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

Abstract

Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

Novel Alleles of Phosphorus-Starvation Tolerance 1 Gene (PSTOL1) from Oryza rufipogon Confers High Phosphorus Uptake Efficiency

“…Two of the O. rufipogon accessions under H17 and H11 were found performing better than the positive control under phosphorus-deficient conditions. Functional allelic variants were observed and utilized for improving various agronomically important traits in cereal crops (Ellis and Setter, 1999; Bhullar et al, 2010; Ravensdale et al, 2012; Vasudevan et al, 2014; Ashkani et al, 2015). The wheat powdery mildew resistance gene Pm3 with 17 identified functional alleles is a remarkable example of natural variations present in GenBank accessions and can be efficiently utilized for conferring broad-spectrum disease resistance.…”

“…The wheat powdery mildew resistance gene Pm3 with 17 identified functional alleles is a remarkable example of natural variations present in GenBank accessions and can be efficiently utilized for conferring broad-spectrum disease resistance. For rice blast resistance gene, functional orthologous have been found in wild rice O. rufipogon accessions (Lv et al, 2013; Xu et al, 2014; Ashkani et al, 2015) defining their utility in widening the genetic base of cultivated rice varieties. A novel allele of PSTOL1 gene is identified in O. glaberrima (CG14) and being transferred to the NERICAs (New Rice for Africa) cultivars using allele-specific markers.…”

Recent Advances in Rice Varietal Development for Durable Resistance to Biotic and Abiotic Stresses through Marker-Assisted Gene Pyramiding

“…About 50% of the rice yield is reduced due to blast when it occurs on a pandemic scale [124]. There are nearly 100 resistance (R) genes/alleles and 500 quantitative trait loci (QTLs) linked to blast resistance in rice [125]. Twenty major R-genes associated with rice blast resistance (Pi1, Pi2, Pi5, Pi9, Pid3, Pi25, Pi36, Pi37, Pi54, Pia/Pi-Co39, Pib, Pid2, Pikm, Pikp, Pik, Pish, Pit, Pita and Pizt) [126][127][128][129][130][131][132][133][134][135] have been cloned and described, as well as two partial resistance genes (Pi21 and Pb1) [136,137].…”

Wheat blast disease: Bangladesh and global perspectives of blast resistance

“…EcoTillering is comparatively easier and costeffective than sequence-based allele mining (Kumar et al, 2010;Ashkani et al, 2015b). Allele mining consists of identification of allele, allelic variation identification, characterization of allelic variation, and identification of haplotype, studying haplotype diversity, evolutionary relationship study, and analysis of similarity and development of molecular markers for identifying and differentiate a specific allele from one another (Ashkani et al, 2015b). So identifying resistant allele by using allele mining is a distinct way of getting resistance from unexamined varieties, landraces, and wild cultivar.…”