title: Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits.
abstract: 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 re-sequencing 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.
authors: National Institute of Plant Genome Research, New Delhi, India.
authors: Chandra Bhan
authors: CB
authors: Yadav
authors: Department of Genetics and Plant Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
authors: Priyanka
authors: P
authors: Bhareti
authors: National Institute of Plant Genome Research, New Delhi, India.
authors: Mehanathan
authors: M
authors: Muthamilarasan
authors: National Institute of Plant Genome Research, New Delhi, India.
authors: Minakshi
authors: M
authors: Mukherjee
authors: National Institute of Plant Genome Research, New Delhi, India.
authors: Yusuf
authors: Y
authors: Khan
authors: Department of Genetics and Plant Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
authors: Pushpendra
authors: P
authors: Rathi
authors: National Institute of Plant Genome Research, New Delhi, India.
authors: Manoj
authors: M
authors: Prasad
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D001483:Base Sequence; D053839:Begomovirus / Q000502:physiology*; D032461:Chromosomes, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D054643:INDEL Mutation / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D010641:Phenotype; D020161:Physical Chromosome Mapping; D010935:Plant Diseases / Q000235:genetics / Q000821:virology*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics* / Q000821:virology*
chemical_list: D009711:Nucleotides