Homoeolog expression bias and expression level dominance in allopolyploids

Grover, Corrinne E.; Gallagher, Joseph P.; Szadkowski, Emmanuel; Yoo, Mi‐Jeong; Flagel, Lex; Wendel, Jonathan F.

doi:10.1111/j.1469-8137.2012.04365.x

Cited by 251 publications

(285 citation statements)

References 61 publications

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“…Although homoeolog expression dominance has been observed in several polyploid species 17,19,22 , a correlation between homoeolog expression dominance and evolutionary rate has not been reported previously. This finding provides important evidence of agricultural selection behavior.…”

Section: Selection In Allopolyploid B Juncea Using Snps From Resequementioning

confidence: 83%

“…The short read lengths of next-generation sequencing hinder assembly through complex regions, and fragmented draft and reference genomes usually lack skewed (G+C)-content sequences and repetitive intergenic sequences. Furthermore, in allopolyploid species, homoeolog expression dominance or bias, and specifically differential homoelog gene expression, has often been detected, for instance in Gossypium [15][16][17] Triticum 18,19 and Arabidopsis 20,21 , but the role of this phenomenon in selection for phenotypic traits remains mechanistically mysterious 22 .…”

Section: 2mentioning

confidence: 99%

“…The reprogramming of allopolyploid transcriptomes is shown to be triggered predominantly by interspecific hybridization 20 , displaying insight into homoeolog gene expression in phenotypic variability and plasticity. Homoeolog expression dominance or bias appears to be a consequence of genome merger and doubling 22 , but the underlying applicability of the homoeolog expression dominance in agriculture trait selection has not been substantiated to date. We found that homoeolog expression dominant genes have higher Ka/Ks than neutral genes in the allopolyploid B. juncea, consistent with these genes as targets of intensified selection for vegetable-and oil-use varieties of this agriculturally important plant.…”

Section: Npgmentioning

confidence: 99%

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The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

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2 2 5The Brassica genus contains a diverse range of oilseed and vegetable crops important for human nutrition 1 . Crops of particular agricultural importance include three diploid species, Brassica rapa (AA), Brassica nigra (BB) and Brassica oleracea (CC), and three allopolyploid species, B. napus (AACC), B. juncea (AABB) and Brassica carinata (BBCC). The evolutionary relationships among these Brassica species are described by what is called the 'triangle of U' model 2 , which proposes how the genomes of the three ancestral Brassica species, B. rapa, B. nigra and Brassica oleracae, combined to give rise to the allopolyploid species of this genus. B. juncea formed by hybridization between the diploid ancestors of B. rapa and B. nigra, followed by spontaneous chromosome doubling. Subsequent diversifying selection then gave rise to the vegetable-and oil-use subvarieties of B. juncea. These subvarieties include vegetable and oilseed mustard in China, oilseed crops in India, canola crops in Canada and Australia, and condiment crops in Europe and other regions 3 . Cultivation of B. juncea began in China about 6,000 to 7,000 years ago 4 , and flourished in India from 2,300 BC onward 5 .The genomes of B. rapa, B. oleracea and their allopolyploid offspring B. napus have been published recently [6][7][8] , and are often used to explain genome evolution in angiosperms [6][7][8] . The genomes of all Brassica species underwent a lineage-specific whole-genome triplication 6,7,9 , followed by diploidization that involved substantial genome reshuffling and gene losses 6,10-13 . In general, plant genomes are typically repetitive, polyploid and heterozygous, which complicates genome assembly 14 . The short read lengths of next-generation sequencing hinder assembly through complex regions, and fragmented draft and reference genomes usually lack skewed (G+C)-content sequences and repetitive intergenic sequences. Furthermore, in allopolyploid species, homoeolog expression dominance or bias, and specifically differential homoelog gene expression, has often been detected, for instance in Gossypium [15][16][17] Triticum 18,19 and Arabidopsis 20,21 , but the role of this phenomenon in selection for phenotypic traits remains mechanistically mysterious 22 .We reported here the draft genomes of an allopolyploid, B. juncea var. tumida, constructed by de novo assembly using shotgun reads, single-molecule long reads (PacBio sequencing), genomic (optical) mapping (BioNano sequencing) and genetic mapping, serving to resolve complicated allopolyploid genomes. The multiuse allopolyploid B. juncea genome offers a distinctive model to study the underlying genomic basis for selection in breeding improvement. These findings place this work into the broader context of plant breeding, highlighting The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-m...

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Section: Selection In Allopolyploid B Juncea Using Snps From Resequementioning

confidence: 83%

Section: 2mentioning

confidence: 99%

Section: Npgmentioning

confidence: 99%

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The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

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“…Another consequence of polyploidization is unequal expression of homoeologous genes in allopolyploids [30][31][32] Table 16). Although the average expression levels and numbers of expressed genes varied among different tissues and developmental stages (Supplementary Fig.…”

Section: Expression Of Homoeologous Genes In Allotetraploid Cottonmentioning

confidence: 99%

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

et al. 2015

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“…Non-additive expression in allopolyploids has been variously described as transcriptome dominance [43], bias [44], nucleolar dominance (in reference to rRNA genes; [45]), genome dominance [42,46] and homeologue expression bias [47]. The factors contributing to these patterns-and what the patterns themselves represent-are complex, as is the terminology [23,47].…”

Section: (C) Novelty In Gene Expressionmentioning

confidence: 99%

Polyploidy and novelty: Gottlieb's legacy

Soltis

Liu

Marchant

et al. 2014

Phil. Trans. R. Soc. B

156

140

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Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30 , 818–830. ( doi:10.2307/2407821 )) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents ( T. dubius and T. porrifolius , and T. dubius and T. pratensis , respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity—the production of novel enzyme forms in the allopolyploids—can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes—with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity—may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.

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Homoeolog expression bias and expression level dominance in allopolyploids

Cited by 251 publications

References 61 publications

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Polyploidy and novelty: Gottlieb's legacy

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