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Open Access Highly Accessed Research article

SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

Swarup K Parida1, Mitali Mukerji2, Ashok K Singh3, Nagendra K Singh1 and Trilochan Mohapatra14*

  • * Corresponding author: Trilochan Mohapatra tm@nrcpb.org

  • † Equal contributors

Author Affiliations

1 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India

2 Institute of Genomics and Integrative Biology, Delhi, 110007, India

3 Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

4 Present Address: Central Rice Research Institute, Cuttack, 753 006, Odisha, India

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BMC Genomics 2012, 13:426  doi:10.1186/1471-2164-13-426

Published: 25 August 2012

Additional files

Additional file 1:

Validation and genotyping of 384 SNPs present in important abiotic and biotic stress-responsive rice genes across a representative set of 91 rice genotypes.

Format: XLS Size: 152KB Download file

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Open Data

Additional file 2:

Chromosome-wise distribution of SNPs validated through GoldenGate genotyping assay.

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Additional file 3:

A non-synonymous SNP validated in a gene containing leucine-rich repeat (LRR) domain (LOC_Os04g19750) showing differentiation between eight known blast resistant indica and 30 blast susceptible indica rice genotypes.

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Open Data

Additional file 4:

Optimization of number of sub-populations (K value) varying from K = 2 to K = 5 to determine the best possible population structure for 91 rice genotypes.

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Additional file 5:

Pair-wise estimates of genetic variance (FST) among four O. sativa sub-populations.

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Additional file 6:

Domesticated and wild Oryza genotypes used in the study and their inferred ancestry coefficients in population genetic structure analysis.

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Additional file 7:

Graphical genotyping using 325 SNP loci validated through Illumina GoldenGate assay across 91 rice genotypes based on their ascending order of physical location (bp) on 12 rice chromosomes giving allele sharing maps of individual rice genotypes.

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Open Data

Additional file 8:

Genomic constitution of rice genotypes based on introgression of indica and japonica alleles on the 12 rice chromosomes.

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Additional file 9:

Graphical genotyping of 12 Tripura Medicinal rice chromosomes.

Format: DOC Size: 540KB Download file

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