Allele mining

Identification and access to allelic variation that affects the plant phenotype is of the utmost importance for the utilization of genetic resources, such as in plant variety development. Considering the huge numbers of accessions that are held collectively by genebanks, genetic resources collections are deemed to harbour a wealth of undisclosed allelic variants. The challenge is how to unlock this variation. Allele mining is a research field aimed at identifying allelic variation of relevant traits within genetic resources collections. For identified genes of known function and basic DNA sequence, genetic resources collections may be screened for allelic variation by e.g. the ’tiling strategy‘ using DNA chip technology. In that approach the basic DNA sequence of a gene is spotted on a chip in the form of large series of sequence-overlapping probes consisting of 15-20 bases. Each base position in a fluorescently labelled sample is then interrogated for the presence of point mutations by monitoring hybridization signals with the spotted probes. Because the sequence of samples is determined in comparison with the primary composition of a gene, this method is also known as ‘re-sequencing’. With this method new point mutations, in relatively large DNA fragments, can be detected. Once allelic variants of interest have been identified, the approach can be optimized by focusing on target sets of polymorphisms, for example by using SNP detection methods.

Suggested reading

Upadhyaya, H.D., B.J. Furman, S.L. Dwivedi, S.M. Udupa, C.L.L. Gowda, M. Baum, J.H. Crouch, H.K. Buhariwalla and S. Singh, 2006. Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea. Plant Genetic Resources: Characterization and Utilization, 4: 13-19.

Latha, R., L. Rubia, J. Bennett, M.S. Swaminathan, 2004. Allele mining for stress tolerance genes in Oryza species and related germplasm. Molecular Biotechnology, 27: 101-108.