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Analysis of 3'-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India.

ABSTRACT: Four strains (NL-1, NL-1n, NL-7 and NL-7n) of Bean common mosaic virus (BCMV) prevalent on common bean (Phaseolus vulgaris) in Himachal Pradesh, a north-western Himalayan state of India were compared at the 3' terminal region of the viral genome to elucidate variation and relationship among these strains. 3' terminal region comprising of partial nuclear inclusion b (NIb) (171-233 bp), complete coat protein (CP) (860 bp) and 3' untranslated region (UTR) (208-244 bp) shared 96-98% nucleotide and 96-99% amino acids identity among various strains of BCMV. Multiple alignment as well as cluster dendrograms of the 3' terminal region placed the test isolates in BCMV species of genus Potyvirus. Phylogenetic analysis of complete CP as well as 3' UTR also showed Indian strains to be distinct strains. Sequence homology, multiple alignment and evolutionary divergence of 3' terminal region could not differentiate the pathogenic strain groups, thereby establishing least role of this region in strain characterization of the virus. Comparisons of CP and 3' UTR region of BCMV strains and other members of genus Potyvirus clearly indicated the little utility of 3' terminal region in distinction of virus strains. Implications of coat protein region in viral strain distinction are also discussed.

SUBMITTER: Sharma P

PROVIDER: S-EPMC3550725 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

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Analysis of 3'-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India.

Sharma Prachi P Sharma P N PN Kapil Renu R Sharma S K SK Sharma O P OP

Indian journal of virology : an official organ of Indian Virological Society 20110621 1

Four strains (NL-1, NL-1n, NL-7 and NL-7n) of Bean common mosaic virus (BCMV) prevalent on common bean (Phaseolus vulgaris) in Himachal Pradesh, a north-western Himalayan state of India were compared at the 3' terminal region of the viral genome to elucidate variation and relationship among these strains. 3' terminal region comprising of partial nuclear inclusion b (NIb) (171-233 bp), complete coat protein (CP) (860 bp) and 3' untranslated region (UTR) (208-244 bp) shared 96-98% nucleotide and 9 ...[more]

PMID: 23637500

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Project description:BACKGROUND: Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV). RESULTS: We physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study. CONCLUSIONS: We demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS.

Dataset Information

Analysis of 3'-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India.

Publications

Analysis of 3'-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India.

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