Haplotype-Assisted Breeding in Rice

Breeding assisted by haplotype is currently one of the promising crop improvement methods. A haplotype is a specific DNA markers combination or nucleotides that are jointly inherited from polymorphic regions, such as polymorphic Single Nucleotide Polymorphisms (SNPs), that have a low probability of current recombination between them, i.e., substantial linkage disequilibrium (LD). Rice is the most important staple food crop grown all over the world; extensive work has been done and is currently going on, with all these available huge data of genome sequence of rice, sequencing-based trait mapping data, and next-generation sequencing (NGS) technologies equipped with precise phenotyping were useful in the identification of haplotypes indirectly. Still, the expense and duration of haplotyping are increased since it necessitates certain statistical conclusions from genotypic data. On the other hand, third-generation sequencing systems, including from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), may create lengthy reads that can be used to directly identify haplotypes. The technique of generating haplotypes from sequencing data via estimation of haplotype is known as phasing. In recent times, numerous phasing techniques have been created. When compared to single SNP markers, the usage of these haplotypes had been shown to significantly improve the accuracy of prediction of quantitative traits that are low-heritable in rice. It is also more effective in identifying candidate genes and genomic regions regulating rice traits of interest, like many quantitative and qualitative traits of rice. This illustrates how effective gene identification and GS are. Using haplotype markers can handle complicated features more effectively than individual SNP markers. Haplotype-assisted breeding could be used as an effective advanced tool to develop genotypes that can prevail in current changing climatic conditions, which might help tackle the adverse effects of many biotic and abiotic stresses.