Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Abstract

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids

“…Although the SNP patterns in regions that have experienced HE should be identical to those that have experienced hGC, other attributes of these sites not explored here (for example, analyzing the distribution of hGC or HE tract length sizes compared to the distribution of haplotype block sizes genome-wide, or through the direct tracking of recombination events through the use of ancestral recombination graphs ( 51)) offer a potential opportunity to distinguish these intertwined phenomena. Analytical methods for population-level processes in allotetraploids (e.g., demographic history, interploidy introgression) has received recent attention (52,53), and we suggest that studying hGC and HE at the population level may offer additional insights that are not possible with our phylogenetic SNP-based approach.…”

Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus

“…In addition to these two ancient WGD events, maize experienced its most recent round of WGD about 5 million to 12 million years ago [ 4 ]. Most newly formed polyploids undergo a differentiation process that includes gene losses, genome rearrangement, and epigenetic changes [ 5 ]. Theoretical studies maintain that the most likely fate of duplicated genes is the loss or pseudogenization of one of them [ 2 ].…”

The emerging importance of cross‐ploidy hybridisation and introgression

“…On occasion, however, some species differing in ploidy do produce hybrid offspring. The importance of such events is not to be underestimated; for example, cross-ploidy hybridisation has led to some very recently originated plant species, which are now models for the study of polyploid speciation (Vallejo-Marin & Hiscock, 2016), and also to the origin of some of our most important crop plants, including wheat, sweet potato, sugar cane, and oilseed rape (Matsuoka, 2011;Wang et al, 2023;Yang et al, 2017;Zhang et al, 2018). Nonetheless, the frequency of cross-ploidy (or interploidy) hybridisation in the wild is a neglected topic with information scattered through the literature.…”