Detectingde NovoHomoeologous Recombination Events in CultivatedBrassica napusUsing a Genome-Wide SNP Array

Abstract

The heavy selection pressure due to intensive breeding of Brassica napus has created a narrow gene pool, limiting the ability to produce improved varieties through crosses between B. napus cultivars. One mechanism that has contributed to the adaptation of important agronomic traits in the allotetraploid B. napus has been chromosomal rearrangements resulting from homoeologous recombination between the constituent A and C diploid genomes. Determining the rate and distribution of such events in natural B. napus will assist efforts to understand and potentially manipulate this phenomenon. The Brassica high-density 60K SNP array, which provides genome-wide coverage for assessment of recombination events, was used to assay 254 individuals derived from 11 diverse cultivated spring type B. napus. These analyses identified reciprocal allele gain and loss between the A and C genomes and allowed visualization of de novo homoeologous recombination events across the B. napus genome. The events ranged from loss/gain of 0.09 Mb to entire chromosomes, with almost 5% aneuploidy observed across all gametes. There was a bias toward sub-telomeric exchanges leading to genome homogenization at chromosome termini. The A genome replaced the C genome in 66% of events, and also featured more dominantly in gain of whole chromosomes. These analyses indicate de novo homoeologous recombination is a continuous source of variation in established Brassica napus and the rate of observed events appears to vary with genetic background. The Brassica 60K SNP array will be a useful tool in further study and manipulation of this phenomenon.

Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus

“…The recent allopolyploid crop species B. napus shows a strong abundance of SV and genomic rearrangements 18,31 . In maize, Beló et al 32 used comparative genomic hybridization arrays for detailed genome-wide analysis of SV, and a more recent study discovered some degree of CNV between 100 analyzed lines across more than 90% of the maize genome 33 .…”

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

“…We identified 26,114 syntenic orthologs (homoeologs) between the A (BnA) and C (BnC) subgenome, and shifts in read depth coverage between these gene pairs allowed us to pinpoint changes in gene dosage across each of the six lines and over the ten generations. Changes in gene dosage occur through homoeologous exchanges, where non-reciprocal homoeologous recombination between syntenic regions of the parental subgenomes replace one homoeolog with another (35) . Previous studies of this resynthesized B. napus population using a handful of DNA or cytogenetic markers identified extensive homoeologous exchanges that resulted in immense phenotypic variation in both plant height and pollen count (36,37) .…”

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

“…The most pervasive and immediate genetic consequence of nascent polyploidy is disruption of normal meiosis due to mismatches between the meiotic machinery of diploids that now must adapt to handle the abruptly doubled chromosome set (Hollister, ; Mercier et al ., ; Bomblies et al ., ). Consequently, multivalents and univalents occur due to compromised pairing fidelity, resulting in homoeologous exchanges (HEs) and aneuploidy (Pecinka et al ., ; Higgins et al ., ; Lloyd et al ., ). Conceivably, while most aneuploidies that cause deficiency and/or chromosome‐wide dosage imbalance will be rapidly purged due to lethality or lack of fitness, many progenies with HEs may remain and be transgenerationally persistent due to the frequent (Gou et al ., ), but not ever‐present (Zhang et al ., ; Gong et al ., ; Lloyd et al ., ), mutual functional compensation of homoeologs (Xiong et al ., ; Chester et al ., ).…”