Allele Mining for Stress Tolerance Genes in <I>Oryza</I> Species and Related Germplasm

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.

Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativaL.)

“…Therefore, to date, many global crop research institutes are adopting with allele mining strategies. Identification of allelic variants among germplasm collections provides new germplasm for the novel alleles to target trait improvement but additionally categorises the germplasm entries because of their conservation (Latha et al, 2004). The international project to sequence the genome of O. sativa L cv.…”

“…The DNA bank could be developed to utilise allele mining to determine unique germplasm that contains novel alleles as well as allele combinations. Allele mining has been performed in unique family genes that are involved in a particular mechanism of stress tolerance exhibited by identified accessions (Latha et al, 2004).…”

“…Using sequence information from allele mining studies, syntenic relationships can be analysed for the identified loci/genes over the species. Allele mining exploits the particular DNA sequence of a single genotype to isolate useful alleles from related genotypes (Latha et al, 2004). The accessibility of the sequences of the candidate genes that underlie agronomic traits may help the practical genebased use of genetic resources (Graner, 2006).…”

Genotypic response of silicon uptake ability in upland varieties of indica rice (Oryza sativa L.) and in silico analysis of silicon transporter gene (Lsi2) in var. Ghanteswari.

“…A significant amount of natural allelic variation is known to exist for a given gene and such small polymorphic variation are implicated in evolutionary relationship between the gene and the trait in question. Thus this type of studies provides the raw materials for plant breeding programmes and translational genomic approaches (Latha et al 2004). …”

Molecular approaches for characterization and use of natural disease resistance in wheat

“…This led to the identification of 166 accessions with superior alleles, suggesting that the improvement of malting quality in barley could be achieved by introducing these alleles into breeding programmes. Latha et al (2004) used the rice calmodulin genes and a saltinducible rice gene for allele mining of stress tolerance genes on identified accessions of rice and related germplasm. They examined the feasibility of allele mining using PCR primers based on the 5′-and 3′-untranslated regions of genes and found that these primers were sufficiently conserved to be effective over the entire range of germplasm in rice.…”