Future Prospects for Structural, Functional, and Evolutionary Genomics

Abstract

Completion of the genome assemblies of the first three Brassica napus genotypes provided a reference for genome evolution research, gene discovery, and breeding of Brassica crops—in particular the availability of a reference genome has greatly facilitated mapping of trait loci. After the previous chapters, this chapter provides future prospects on three aspects: (1) Structural genomics—The current B. napus reference genomes remain a great space for improvement. This is urgent need for at least one chromosome-level assembly should be achieved which corrects collapsed genomic regions such as highly repeated sequences from the previous versions. Highly structural variation also necessitated construction of a B. napus pan-genome which describes species-level structural variation in as much detail as possible. Meanwhile, substantial improvement should be undertaken to the annotations of genomic composition and gene models, in order to provide a set of comprehensive annotations including non-coding RNA and alternative splicing transcripts. (2) Functional genomics—There are many ways for making use of the B. napus genome resources to assist genetics-related research. With genome resources and related technologies, one can further speed up discovery of molecular markers and functional genes by linkage mapping, association mapping, syntenic comparison approaches, and their combination (among themselves and with other omics data). (3) Genome evolution—This gives insight into allopolyploid B. napus genome origin, its dynamic genome structure variation, genetic diversity, and selection patterns. Insight into the processes of multiple cycles of “whole-genome duplication and subsequent diploidization”, such as structural variation and its underlying mechanism, patterns and origins of duplicate gene expression changes, the relative contributions of duplicate genes to trait expression, and asymmetrical recombination and selection between B. napus subgenomes and regional “hot” and “cold” spots, will broaden our understanding of B. napus polyploid genetic diversity and benefit breeding method innovation.