Research review paperAllele mining in crops: Prospects and potentials
Introduction
Progress in plant breeding in terms of development of superior and high yielding varieties of agricultural crops was 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 utilized as these were left behind during evolution and domestication. This untapped genetic variation existing in wild relatives and land races of crop plants could be exploited gainfully for development of agronomically superior cultivars. Introgressions of novel alleles from wild relatives of crop plants into cultivated varieties (deVicente and Tanksley, 1993, Xiao et al., 1996, Xiao et al., 1998, McCouch et al., 2007) have clearly demonstrated that certain alleles and their combinations potentially make dramatic changes in trait expression when moved to a suitable genetic background by overcoming the genetic bottlenecks which restricted their introgression to cultivars. Hence, the vast germplasm resources need to be re-looked for novel alleles to further enhance the genetic potential of crop varieties for various agronomic traits.
Enormous progress has been made in the last 15 years in depositing an exponential amount of sequence information into GenBank (Chan, 2005, Mardis, 2008). With rapid accumulation of sequence and expression data in various genomic databases, accelerated discovery and annotation of new genes can be expected which would enable the development of allele-specific markers (Spooner et al., 2005). Based on gene and genome sequences, polymerase chain reaction (PCR) strategies are devised to isolate useful alleles of genes from a wide range of species (Latha et al., 2004). This capability enables direct access to key alleles conferring resistance to biotic and abiotic stresses, greater nutrient use efficiency, enhanced yield and improved quality. Using novel genomic tools, similar alleles responsible for a given trait and their variants in other genotypes can be identified. This is often referred to as ‘dissection of naturally occurring variation at candidate genes/loci’ or simply ‘allele mining’. Identification of allelic variants from germplasm collections not only provides new germplasm for delivering novel alleles to targeted trait improvement but also categorizes the germplasm entries for their conservation.
Realizing the importance of allele mining in genomics-driven plant breeding era, we discuss the concept of allele mining and its strategies along with the prospects and challenges.
Section snippets
Evolution of new alleles
Mutation is considered as an evolutionary driving force which underlies existing allelic diversity in any crop species. For creation of new alleles or causing variations in the existing allele and allelic combinations, mutations in the genic regions of the genome either as single nucleotide polymorphism (SNP) or as insertion and deletion (InDel) are important. The mutations in coding regions and/or regulatory regions may have tremendous effect on the phenotype by altering the encoded protein
‘True’ allele mining
Initial studies of allele mining have focused only on the identification of SNPs/InDels at coding sequences or exons of the gene, since these variations were expected to affect the encoded protein structure and/or function. Ample examples are available to demonstrate the effect of such sequence variations in genic regions in altering the phenotypes. However, recent reports indicate that the nucleotide changes in non-coding regions (5′ UTR) including promoter, introns and 3′ UTR) also have
Applications
Allele mining can be effectively used for discovery of superior alleles, 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. In addition, the rate of evolution of alleles; allelic similarity/dissimilarity at a candidate gene and allelic synteny with other members of the family can also be studied. Allele mining may also pave
Challenges
Considering the huge number of accessions that are held collectively in various gene banks, genetic resources collections are deemed to harbour a wealth of undisclosed allelic variants. Now the challenge is to efficiently identify and exploit the useful variation for crop improvement. Here, we describe the challenges in allele mining and suggest the ways to overcome them in order to increase the efficiency.
Perspective
Due to its tremendous potentials and applications, allele mining can be visualized as a vital link between effective utilization of genetic and genomic resources in genomics-driven modern plant breeding. In order to keep pace with ever increasing sequence data in GenBank and ever expanding crop gene banks, it is highly imperative to evolve novel and efficient ‘mining’ strategies. Efforts to develop tools and strategies should be equally focused on handling both genetic and genome resources.
Acknowledgments
Research in our laboratory on this topic is funded by the Department of Biotechnology, Government of India, New Delhi. We thank Dr. P. Rajendrakumar, NRCS, Hyderabad for his critical review of the manuscript. We also thank the anonymous reviewers whose suggestions have helped to improve the manuscript to the present form.
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These authors have contributed equally.