Haplotype-Resolved Genomics for Complex Crop Genomes: Technologies, Insights, and Breeding Applications
Bobbali Madhavi *
Department of Genetics and Plant Breeding, School of Agriculture, Lovely Professional University, Phagwara, Punjab-144411, India.
Mohammad Amir
Department of Genetics and Plant Breeding, School of Agriculture, Lovely Professional University, Phagwara, Punjab-144411, India.
Yakanna Lavudya
Anglia Ruskin University, Writtle, Chelmsford, United Kingdom.
Varsha Reddy Patlolla
Department of Genetics and Plant Breeding, School of Agriculture, Lovely Professional University, Phagwara, Punjab-144411, India.
Thulasi Satya Laxmi Devi Balam
Department of Genetics and Plant Breeding, School of Agriculture, Lovely Professional University, Phagwara, Punjab-144411, India.
*Author to whom correspondence should be addressed.
Abstract
The significance of haplotype-resolved genome assemblies, which enable the reconstruction of individual chromosomal copies while preserving allele-specific variation, has been brought to light by recent advances in plant genomics. The techniques provide a better representation of genetic variation than traditional genome assemblies, which recombine the homologous sequences into one consensus, especially in heterozygous and polyploid crops. This review explains the role of haplotype-resolved assemblies in enhancing our understanding of genome evolution, conducting research on allele-specific expression, and improving the accuracy of genomes. Important technologies are also discussed, including trio binning and phasing techniques, long-read sequencing (PacBio HiFi and Nanopore), and Hi-C scaffolding. They have been used to detect key characteristics and support the breeding process of crops like potatoes, wheat, grapevine, and cassava. All things considered, these methods have a great deal of potential to generate high-yielding, stress-tolerant cultivars and accelerate crop improvement.
Keywords: Pangenome, heterozygosity and polyploidy, allele-specific variation, genome sequencing, haplotype-resolved genome assembly