Allele mining for stress tolerance genes in Oryza species and related germplasm |
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Authors: | R. Latha L. Rubia J. Bennett M. S. Swaminathan |
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Affiliation: | (1) MS Swaminathan Research Foundation, Taramani Institutional Area, 3rd Cross Street, 600 113 Chennai, India;(2) Biotechnology and Bioresources Division, Darbar, Seth Block, The Energy and Resources Institute, Habitat Place, Lodhi Road, 1210 002 New Delhi, India;(3) Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines |
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Abstract: | Allele mining exploits the deoxyribonucleic acid (DNA) sequence of one genotype to isolate useful alleles from related genotypes. The international project to sequence the genome of Oryza sativa L cv. Nipponbare will make allele mining possible for all genes of rice and possibly related cereals. We used a rice calmodulin gene, a rice gene encoding a late embryogenesis-associated protein, and salt-inducible rice gene to optimize the polymerase chain reaction (PCR) for allele mining of stress tolerance genes on identified accessions of rice and related germplasm. Two sets of PCR primers were designed for each gene. Primers based on the 5′ and 3′ untranslated region of genes were found to be sufficiently conserved so as to be effective over the entire range of germplasm in rice for which the concept of allelism is applicable. However, the primers based on the adjacent amino (N) and carboxy (C) termini amplify additional loci. |
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Keywords: | Allele mining Oryza species PCR stress-tolerance genes |
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