Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Abstract

SummaryGenomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high‐density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole‐genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC‐FISH) coupled with PCR using primers specific to the rearranged region. Using a well‐known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

“…Functional annotation of the HE-related PAV genes suggests their involvement in defence, stress and auxin pathways (Table S12), similar to observations of variable genes in other species, although their association with HEs has not been previously reported. HEs have been shown to impact agronomic traits Schiessl et al, 2017a,b;Stein et al, 2017;Szadkowski et al, 2010;Zou et al, 2011), including the flowering time regulators PHYTOCHROME A (PHYA), gibberellin 3-beta-dioxygenase (GA3ox1) and FLOWER-ING LOCUS C (FLC) (Schiessl et al, 2017b). Here, we confirm that PHYA and GA3ox1 are present on chromosome A09, but absent on the homoeologous portion of chromosome C08 in the majority of swede accessions from the ERANET-ASSYST population as previously reported (Schiessl et al, 2017b), suggesting a potential split between swede and nonswede types (Data S2).…”

“…The B. napus gene pool includes synthetic lines, which are produced from interspecific crossing between B. rapa and B. oleracea (Gaeta et al ., ), and is a source of novel genetic diversity (Cheung et al ., ; Gaeta et al ., ; Osborn et al ., ; Sharpe et al ., ), which is valuable for crop breeding. The meiotic chromosome pairing that occurs between homoeologous chromosomes which share a high degree of sequence identity leads to increased homoeologous exchanges (HEs) and gene conversion events (Gaeta and Chris Pires, ; Stein et al ., ), and synthetic B. napus has been shown to exhibit a higher frequency of HEs than nonsynthetic B. napus (Liu et al ., ; Rousseau‐Gueutin et al ., ; Sharpe et al ., ), making it an interesting model to study the impact of polyploidization on genome structure (Chalhoub et al ., ; Clarke et al ., ; Gaeta et al ., ; Nicolas et al ., ; Osborn et al ., ; Parkin et al ., ; Schmutzer et al ., ; Stein et al ., ; Szadkowski et al ., ; Udall et al ., ) and agronomic traits (Rousseau‐Gueutin et al ., ; Schiessl et al ., ; Stein et al ., ; Zou et al ., ).…”

The causes and consequences of subgenome dominance in hybrids and recent polyploids

“…HEs have also been shown to impact the expression abundance of a homoeolog proportional to the gene copy number (Lloyd et al, 2018). Thus, HEs probably play an important role in producing novel, favorable traitsan argument reinforced by the finding that HEs underlie quantitative trait loci (QTLs) related to seed quality in B. napus (Stein et al, 2017).…”

“…Alleles associated with favorable agronomic traits may be masked if they are introgressed into a more dominant genome background, or undesirable alleles may be unmasked from a newly dominant subgenome. Recent evidence of HEs underlying QTLs and contributing to presence/absence variation in B. napus (Hurgobin et al, 2017;Stein et al, 2017) shows that QTLs can fall within regions with frequent HE and may be removed or fixed unexpectedly. This factor should be accounted for during introgression.…”

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

“…41 visualization based on mRNAseq data (He et al, 2017) or deletion calling from SNP array 55 data (Gabur et al, 2018;Grandke et al, 2016). Critically, numerous examples have 56 connected genome SV in B. napus to important agronomic traits (Gabur et al, 2018; Gabur et 57 al., 2019;Liu et al, 2012;Stein et al, 2017). These studies revealed the important role of SV 58 in the creation of de novo variation for adaptation and breeding, however the methods used 59were not yet capable of resolving SV at gene scale.…”