Modelling of gene loss propensity in the pangenomes of three <i>Brassica</i> species suggests different mechanisms between polyploids and diploids

Bayer, Philipp E.; Scheben, Armin; Golicz, Agnieszka A.; Yuan, Yuxuan; Faure, Sébastien; Lee, HueyTyng; Chawla, Harmeet Singh; Anderson, Robyn; Bancroft, Ian; Raman, Harsh; Lim, Yong Pyo; Robbens, Steven; Jiang, Lixi; S, Liu; Barker, Michael S.; Schranz, M. Eric; Wang, Xiaowu; King, Graham J.; Pires, J. Chris; Chalhoub, Boulos; Snowdon, Rod J.; Batley, Jacqueline; Edwards, David

doi:10.1111/pbi.13674

Cited by 55 publications

(55 citation statements)

References 86 publications

(160 reference statements)

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“…These barley PAV tags will help construct future barley pangenomes and can be applied to association analysis. Pangenomics ML has also been applied to understand gene loss mechanisms in Brassica [ 134 ]. It was demonstrated that gene loss was mainly associated with transposable elements in the diploid B. oleracea and B. rapa, while in the polyploid B. napus, the loss of genes was mostly associated with homoeologous recombination.…”

Section: The Breeding Potential Of Under-utilised Crop Speciesmentioning

confidence: 99%

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Fernandez

Nestor

Danilevicz

et al. 2022

IJMS

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Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.

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Section: The Breeding Potential Of Under-utilised Crop Speciesmentioning

confidence: 99%

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Fernandez

Nestor

Danilevicz

et al. 2022

IJMS

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“…The increasing availability of reference genome assemblies made it clear that there is significant presence/absence variation (PAV) between individuals (9)(10)(11)(12). This insight has led to the production of pangenomes that reflect the gene content of a species rather than an individual (10,(13)(14)(15)(16)(17)(18)(19)(20).…”

Section: Introductionmentioning

confidence: 99%

“…The increasing availability of reference genome assemblies made it clear that there is significant presence/absence variation (PAV) between individuals (9–12). This insight has led to the production of pangenomes that reflect the gene content of a species rather than an individual (10,13–20). Pangenomes are now available for several plant species; the first bread what pangenome representing the gene content of 16 bread wheat cultivars was published in 2017 (18).…”

Section: Introductionmentioning

confidence: 99%

Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes

Bayer

Petereit

Durant

et al. 2022

Preprint

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Bread wheat is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence/absence variation between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate due to the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess presence/absence variation between bread wheat genomes. Database URL: http://www.appliedbioinformatics.com.au/wheat_panache .

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“…Additionally, homoeologous exchanges often underlie gene presence-absence variation and agronomically valuable quantitative trait loci in Brassica napus (Stein et al 2017;Samans et al 2017;Hurgobin et al 2017;Bayer et al 2021) and generate novel, chimeric transcripts in multiple polyploid species (Zhang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Bird

Pires

VanBuren

et al. 2021

Preprint

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Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Frequently, allopolyploids exhibit genomic rearrangements that recombine, duplicate, or delete homoeologous regions of the newly formed genome. While decades of investigation have focused on how genome duplication leads to systematic differences in the retention and expression of duplicate genes, the impact of genomic rearrangements on genome evolution has received less attention. We used genomic and transcriptomic data for six independently resynthesized, isogenic Brassica napus lines in the first, fifth, and tenth generation to identify genomic rearrangements and assess their impact on gene expression dynamics related to subgenome dominance and gene dosage constraint. We find that dosage constraints on the gene expression response to polyploidy begin to loosen within the first ten generations of evolution and systematically differ between dominant and non-dominant subgenomes. We also show that genomic rearrangements can bias estimation of homoeolog expression bias, but fail to fully obscure which subgenome is dominantly expressed. Finally, we demonstrate that dosage-sensitive genes exhibit the same kind of coordinated response to homoeologous exchange as they do for genome duplication, suggesting constraint on dosage balance also acts on these changes to gene dosage.

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Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Cited by 55 publications

References 86 publications

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes

Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

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