Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in<i>Brassica rapa</i>

Qi, Xuchen; An, Hong; Hall, Tara E.; Di, Chenlu; Blischak, Paul D.; Pires, J. Chris; Barker, Michael S.

doi:10.1101/842351

Cited by 11 publications

(16 citation statements)

References 104 publications

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“…In the cabbage comparisons, DEG were enriched among syntenic genes while being depleted in non-syntenic genes ( Figure 4 ). This aligns with recent findings that genes derived from the ancient Brassica polyploidy are also more likely involved in domestication in B. rapa ( Qi et al, 2019 ). However, in the kale–TO1000 comparison, no such enrichment was found.…”

Section: Discussionsupporting

confidence: 92%

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

et al. 2021

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Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.

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Section: Discussionsupporting

confidence: 92%

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

et al. 2021

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“…5). This aligns with recent findings that genes derived from the ancient Brassica polyploidy are more likely involved in domestication in B. rapa (Qi et al, 2019). We focused our search on DEGs that were amongst comparisons with kale, reasoning that these were more likely to underly the unique characteristics of kale.…”

Section: Discussionsupporting

confidence: 92%

The molecular basis of Kale domestication: Transcription profiling of leaves and meristems provides new insights into the evolution of aBrassica oleraceavegetative morphotype

Arias

Niederhuth

McSteen

et al. 2020

Preprint

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Premise of the study: Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales ornate leaves, delayed flowering, and nutritional quality are some of the characters potentially selected by humans during domestication. Methods: We used a combination of developmental studies and RNAseq experiments to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNAseq experiments were used to understand the global pattern of expressed genes during one single phase of development in kale, cabbage and the rapid cycling kale line TO1000. Key Results: We identified gene expression patterns that differ among morphotypes, and estimate the contribution of morphotype-specific gene expression that sets kale apart (2378 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plan architecture, defense and nutrition were differentially expressed in kale. Conclusions: RNA-Seq experiments allow the discovery of novel candidate genes involved in the kale domestication syndrome. We identified candidate genes differentially expressed in kale that could be responsible for variation in flowering times, taste and herbivore defense, variation in leaf morphology, plant architecture, and nutritional value. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.

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“…We tested for associations between genes' subgenome of origin and their propensity to experience recent selective sweeps. Data on these sweeps was taken from a recent scan in B. rapa by Qi et al (Qi et al 2019). No subgenome had either an excess or a deficit of observed sweeps relative to the other two (Supplementary Figure S7).…”

Section: Subgenome Of Origin Does Not Affect the Propensity To Experimentioning

confidence: 99%

“…Association between recent selective sweeps in B. rapa and subgenomes origin B. rapa genes were divided into those in the regions of selective sweeps detected by SweeD (Pavlidis et al 2013) in either turnip, toria, Indian sarson, pak choi or Chinese cabbage (vegetable types of B. rapa), and those showing no such signatures (Qi et al 2017(Qi et al , 2021. We tested whether particular subgenomes (posterior probability  0.95) were unusually likely or unlikely to have experienced a selective sweep using chi-square test.…”

Section: Brassica Rapa Co-expression Network Analysismentioning

confidence: 99%

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

Hao

Mabry

Edger

et al. 2020

Preprint

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The members of the tribe Brassiceae share an ancient whole genome triplication (WGT), and plants in this tribe display extraordinarily high within-species morphological diversity. One proposed model for the formation of these hexaploid Brassiceae is that they result from a “two-step” pair of hybridizations. However, direct evidence supporting this model of formation has been lacking; meanwhile, the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. After adding this new genome to three others that are also descended from the ancient hexaploidy, we traced the history of gene loss after the WGT using a phylogenomic pipeline called POInT (the Polyploidy Orthology Inference Tool). This approach allowed us to confirm the two-step model of hexaploidy formation and to assign statistical confidence to our parental “subgenome” assignments for >90,000 individual genes. We show that each subgenome has a statistically distinguishable rate of homeolog losses. Moreover, our modeling allowed us to infer that there was a significant temporal gap between the two allopolyploidizations, with about one third of the total shared gene losses between the four analyzed Brassiceae species in the first two subgenomes prior to the arrival of the third subgenome. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a “mix and match” model of allopolyploidy, where subgenome origin drives homeolog loss propensities but where genes from different subgenomes function together without difficulty.

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Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication inBrassica rapa

Cited by 11 publications

References 104 publications

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

The molecular basis of Kale domestication: Transcription profiling of leaves and meristems provides new insights into the evolution of aBrassica oleraceavegetative morphotype

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

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