance/genetics
KW - Gene Expression Regulation, Plant
KW - Genes, Plant
KW - Genome, Plant
KW - INDEL Mutation/genetics
KW - Molecular Sequence Annotation
KW - Molecular Sequence Data
KW - Nucleotides/genetics
KW - Phenotype
KW - Physical Chromosome Mapping
KW - Plant Diseases/genetics
KW - Polymerase Chain Reaction
KW - Polymorphism, Single Nucleotide/genetics
KW - Quantitative Trait Loci
KW - Quantitative Trait, Heritable
KW - Reproducibility of Results
KW - Sequence Alignment
KW - Sequence Analysis, DNA
KW - Soybeans/genetics
UR - https://www.scopus.com/pages/publications/84928820447
U2 - 10.1371/journal.pone.0123897
DO - 10.1371/journal.pone.0123897
M3 - Article
C2 - 25875830
SN - 1932-6203
VL - 10
JO - PLoS ONE
JF - PLoS ONE
IS - 4
M1 - e0123897
ER -