Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species

Abstract

Summary Brassica napus (A n A n C n C n ) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of Brassica rapa (A r A r ) and 74 accessions of Brassica carinata (B c B c C c C c ) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high‐throughput SNP /Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses.

Multi-omics-based prediction of hybrid performance in canola

“…However, in oilseed rape heterotic groups (Melchinger and Gumber 1998 ) are not yet well established, and genetic distances between pools are not as large (Qian et al 2007 ; Rincent et al 2014 ) as for instance in the flint and dent populations of European maize (Younas et al 2012 ; Liu et al 2019 ). This can be attributed in particular to a less intensive and shorter breeding history of canola compared to maize (Chalhoub et al 2014 ; Hu et al 2019 ).…”

Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun

“…The lower levels of nucleotide diversity suggest stronger genetic bottlenecks during domestication of B. carinata than for B. napus. Although the two species followed a similar evolutionary path, each likely formed from a limited number of hybridization events 36,37 . The B. carinata population was clustered into two distinct groups (SP1 and SP2) based on breeding history rather than natural selection.…”

“…The lower levels of nucleotide diversity suggest stronger genetic bottlenecks during domestication of B. carinata than for B. napus . Although the two species followed a similar evolutionary path, each likely formed from a limited number of hybridization events between progenitor diploid species leading to small effective population sizes; however, B. napus benefited from introgression with extant diploid species 36 , 37 .…”

Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid B. napus

“…Established B. napus cultivars have limited genetic diversity as a result of few hybridization events between the diploid B. rapa and B. oleracea parents as well as strong breeding selection for zero seed erucic acid and low glucosinolate content (Delourme et al 2013). Therefore, broadening its genetic diversity is necessary for sustainable rapeseed breeding (Hu et al 2019).…”