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Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits

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Title Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits
 
Creator Yadav, Chandra Bhan
Bhareti, Priyanka
Muthamilarasan, Mehanathan
Mukherjee, Minakshi
Khan, Yusuf
Rathi, Pushpendra
Prasad, Manoj
 
Subject Mungbean yellow mosaic India virus
Soybean
 
Description Accepted date: March 3, 2015
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.
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.
 
Date 2016-01-27T05:34:06Z
2016-01-27T05:34:06Z
2015
 
Type Article
 
Identifier PLoS One, 10(4): e0123897
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/593
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123897
10.1371/journal.pone.0123897
 
Language en_US
 
Publisher PLOS