Allele Mining in Crop Improvement

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International Journal of Development Research

Allele Mining in Crop Improvement

Abstract: 

Development of superior and high yielding varieties made possible by accumulation of beneficial alleles from vast plant genetic resources existing worldwide. Still, a significant portion of these beneficial/ superior alleles were not used as these were left behind during evolution and domestication. Introducing novel alleles from wild crop plants to cultivated varieties have clearly demonstrated that certain alleles and their combinations potentially make dramatic changes in trait expression. Hence, the vast germplasm resources need to be relooked for novel alleles to further enhance the genetic potential of crop varieties for various agronomic traits. Alleles are alternative forms of a gene occupying a given locus on a chromosome. Allele mining exploits the deoxy-ribonucleic acid (DNA) sequence of one genotype to isolate useful alleles from related genotypes. It helps in tracing the evolution of alleles, identification of new haplotypes and development of allele-specific markers for use in marker-assisted selection. Allele mining is a way to find out the superior alleles from related genotypes. This is made possible as enormous sequence information is available in public databases as a result of sequencing of diverse crop genomes. It is important to use this genomic information for the identification and isolation of novel and superior alleles of agronomically important genes from crop gene pools to suitably organize for the development of improved cultivars. Alleles such as Sh (grain shattering), Rc (grain pericarp color), Wx for Granule-Bound Starch Synthase (GBSS) and GS (grain size) have led to significant improvements in rice. In allele mining, different softwares are used for identifying the nucleotide variation and prediction of amino acid changes which is responsible for encoding protein structure and functions. Some of the bioinformatics softwares used are ClustalW, DCPD, Fast PCR and Plant CARE. Allele mining can be effectively used for discovery of superior alleles are through ‘mining’ the gene of interest from diverse genetic resources. It can also provide insight into molecular basis of novel trait variations and identify the nucleotide sequence changes associated with superior alleles. It will help to trace the evolution of alleles, identification of new haplotypes and development of allele-specific markers for use in marker-assisted selection. Realizing the immense potential of allele mining, concerted allele mining efforts are underway in many international crop research institutes.

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