Allelic Variation for Rice Improvement

Abstract

Genetic improvement of rice (Oryza sativa L.) is accelerated by precise exploitation of novel allelic variation. Wild and cultivated rice germplasm harbours valuable allelic variation that can be leveraged to enhance agronomic traits and overall crop performance. This untapped allelic variation can be unlocked through an allele mining (AM) approach. It is an efficient tool in rice researchers' hands to finding superior alleles by ‘mining’ the gene of interest. It also aids in identifying the nucleotide sequence variations associated with novel alleles and providing an understanding of the molecular basis of variation for new traits. This article discussed the challenges of the AM project: sample collection (core or mini core collection), total genomic DNA extraction, primer design, PCR amplification, that is an immense task, and alternative potential solutions to improve efficiency. Apart from that, AM challenges are genetic complexity of trait, poor annotation, rare variants, phenotyping limits and data integration difficulties, furthermore, discussed about the solution of them. To date, significant progress has been made in AM for important traits in rice, including agronomic traits (plant height, heading date and phosphorus uptake efficiency), biotic stress resistance (blast and rice yellow mottle virus), abiotic stress tolerance (drought and submergence), grain-related traits (grain number, weight and size), physiological traits (pericarp colour and apiculus coloration) and quality traits (fragrance, amylose content, rice bran oil and cooking qualities). Additionally, discussed how AM can integrate with other breeding strategies to develop climate-resilient cultivars. The integration of AM, mainly haplotype-based approaches, with GWAS, MAS, GS, miRNA-based functional markers, genome editing–based AM and alongside genomic platforms like RiceNavi, presents a robust framework for accelerating AM and enhancing genetic improvement in rice. In future, exploration of natural allelic variation for important genes related to yield, biotic and abiotic stress tolerance is highly indispensable for rice breeding programs.