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

Hurgobin, Bhavna; Golicz, Agnieszka A.; Bayer, Philipp E.; Chan, Chon‐Kit Kenneth; Tirnaz, Soodeh; Dolatabadian, Aria; Schiessl, Sarah; Samans, Birgit; Montenegro, Juan D.; Parkin, Isobel A. P.; Pires, J. Chris; Chalhoub, Boulos; King, Graham J.; Snowdon, Rod J.; Batley, Jacqueline; Edwards, David

doi:10.1111/pbi.12867

Cited by 224 publications

(272 citation statements)

References 59 publications

(88 reference statements)

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“…In this study, the synthetic lines were shown to exhibit more RGAs than non‐synthetic lines, whereas non‐synthetics lines have lost more RGAs, making them an interesting model to study the impact of polyploidization on genome structure, disease resistance genes and their potential associated with agronomic traits. Greater genetic diversity in synthetic B. napus lines compared with non‐synthetic lines has previously been reported (Golicz et al ., 2016b; Hurgobin et al ., ; Li et al ., ). This difference has been attributed to the incorporation of novel alleles from diverse progenitor genomes and highlights the potential of using synthetic B. napus accessions as a source of novel genetic structural variation for breeding improved varieties (Hurgobin et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…Greater genetic diversity in synthetic B. napus lines compared with non‐synthetic lines has previously been reported (Golicz et al ., 2016b; Hurgobin et al ., ; Li et al ., ). This difference has been attributed to the incorporation of novel alleles from diverse progenitor genomes and highlights the potential of using synthetic B. napus accessions as a source of novel genetic structural variation for breeding improved varieties (Hurgobin et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…Gene PAV discovery was performed using the SGSGeneLoss package (Golicz et al ., ) as described in Hurgobin et al . () and Bayer et al . ().…”

Section: Methodsmentioning

confidence: 97%

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Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Dolatabadian

Bayer

Tirnaz

et al. 2019

Plant Biotechnology Journal

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104

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Summary Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor‐bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R‐genes harbour more SNPs than variable genes. More nucleotide binding site‐leucine‐rich repeat (NBS‐LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics‐based improvement and improved disease resistance.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Dolatabadian

Bayer

Tirnaz

et al. 2019

Plant Biotechnology Journal

Self Cite

104

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“…Furthermore, a recently developed pangenome of B. napus revealed high gene presence/absence variation among diverse cultivars as a result of HEs involving genes encoding important agronomic traits, including flowering time, disease resistance and chemical defenses (Hurgobin et al, 2017). HEs have also been shown to impact the expression abundance of a homoeolog proportional to the gene copy number (Lloyd et al, 2018).…”

Section: Subgenome Biases In Homoeologous Exchangesmentioning

confidence: 99%

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

et al. 2018

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Contents Summary 87 I. Introduction 87 II. Evolution in action: subgenome dominance within newly formed hybrids and polyploids 88 III. Summary and future directions 90 Acknowledgements 92 References 92 SUMMARY: The merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a 'genomic shock' that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to extant parental progenitors have allowed for major strides in understanding the mechanistic basis for subgenome dominance. In particular, our understanding of the role that homoeologous exchange might play in subgenome dominance and genome evolution is quickly growing. Here we describe recent discoveries uncovering the underlying mechanisms and provide a framework to predict subgenome dominance in hybrids and allopolyploids with far-reaching implications for agricultural, ecological, and evolutionary research.

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“…Based on the results described above, the inference is that homologous exchange events occurred between the B and A/C genomes. In addition, brand‐new variation could be generated during the change from hexaploid (AABBCC) to tetraploid (AACC) because of chromosomal breakage or fusion, autosyndetic chromosome rearrangement, homologous exchange and retrotransposon activation as reported in previous studies of resynthesized B. napus (Hurgobin et al ., ; Xiong et al ., ; Zou et al ., , ). Rich new alleles and frequent deletion and duplication events were demonstrated in the inbred lines from the A r and C c polymorphism subpopulations (Xiao et al ., ; Zou et al ., , ).…”

Section: Discussionmentioning

confidence: 99%

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

Zhang

et al. 2019

Plant Biotechnology Journal

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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.

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

Cited by 224 publications

References 59 publications

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

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

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

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