| Literature DB >> 35873727 |
Zheng Wang1, Jinghua Yang2, Feng Cheng3, Peirong Li1, Xiaoyun Xin1, Weihong Wang1, Yangjun Yu1, Deshuang Zhang1, Xiuyun Zhao1, Shuancang Yu1, Fenglan Zhang1, Yang Dong4, Tongbing Su1.
Abstract
Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.Entities:
Year: 2022 PMID: 35873727 PMCID: PMC9297153 DOI: 10.1093/hr/uhac090
Source DB: PubMed Journal: Hortic Res ISSN: 2052-7276 Impact factor: 7.291
Figure 1A phylogenetic tree of plants showing the association of WGDs with morphological innovations. A simplified phylogeny displaying the evolutionary relationship between representative plant species. Mapping of WGDs and key morphological innovations on the phylogeny is based on information from published data (Van de Peer et al., 2017; Cheng et al., 2018; [24, 36]). WGDs estimated to be between 55 and 75 million years old are shown in purple rectangular boxes, while others are shown in red rectangular boxes. The K–Pg boundary is indicated by a grey shaded area.
Figure 2Subgenome dominance and its evolutionary implications in plants. a Establishment of subgenome dominance and its evolutionary implications in crop domestication and intraspecific diversification. Subgenome dominance was initially shaped and influenced by TE density, epigenetic modification, HE, and other unexplored factors when two distinct subgenomes merge. (Dotted box) To better understand the effects of subgenome dominance on intraspecific diversification, we assumed an intermediate status during the shaping of subgenome dominance, which actually does not exist during evolution. b Polyploidization and subgenome dominance constitute the fundamental driving force for evolution and morphotypization of B. rapa.
Summary of candidate genes related to important agricultural traits in Brassica rapa
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| BraA07g030650.3C | A07 | 21 870 249 | LF | Selection sweep |
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| BraA07g029180.3C | A07 | 21 145 989 | / | Selection sweep |
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| BraA01g019170.3C | A01 | 10 320 303 | LF | Selection sweep |
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| BraA01g025930.3C | A01 | 15 373 141 | MF1 | Selection sweep |
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| BraA04g024390.3C | A04 | 17 723 081 | LF | Selection sweep |
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| BraA10g018230.3C | A10 | 13 535 905 | LF | Selection sweep |
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| BraA09g032840.3C | A09 | 25 471 282 | LF | Selection sweep |
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| BraA05g023490.3C | A05 | 17 380 156 | MF2 | Selection sweep |
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| BraA09g033250.3C | A09 | 25 879 277 | LF | Selection sweep |
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| BraA08g009040.3C | A08 | 7 993 035 | MF1 | Selection sweep |
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| BraA05g002720.3C | A05 | 1 497 805 | LF | Homologous cloning | Wang | |
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| BraA07g042410.3C | A07 | 28 393 881 | LF | MutMap analysis |
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| BraA06g007950.3C | A06 | 4 363 461 | LF | Selection sweep |
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| BraA09g061400.3C | A09 | 42 842 596 | MF2 | Selection sweep |
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| BraA03g054290.3C | A03 | 28 172 489 | MF1 | Selection sweep |
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| BraA07g026700.3C | A07 | 20 256 386 | MF2 | QTL; MutMap analysis |
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| BraA10g027720.3C | A10 | 18 122 666 | LF | QTL; domestication | Yuan |
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| BraA02g003340.3C | A02 | 1 616 321 | MF2 | QTL; domestication | Xiao | |
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| BraA03g015950.3C | A03 | 7 336 775 | MF2 | QTL | Xi | |
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| BraA06g040160.3C | A06 | 26 686 911 | MF2 | QTL; selection sweep | Su | |
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| BraA02g016700.3C | A02 | 8 897 950 | MF1 | QTL; selection sweep | Su | |
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| BraA04g017190.3C | A04 | 13 126 173 | MF1 | EMS; Map-based cloning | Huang | |
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| BraA07g040740.3C | A07 | 27 592 362 | MF1 | EMS; Map-based Cloning | Fu | |
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| BraA06g037290.3C | A06 | 24 917 368 | LF | GWAS;QTL | Zhang |
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| BraA03g005840.3C | A03 | 2 557 478 | MF1 | EMS; MutMap analysis | Fu |
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| BraA03g050600.3C | A03 | 25 985 593 | MF1 | EMS; MutMap analysis | Wang | |
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| BraA09g063710.3C | A09 | 43 923 664 | MF2 | Map-based cloning | Su | |
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| BraA05g023920.3C | A05 | 17 771 508 | MF2 | Map-based cloning | Su | |
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| BraA07g032100.3C | A07 | 23 201 361 | LF | Map-based cloning | He | |
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| BraA06g006120.3C | A06 | 3 535 037 | LF | GWAS; map-based cloning | Su |