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Shan S, Gitzendanner MA, Boatwright JL, Spoelhof JP, Ethridge CL, Ji L, Liu X, Soltis PS, Schmitz RJ, Soltis DE. Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid Tragopogon miscellus (Asteraceae). THE NEW PHYTOLOGIST 2024; 242:1363-1376. [PMID: 38450804 DOI: 10.1111/nph.19655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/15/2024] [Indexed: 03/08/2024]
Abstract
Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.
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Affiliation(s)
- Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - J Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
| | - Jonathan P Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Xiaoxian Liu
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Bioinformatics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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Suma A, Joseph John K, Bhat KV, Latha M, Lakshmi CJ, Pitchaimuthu M, Nissar VAM, Thirumalaisamy PP, Pandey CD, Pandey S, Kumar A, Gautam RK, Singh GP. Genetic enhancement of okra [ Abelmoschus esculentus (L.) Moench] germplasm through wide hybridization. FRONTIERS IN PLANT SCIENCE 2023; 14:1284070. [PMID: 38023890 PMCID: PMC10654990 DOI: 10.3389/fpls.2023.1284070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction The introgression of genetic material from one species to another through wide hybridization and repeated back-crossing, plays an important role in genetic modification and enriching the cultivated gene-pool with novel genetic variations. Okra (Abelmoschus esculentus [(L.) Moench)] is a popular vegetable crop with high dietary fibre and protein, rich in essential amino acids, lysine and tryptophan. The wild Abelmoschus genepool has many desirable traits like ornamental value, short internodal length, more number of productive branches, extended bearing, perennation tendency, reduced fruit length (more consumer preferred trait), high mucilage content (medicinal value), abiotic stress tolerances such as drought, high temperature and biotic stress resistances such as okra Yellow Vein Mosaic Virus (YVMV) and Enation Leaf Curl Virus (ELCV) diseases. The repeated use of elite breeding lines led to narrowing of the genetic base of the okra crop, one of the major factors attributed to breakdown of resistance/ tolerance to biotic stresses. YVMV and ELCV are the two major diseases, causing significant yield loss in okra. Hence, wide hybridization was attempted to transfer tolerance genes from wild species to the cultivated genepool to widen the genetic base. Material and methods The screening of germplasm of wild Abelmoschus species at hotspots led to the identification of tolerant species (Abelmoschus pungens var. mizoramensis, A. enbeepeegeearensis, A. caillei, A. tetraphyllus and A. angulosus var. grandiflorus), which were further used in a wide-hybridization programme to generate interspecific hybrids with the cultivated okra. Presence of pre- and post-zygotic barriers to interspecific geneflow, differences in ploidy levels and genotype specific variations in chromosome numbers led to varying degrees of sterility in F1 plants of interspecific crosses. This was overcome by doubling the chromosome number of interspecific hybrids by applying Colchicine at the seedling stage. The 113 cross derivatives generated comprising amphidiploids in the F1 generation (30), F3 (14), one each in F2 and F4 generations, back cross generation in BC1F2 (03), BC1F3 (25), and BC2F3 (02), crosses between amphidiploids (27), multi-cross combinations (07) and inter-specific cross (between A. sagittifolius × A. moschatus subsp. moschatus) selfed derivatives at F8 generation (03) were characterized in the present study. Besides they were advanced through selfing and backcrossing. Results and Discussion The amphidiploids were found to possess many desirable genes with a considerable magnitude of linkage drag. Majority of the wide cross derivatives had an intermediate fruit morphology and dominance of wild characters viz., hispid fruits, stem, leaves, tough fruit fibre, vigorous perennial growth habit and prolonged flowering and fruiting. The fruit morphology of three BC progenies exhibited a high morphological resemblance to the cultivated okra, confirming successful transfer of useful genes to the cultivated okra genepool. The detailed morphological characteristics of the various combinations of Abelmoschus amphidiploids and the genetic enhancement of the genepool achieved in this process is reported here.
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Affiliation(s)
- A. Suma
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | - K. Joseph John
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | | | - Madhavan Latha
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | | | | | - V. A. M. Nissar
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | | | | | - Sushil Pandey
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Raj Kumar Gautam
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Wu J, Liang J, Lin R, Cai X, Zhang L, Guo X, Wang T, Chen H, Wang X. Investigation of Brassica and its relative genomes in the post-genomics era. HORTICULTURE RESEARCH 2022; 9:uhac182. [PMID: 36338847 PMCID: PMC9627752 DOI: 10.1093/hr/uhac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/07/2022] [Indexed: 06/16/2023]
Abstract
The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.
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Affiliation(s)
| | | | | | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xinlei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
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DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication. J Adv Res 2022; 42:41-53. [PMID: 35933090 PMCID: PMC9788948 DOI: 10.1016/j.jare.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/05/2022] [Accepted: 07/23/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Polyploidy is a major force in plant evolution and the domestication of cultivated crops. OBJECTIVES The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication. METHODS The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication. RESULTS We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes. CONCLUSION The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.
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Zhang W, Shi H, Zhou Y, Liang X, Luo X, Xiao C, Li Y, Xu P, Wang J, Gong W, Zou Q, Tao L, Kang Z, Tang R, Li Z, Yang J, Fu S. Rapid and Synchronous Breeding of Cytoplasmic Male Sterile and Maintainer Line Through Mitochondrial DNA Rearrangement Using Doubled Haploid Inducer in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:871006. [PMID: 35557722 PMCID: PMC9087798 DOI: 10.3389/fpls.2022.871006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 05/31/2023]
Abstract
When homozygously fertile plants were induced using doubled haploid (DH) induction lines Y3380 and Y3560, the morphology of the induced F1 generation was basically consistent with the female parent, but the fertility was separated, showing characteristics similar to cytoplasmic male sterile (CMS) and maintainer lines. In this study, the morphology, fertility, ploidy, and cytoplasm genotype of the induced progeny were identified, and the results showed that the sterile progeny was polima cytoplasm sterile (pol CMS) and the fertile progeny was nap cytoplasm. The molecular marker and test-cross experimental results showed that the fertile progeny did not carry the restorer gene of pol CMS and the genetic distance between the female parent and the offspring was 0.002. This suggested that those inductions which produced sterile and fertile progeny were coordinated to CMS and maintainer lines. Through the co-linearity analysis of the mitochondrial DNA (mtDNA), it was found that the rearrangement of mtDNA by DH induction was the key factor that caused the transformation of fertility (nap) into sterility (pol). Also, when heterozygous females were induced with DH induction lines, the induction F2 generation also showed the segregation of fertile and sterile lines, and the genetic distance between sterile and fertile lines was approximately 0.075. Therefore, the induction line can induce different types of female parents, and the breeding of the sterile line and the maintainer line can be achieved through the rapid synchronization of sister crosses and self-crosses. The induction of DH inducer in B. napus can provide a new model for the innovation of germplasm resources and open up a new way for its application.
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Affiliation(s)
- Wei Zhang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Haoran Shi
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Ying Zhou
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Xingyu Liang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuan Luo
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaowen Xiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yun Li
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jisheng Wang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Wanzhuo Gong
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Qiong Zou
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Lanrong Tao
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Zeming Kang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Rong Tang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Zhuang Li
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Jin Yang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Shaohong Fu
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
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Specificities and Dynamics of Transposable Elements in Land Plants. BIOLOGY 2022; 11:biology11040488. [PMID: 35453688 PMCID: PMC9033089 DOI: 10.3390/biology11040488] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Transposable elements are dynamic components of plant genomes, and display a high diversity of lineages and distribution as the result of evolutionary driving forces and overlapping mechanisms of genetic and epigenetic regulation. They are now regarded as main contributors for genome evolution and function, and important regulators of endogenous gene expression. In this review, we survey recent progress and current challenges in the identification and classification of transposon lineages in complex plant genomes, highlighting the molecular specificities that may explain the expansion and diversification of mobile genetic elements in land plants. Abstract Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.
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Xiao L, Lu L, Zeng W, Shang X, Cao S, Yan H. DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava. FRONTIERS IN PLANT SCIENCE 2022; 13:915056. [PMID: 35860527 PMCID: PMC9289687 DOI: 10.3389/fpls.2022.915056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 05/16/2023]
Abstract
Whole genome duplication (WGD) increases the dosage of all coding and non-coding genes, yet the molecular implications of genome-dosage effects remain elusive. In this study, we generated integrated maps of the methylomes and lncRNAomes for diploid and artificially generated autotetraploid cassava (Manihot esculenta Crantz). We found that transposable elements (TEs) suppressed adjacent protein coding gene (PCG)-expression levels, while TEs activated the expression of nearby long non-coding RNAs (lncRNAs) in the cassava genome. The hypermethylation of DNA transposons in mCG and mCHH sites may be an effective way to suppress the expression of nearby PCGs in autotetraploid cassava, resulting in similar expression levels for most of PCGs between autotetraploid and diploid cassava. In the autotetraploid, decreased methylation levels of retrotransposons at mCHG and mCHH sites contributed to reduced methylation of Gypsy-neighboring long intergenic non-coding RNAs, potentially preserving diploid-like expression patterns in the major of lncRNAs. Collectively, our study highlighted that WGD-induced DNA methylation variation in DNA transposons and retrotransposons may be as direct adaptive responses to dosage of all coding-genes and lncRNAs, respectively.
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Affiliation(s)
- Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- *Correspondence: Huabing Yan,
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Zhang L, Hua C, Pruitt RN, Qin S, Wang L, Albert I, Albert M, van Kan JAL, Nürnberger T. Distinct immune sensor systems for fungal endopolygalacturonases in closely related Brassicaceae. NATURE PLANTS 2021; 7:1254-1263. [PMID: 34326531 DOI: 10.1038/s41477-021-00982-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/07/2021] [Indexed: 05/23/2023]
Abstract
Plant pattern recognition receptors (PRRs) facilitate recognition of microbial patterns and mediate activation of plant immunity. Arabidopsis thaliana RLP42 senses fungal endopolygalacturonases (PGs) and triggers plant defence through complex formation with SOBIR1 and SERK co-receptors. Here, we show that a conserved 9-amino-acid fragment pg9(At) within PGs is sufficient to activate RLP42-dependent plant immunity. Structure-function analysis reveals essential roles of amino acid residues within the RLP42 leucine-rich repeat and island domains for ligand binding and PRR complex assembly. Sensitivity to pg9(At), which is restricted to A. thaliana and exhibits scattered accession specificity, is unusual for known PRRs. Arabidopsis arenosa and Brassica rapa, two Brassicaceae species closely related to A. thaliana, respectively perceive immunogenic PG fragments pg20(Aa) and pg36(Bra), which are structurally distinct from pg9(At). Our study provides evidence for rapid evolution of polymorphic PG sensors with distinct pattern specificities within a single plant family.
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Affiliation(s)
- Lisha Zhang
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany.
| | - Chenlei Hua
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Rory N Pruitt
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Si Qin
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Lei Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Isabell Albert
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
- Institute of Molecular Plant Physiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Markus Albert
- Institute of Molecular Plant Physiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany.
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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11
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Zhou C, Liu X, Li X, Zhou H, Wang S, Yuan Z, Zhang Y, Li S, You A, Zhou L, He Z. A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling. RICE (NEW YORK, N.Y.) 2021; 14:72. [PMID: 34347189 PMCID: PMC8339180 DOI: 10.1186/s12284-021-00515-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/27/2021] [Indexed: 05/16/2023]
Abstract
Evolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.
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Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan, 430056, China
| | - Xinglei Li
- Bioacme Biotechnology Co., Ltd., Wuhan, 430056, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Sijia Wang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Zhu Yuan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, 442000, China
| | - Sanhe Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lei Zhou
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
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12
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Chu Y, Bertioli D, Levinson CM, Stalker HT, Holbrook CC, Ozias-Akins P. Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaënsis × Arachis correntina4x and its derivatives. G3-GENES GENOMES GENETICS 2021; 11:6162164. [PMID: 33693764 PMCID: PMC8759810 DOI: 10.1093/g3journal/jkab066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/21/2021] [Indexed: 11/13/2022]
Abstract
Genome instability in newly synthesized allotetraploids of peanut has breeding implications that have not been fully appreciated. Synthesis of wild species-derived neo-tetraploids offers the opportunity to broaden the gene pool of peanut; however, the dynamics among the newly merged genomes creates predictable and unpredictable variation. Selfed progenies from the neo-tetraploid Arachis ipaënsis × Arachis correntina (A. ipaënsis × A. correntina)4x and F1 hybrids and F2 progenies from crosses between A. hypogaea × [A. ipaënsis × A. correntina]4x were genotyped by the Axiom Arachis 48 K SNP array. Homoeologous recombination between the A. ipaënsis and A. correntina derived subgenomes was observed in the S0 generation. Among the S1 progenies, these recombined segments segregated and new events of homoeologous recombination emerged. The genomic regions undergoing homoeologous recombination segregated mostly disomically in the F2 progenies from A. hypogaea × [A. ipaënsis × A. correntina]4x crosses. New homoeologous recombination events also occurred in the F2 population, mostly found on chromosomes 03, 04, 05, and 06. From the breeding perspective, these phenomena offer both possibilities and perils; recombination between genomes increases genetic diversity, but genome instability could lead to instability of traits or even loss of viability within lineages.
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Affiliation(s)
- Ye Chu
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
| | - Chandler M Levinson
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - H Thomas Stalker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - C Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
| | - Peggy Ozias-Akins
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
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13
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Yin L, Zhu Z, Huang L, Luo X, Li Y, Xiao C, Yang J, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.). HORTICULTURE RESEARCH 2021; 8:142. [PMID: 34193846 PMCID: PMC8245426 DOI: 10.1038/s41438-021-00576-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/29/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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Affiliation(s)
- Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Chaowen Xiao
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
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14
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Zhang Q, Guan P, Zhao L, Ma M, Xie L, Li Y, Zheng R, Ouyang W, Wang S, Li H, Zhang Y, Peng Y, Cao Z, Zhang W, Xiao Q, Xiao Y, Fu T, Li G, Li X, Shen J. Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus. MOLECULAR PLANT 2021; 14:604-619. [PMID: 33387675 DOI: 10.1016/j.molp.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/28/2020] [Accepted: 12/28/2020] [Indexed: 05/20/2023]
Abstract
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization, which drives genome evolution and contributes to the increased adaptability to diverse environments. However, a comprehensive epigenome map of Brassica napus is still unavailable. In this study, we performed integrative analysis of five histone modifications, RNA polymerase II occupancy, DNA methylation, and transcriptomes in two B. napus lines (2063A and B409), and established global maps of regulatory elements, chromatin states, and their dynamics for the whole genome (including the An and Cn subgenomes) in four tissue types (young leaf, flower bud, silique, and root) of these two lines. Approximately 65.8% of the genome was annotated with different epigenomic signals. Compared with the Cn subgenome, the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks. Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes. Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns. We identified a novel bivalent chromatin state (with H3K4me1 and H3K27me3) in B. napus that is associated with tissue-specific gene expression. Furthermore, we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels. Collectively, our findings provide a valuable epigenetic resource for allopolyploid plants.
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Affiliation(s)
- Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengpeng Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqin Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shunyao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmeijuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanling Xiao
- National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Lv Z, Li Z, Wang M, Zhao F, Zhang W, Li C, Gong L, Zhang Y, Mason AS, Liu B. Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition. BMC Biol 2021; 19:42. [PMID: 33750361 PMCID: PMC7944620 DOI: 10.1186/s12915-021-00985-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidy has played a prominent role in the evolution of plants and many other eukaryotic lineages. However, how polyploid genomes adapt to the abrupt presence of two or more sets of chromosomes via genome regulation remains poorly understood. Here, we analyzed genome-wide histone modification and gene expression profiles in relation to domestication and ploidy transition in the A and B subgenomes of polyploid wheat. RESULTS We found that epigenetic modification patterns by two typical euchromatin histone markers, H3K4me3 and H3K27me3, for the great majority of homoeologous triad genes in A and B subgenomes were highly conserved between wild and domesticated tetraploid wheats and remained stable in the process of ploidy transitions from hexaploid to extracted tetraploid and then back to resynthesized hexaploid. However, a subset of genes was differentially modified during tetraploid and hexaploid wheat domestication and in response to ploidy transitions, and these genes were enriched for particular gene ontology (GO) terms. The extracted tetraploid wheat manifested higher overall histone modification levels than its hexaploid donor, and which were reversible and restored to normal levels in the resynthesized hexaploid. Further, while H3K4me3 marks were distally distributed along each chromosome and significantly correlated with subgenome expression as expected, H3K27me3 marks showed only a weak distal bias and did not show a significant correlation with gene expression. CONCLUSIONS Our results reveal overall high stability of histone modification patterns in the A and B subgenomes of polyploid wheat during domestication and in the process of ploidy transitions. However, modification levels of a subset of functionally relevant genes in the A and B genomes were trans-regulated by the D genome in hexaploid wheat.
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Affiliation(s)
- Zhenling Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Department of Plant Breeding, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Changping Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yijng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Department of Plant Breeding, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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16
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Braz GT, Yu F, Zhao H, Deng Z, Birchler JA, Jiang J. Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize. THE NEW PHYTOLOGIST 2021; 229:3294-3302. [PMID: 33222183 DOI: 10.1111/nph.17098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well-established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing. We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide-based haplotype-specific chromosome painting. We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation. We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids.
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Affiliation(s)
- Guilherme T Braz
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Fan Yu
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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17
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Xiong Z, Gaeta RT, Edger PP, Cao Y, Zhao K, Zhang S, Pires JC. Chromosome inheritance and meiotic stability in allopolyploid Brassica napus. G3-GENES GENOMES GENETICS 2021; 11:6044140. [PMID: 33704431 PMCID: PMC8022990 DOI: 10.1093/g3journal/jkaa011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/05/2020] [Indexed: 12/23/2022]
Abstract
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosomes during meiosis can be compared by unambiguous chromosome identification between resynthesized and natural B. napus. Compared with natural B. napus, resynthesized lines show high rates of nonhomologous centromere association, homoeologous recombination leading to translocation, homoeologous chromosome replacement, and association and breakage of 45S rDNA loci. In both natural and resynthesized B. napus, we observed low rates of univalents, A–C bivalents, and early sister chromatid separations. Reciprocal homoeologous chromosome exchanges and double reductions were photographed for the first time in meiotic telophase I. Meiotic errors were non-uniformly distributed across the genome in resynthesized B. napus, and in particular homoeologs sharing synteny along their entire length exhibited multivalents at diakinesis and polysomic inheritance at telophase I. Natural B. napus appeared to resolve meiotic errors mainly by suppressing homoeologous pairing, resolving nonhomologous centromere associations and 45S rDNA associations before diakinesis, and reducing homoeologous cross-overs.
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Affiliation(s)
- Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China.,Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Robert T Gaeta
- Bayer's Crop Science Division, Chesterfield, MO 63017, USA
| | - Patrick P Edger
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.,Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - Siqi Zhang
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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18
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Pan Q, Zhu B, Zhang D, Tong C, Ge X, Liu S, Li Z. Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus. Front Genet 2020; 10:1279. [PMID: 31921314 PMCID: PMC6931035 DOI: 10.3389/fgene.2019.01279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/21/2019] [Indexed: 11/21/2022] Open
Abstract
Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, AeAe, 2n = 20) obtained from Brassica napus (AnAnCnCn, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (ArAr), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the An-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between An and Cn subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the An and Cn subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.
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Affiliation(s)
- Qi Pan
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Zhu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dawei Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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19
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Lee H, Chawla HS, Obermeier C, Dreyer F, Abbadi A, Snowdon R. Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:496. [PMID: 32411167 PMCID: PMC7202327 DOI: 10.3389/fpls.2020.00496] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/01/2020] [Indexed: 05/19/2023]
Abstract
Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession 'Express 617' using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.
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Affiliation(s)
- HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- *Correspondence: Rod Snowdon,
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20
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Lee H, Chawla HS, Obermeier C, Dreyer F, Abbadi A, Snowdon R. Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:496. [PMID: 32411167 DOI: 10.3389/fpls.2020.00496/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/01/2020] [Indexed: 05/21/2023]
Abstract
Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession 'Express 617' using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.
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Affiliation(s)
- HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
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21
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Yan H, Bombarely A, Xu B, Wu B, Frazier TP, Zhang X, Chen J, Chen P, Sun M, Feng G, Wang C, Cui C, Li Q, Zhao B, Huang L. Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5673-5686. [PMID: 31419288 DOI: 10.1093/jxb/erz325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 07/18/2019] [Indexed: 05/16/2023]
Abstract
Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Life Sciences, University of Milan, Milan, Italy
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Bingchao Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Taylor P Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Chenming Cui
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Qi Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Bingyu Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
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22
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Mhiri C, Parisod C, Daniel J, Petit M, Lim KY, Dorlhac de Borne F, Kovarik A, Leitch AR, Grandbastien MA. Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids. THE NEW PHYTOLOGIST 2019; 221:1619-1633. [PMID: 30220091 DOI: 10.1111/nph.15484] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/06/2018] [Indexed: 05/29/2023]
Abstract
The genomic shock hypothesis suggests that allopolyploidy is associated with genome changes driven by transposable elements, as a response to imbalances between parental insertion loads. To explore this hypothesis, we compared three allotetraploids, Nicotiana arentsii, N. rustica and N. tabacum, which arose over comparable time frames from hybridisation between increasingly divergent diploid species. We used sequence-specific amplification polymorphism (SSAP) to compare the dynamics of six transposable elements in these allopolyploids, their diploid progenitors and in corresponding synthetic hybrids. We show that element-specific dynamics in young Nicotiana allopolyploids reflect their dynamics in diploid progenitors. Transposable element mobilisation is not concomitant with immediate genome merger, but occurs within the first generations of allopolyploid formation. In natural allopolyploids, such mobilisations correlate with imbalances in the repeat profile of the parental species, which increases with their genetic divergence. Other restructuring leading to locus loss is immediate, nonrandom and targeted at specific subgenomes, independently of cross orientation. The correlation between transposable element mobilisation in allopolyploids and quantitative imbalances in parental transposable element loads supports the genome shock hypothesis proposed by McClintock.
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Affiliation(s)
- Corinne Mhiri
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Christian Parisod
- Ecological Genomics, Institute of Plant Sciences, University of Bern, Bern, CH-3013, Switzerland
| | - Julien Daniel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Maud Petit
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - K Yoong Lim
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | | | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Marie-Angèle Grandbastien
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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Goswami G, Nath UK, Park JI, Hossain MR, Biswas MK, Kim HT, Kim HR, Nou IS. Transcriptional regulation of anthocyanin biosynthesis in a high-anthocyanin resynthesized Brassica napus cultivar. JOURNAL OF BIOLOGICAL RESEARCH (THESSALONIKE, GREECE) 2018; 25:19. [PMID: 30505808 PMCID: PMC6258291 DOI: 10.1186/s40709-018-0090-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/09/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Anthocyanins are plant secondary metabolites with key roles in attracting insect pollinators and protecting against biotic and abiotic stresses. They have potential health-promoting effects as part of the human diet. Anthocyanin biosynthesis has been elucidated in many species, enabling the development of anthocyanin-enriched fruits, vegetables, and grains; however, few studies have investigated Brassica napus anthocyanin biosynthesis. RESULTS We developed a high-anthocyanin resynthesized B. napus line, Rs035, by crossing anthocyanin-rich B. rapa (A genome) and B. oleracea (C genome) lines, followed by chromosome doubling. We identified and characterized 73 and 58 anthocyanin biosynthesis genes in silico in the A and C genomes, respectively; these genes showed syntenic relationships with 41 genes in Arabidopsis thaliana and B. napus. Among the syntenic genes, twelve biosynthetic and six regulatory genes showed transgressively higher expression in Rs035, and eight structural genes and one regulatory gene showed additive expression. We identified three early-, four late-biosynthesis pathways, three transcriptional regulator genes, and one transporter as putative candidates enhancing anthocyanin accumulation in Rs035. Principal component analysis and Pearson's correlation coefficients corroborated the contribution of these genes to anthocyanin accumulation. CONCLUSIONS Our study lays the foundation for producing high-anthocyanin B. napus cultivars. The resynthesized lines and the differentially expressed genes we have identified could be used to transfer the anthocyanin traits to other commercial rapeseed lines using molecular and conventional breeding.
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Affiliation(s)
- Gayatri Goswami
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Mohammad Rashed Hossain
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
- University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Hye Ran Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
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24
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Shao GM, Li XY, Wang Y, Wang ZW, Li Z, Zhang XJ, Zhou L, Gui JF. Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp. Genome Biol Evol 2018; 10:2394-2407. [PMID: 30085110 PMCID: PMC6143163 DOI: 10.1093/gbe/evy165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid animals is scarce. In this study, the genome constitution and DNA methylation inheritance in a newly synthetic allopolyploid of gynogenetic gibel carp were analyzed. The incorporation of a whole genome of paternal common carp sperm in the allopolyploid was confirmed by genomic in situ hybridization, chromosome localization of 45S rDNAs, and sequence comparison. Pooled sample-based methylation sensitive amplified polymorphism (MSAP) revealed that an overwhelming majority (98.82%) of cytosine methylation patterns in the allopolyploid were inherited from its parents of hexaploid gibel carp clone D and common carp. Compared to its parents, 11 DNA fragments in the allopolyploid were proved to be caused by interindividual variation, recombination, deletion, and mutation through individual sample-based MSAP and sequencing. Contrast to the rapid and remarkable epigenetic changes in most of analyzed neopolyploids, no cytosine methylation variation was detected in the gynogenetic allopolyploid. Therefore, the newly synthetic allopolyploid of gynogenetic gibel carp combined genomes from its parents and maintained genetic and epigenetic stability after its formation and subsequently seven successive gynogenetic generations. Our current results provide a paradigm for recurrent polyploidy consequences in the gynogenetic allopolyploid animals.
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Affiliation(s)
- Guang-Ming Shao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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25
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Liu Y, Xu C, Tang X, Pei S, Jin D, Guo M, Yang M, Zhang Y. Genomic methylation and transcriptomic profiling provides insights into heading depression in inbred Brassica rapa L. ssp. pekinensis. Gene 2018; 665:119-126. [PMID: 29705127 DOI: 10.1016/j.gene.2018.04.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape. Transcriptome analysis by RNA-Seq revealed that genes in auxin-response and synthesis pathways were differentially expressed in the inbreeding depression lines. Interestingly, methylation levels of some of those genes were also changed. Furthermore, endogenous IAA content was decreased in inbred plants, in agreement with expression and methylation data. Chemical inhibition of auxin also replicated the degenerated phenotype in normal plants, while exogenous IAA application had no effect in inbred depression plants, suggesting a more complex mechanism. These data indicate DNA methylation-regulated auxin pathways play a role in establishing inbred depression phenotypes in plants. Our findings reveal new insights into inbreeding depression and leafy head development in Chinese cabbage.
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Affiliation(s)
- Yan Liu
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Cui Xu
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Xuebing Tang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, PR China
| | - Di Jin
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Minghao Guo
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Meng Yang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Yaowei Zhang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin 150030, PR China.
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26
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Kalinka A, Achrem M. Reorganization of wheat and rye genomes in octoploid triticale (× Triticosecale). PLANTA 2018; 247:807-829. [PMID: 29234880 PMCID: PMC5856900 DOI: 10.1007/s00425-017-2827-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/03/2017] [Indexed: 06/01/2023]
Abstract
The analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations. This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes. Wheat chromosomes were eliminated to a higher extent. The lower content of telomeric heterochromatin was also found in rye chromosomes in comparison with parental rye. Studying the location of selected retrotransposons from Ty1-copia and Ty3-gypsy families using fluorescence in situ hybridization revealed additional locations of these retrotransposons that were not present in chromosomes of parental species. ISSR, IRAP and REMAP analyses showed significant changes at the level of specific DNA nucleotide sequences. In most cases, the disappearance of certain types of bands was observed, less frequently new types of bands appeared, not present in parental species. This demonstrates the scale of genome rearrangement and, above all, the elimination of wheat and rye sequences, largely due to the reduction of chromosome number. With regard to the proportion of wheat to rye genome, the rye genome was more affected by the changes, thus this study was focused more on the rye genome. Observations suggest that genome reorganization is not finished in the F5 generation but is still ongoing in the F8 generation.
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Affiliation(s)
- Anna Kalinka
- Department of Cell Biology, Faculty of Biology, Institute for Research on Biodiversity, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
- Faculty of Biology, Molecular Biology and Biotechnology Center, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Magdalena Achrem
- Department of Cell Biology, Faculty of Biology, Institute for Research on Biodiversity, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
- Faculty of Biology, Molecular Biology and Biotechnology Center, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
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27
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Wang X, Dong Q, Li X, Yuliang A, Yu Y, Li N, Liu B, Gong L. Cytonuclear Variation of Rubisco in Synthesized Rice Hybrids and Allotetraploids. THE PLANT GENOME 2017; 10. [PMID: 29293814 DOI: 10.3835/plantgenome2017.05.0041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The allopolyploid speciation process faces the genomic challenge of stoichiometric disruption caused by merging biparental nuclear genomes with only one (usually maternal) of the two sets of progenitor cytoplasmic genomes. The photosynthetic protein 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is composed of nuclear-encoded small subunits (SSUs) and plastome-encoded large subunits (LSUs), making it an ideal enzyme to explore the evolution process of cytonuclear accommodation. We investigated the variation of SSUs and their encoding genes in synthetic nascent rice ( L.) allotetraploid lineages, formed from the parental subspecies and of Asian rice. The evolution of genes in rice subspecies involves both mutation and concerted homogenization. Within reciprocal rice hybrids and allopolyploids, there was no consistent pattern of biased expression of alleles or homeologs, nor was there biased gene conversion favoring the maternal gene copies. Instead, we observed an apparently stochastic pattern of intergenomic gene conversions and biased expression of homeologs. We conclude that in young rice allopolyploids, cytonuclear coordination either is not selectively favored because of high parental sequence similarity or because there has been insufficient time for subtle selective effects to become observable.
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28
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Seo MS, Kim JS. Understanding of MYB Transcription Factors Involved in Glucosinolate Biosynthesis in Brassicaceae. Molecules 2017; 22:molecules22091549. [PMID: 28906468 PMCID: PMC6151624 DOI: 10.3390/molecules22091549] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 02/06/2023] Open
Abstract
Glucosinolates (GSLs) are widely known secondary metabolites that have anticarcinogenic and antioxidative activities in humans and defense roles in plants of the Brassicaceae family. Some R2R3-type MYB (myeloblastosis) transcription factors (TFs) control GSL biosynthesis in Arabidopsis. However, studies on the MYB TFs involved in GSL biosynthesis in Brassica species are limited because of the complexity of the genome, which includes an increased number of paralog genes as a result of genome duplication. The recent completion of the genome sequencing of the Brassica species permits the identification of MYB TFs involved in GSL biosynthesis by comparative genome analysis with A. thaliana. In this review, we describe various findings on the regulation of GSL biosynthesis in Brassicaceae. Furthermore, we identify 63 orthologous copies corresponding to five MYB TFs from Arabidopsis, except MYB76 in Brassica species. Fifty-five MYB TFs from the Brassica species possess a conserved amino acid sequence in their R2R3 MYB DNA-binding domain, and share close evolutionary relationships. Our analysis will provide useful information on the 55 MYB TFs involved in the regulation of GSL biosynthesis in Brassica species, which have a polyploid genome.
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Affiliation(s)
- Mi-Suk Seo
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea.
| | - Jung Sun Kim
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea.
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29
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Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Washburn JD, Schmitz RJ, Smith GD, Pires JC, Puzey JR. Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower. THE PLANT CELL 2017; 29:2150-2167. [PMID: 28814644 PMCID: PMC5635986 DOI: 10.1105/tpc.17.00010] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/25/2017] [Accepted: 08/13/2017] [Indexed: 05/18/2023]
Abstract
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are reduced in regions near genes and within TEs in the first-generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. Subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events and may also contribute to uncovering the mechanistic basis of heterosis and subgenome dominance.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
- Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824
| | - Ronald Smith
- Department of Applied Science, The College of William and Mary, Williamsburg, Virginia 23185
| | | | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington 99362
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Yaowu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Adrian E Platts
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan 48824
| | - Jacob D Washburn
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Gregory D Smith
- Department of Applied Science, The College of William and Mary, Williamsburg, Virginia 23185
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Joshua R Puzey
- Department of Biology, The College of William and Mary, Williamsburg, Virginia 23185
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Carlson KD, Fernandez-Pozo N, Bombarely A, Pisupati R, Mueller LA, Madlung A. Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica. BMC Genomics 2017; 18:653. [PMID: 28830347 PMCID: PMC5567635 DOI: 10.1186/s12864-017-4067-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can lead to instant speciation. Arabidopsis suecica is a relatively recent allopolyploid species, suggesting that its natural accessions might be genetically very similar to each other. Nonetheless, subtle phenotypic differences have been described between different geographic accessions of A. suecica grown in a common garden. RESULTS To determine the degree of genomic similarity between different populations of A. suecica, we obtained transcriptomic sequence, quantified SNP variation within the gene space, and analyzed gene expression levels genome-wide from leaf material grown in controlled lab conditions. Despite their origin from the same progenitor species, the two accessions of A. suecica used in our study show genomic and transcriptomic variation. We report significant gene expression differences between the accessions, mostly in genes with stress-related functions. Among the differentially expressed genes, there are a surprising number of homoeologs coordinately regulated between sister accessions. CONCLUSIONS Many of these homoeologous genes and other differentially expressed genes affect transpiration and stomatal regulation, suggesting that they might be involved in the establishment of the phenotypic differences between the two accessions.
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Affiliation(s)
- Keisha D. Carlson
- Department of Biology, University of Puget Sound, 1500 N Warner St, CMB 1088, Tacoma, WA 98416 USA
| | | | - Aureliano Bombarely
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853 USA
- Present Address: Virginia Tech, Department of Horticulture, 216 Latham Hall, Blacksburg, VA 24061 USA
| | - Rahul Pisupati
- Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | | | - Andreas Madlung
- Department of Biology, University of Puget Sound, 1500 N Warner St, CMB 1088, Tacoma, WA 98416 USA
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Rana K, Atri C, Gupta M, Akhatar J, Sandhu PS, Kumar N, Jaswal R, Barbetti MJ, Banga SS. Mapping resistance responses to Sclerotinia infestation in introgression lines of Brassica juncea carrying genomic segments from wild Brassicaceae B. fruticulosa. Sci Rep 2017; 7:5904. [PMID: 28724956 PMCID: PMC5517529 DOI: 10.1038/s41598-017-05992-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/07/2017] [Indexed: 11/30/2022] Open
Abstract
Sclerotinia stem rot (Sclerotinia sclerotiorum) is a major disease of Brassica oilseeds. As suitable donors to develop resistant cultivars are not available in crop Brassicas, we introgressed resistance from a wild Brassicaceae species, B. fruticulosa. We produced 206 B. juncea-B. fruticulosa introgression lines (ILs). These were assessed for pollen grain fertility, genome size variations and resistance responses to Sclerotinia following stem inoculations under disease-conducive conditions. Of these, 115 ILs showing normal fertility and genome size were selected for cytogenetic characterization using florescent genomic in situ hybridization (Fl-GISH). B. fruticulosa segment substitutions were indicated in 28 ILs. These were predominantly terminal and located on B-genome chromosomes. A final set of 93 highly fertile and euploid (2n = 36) ILs were repeat-evaluated for their resistance responses during 2014-15. They were also genotyped with 202 transferable and 60 candidate gene SSRs. Association mapping allowed detection of ten significant marker trait associations (MTAs) after Bonferroni correction. These were: CNU-m157-2, RA2G05, CNU-m353-3, CNU-m442-5, ACMP00454-2, ACMP00454-3, EIN2-3-1, M641-1, Na10D09-1 and Na10D11-1. This is the first time such a molecular mapping technique has been deployed with introgression lines carrying genomic segments from B. fruticulosa, and the first to show that they possess high levels of resistance against S. sclerotiorum.
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Affiliation(s)
- Kusum Rana
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Chhaya Atri
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mehak Gupta
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Javed Akhatar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Prabhjodh S Sandhu
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Nitin Kumar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Ravinder Jaswal
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Surinder S Banga
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
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Pelé A, Falque M, Trotoux G, Eber F, Nègre S, Gilet M, Huteau V, Lodé M, Jousseaume T, Dechaumet S, Morice J, Poncet C, Coriton O, Martin OC, Rousseau-Gueutin M, Chèvre AM. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genet 2017; 13:e1006794. [PMID: 28493942 PMCID: PMC5444851 DOI: 10.1371/journal.pgen.1006794] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 05/25/2017] [Accepted: 05/02/2017] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Matthieu Falque
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Sylvain Dechaumet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Olivier Coriton
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Olivier C. Martin
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- * E-mail:
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Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica. Sci Rep 2016; 6:37416. [PMID: 27874043 PMCID: PMC5118723 DOI: 10.1038/srep37416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/27/2016] [Indexed: 11/08/2022] Open
Abstract
Raphanobrassica is an allopolyploid species derived from inter-generic hybridization that combines the R genome from R. sativus and the C genome from B. oleracea var. alboglabra. In the present study, we used a high-throughput sequencing method to identify the mRNA and miRNA profiles in Raphanobrassica and its parents. A total of 33,561 mRNAs and 283 miRNAs were detected, 9,209 mRNAs and 134 miRNAs were differentially expressed respectively, 7,633 mRNAs and 39 miRNAs showed ELD expression, 5,219 mRNAs and 57 miRNAs were non-additively expressed in Raphanobrassica. Remarkably, differentially expressed genes (DEGs) were up-regulated and maternal bias was detected in Raphanobrassica. In addition, a miRNA-mRNA interaction network was constructed based on reverse regulated miRNA-mRNAs, which included 75 miRNAs and 178 mRNAs, 31 miRNAs were non-additively expressed target by 13 miRNAs. The related target genes were significantly enriched in the GO term 'metabolic processes'. Non-additive related target genes regulation is involved in a range of biological pathways, like providing a driving force for variation and adaption in this allopolyploid. The integrative analysis of mRNA and miRNA profiling provides more information to elucidate gene expression mechanism and may supply a comprehensive and corresponding method to study genetic and transcription variation of allopolyploid.
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Fu Y, Xiao M, Yu H, Mason AS, Yin J, Li J, Zhang D, Fu D. Small RNA changes in synthetic Brassica napus. PLANTA 2016; 244:607-622. [PMID: 27107747 DOI: 10.1007/s00425-016-2529-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/09/2016] [Indexed: 06/05/2023]
Abstract
Small RNAs and microRNAs were found to vary extensively in synthetic Brassica napus and subsequent generations, accompanied by the activation of transposable elements in response to hybridization and polyploidization. Resynthesizing B. napus by hybridization and chromosome doubling provides an approach to create novel polyploids and increases the usable genetic variability in oilseed rape. Although many studies have shown that small RNAs (sRNAs) act as important factor during hybridization and polyploidization in plants, much less is known on how sRNAs change in synthetic B. napus, particularly in subsequent generations after formation. We performed high-throughput sequencing of sRNAs in S1-S4 generations of synthetic B. napus and in the homozygous B. oleracea and B. rapa parent lines. We found that the number of small RNAs (sRNAs) and microRNAs (miRNAs) doubled in synthetic B. napus relative to the parents. The proportions of common sRNAs detected varied from the S1 to S4 generations, suggesting sRNAs are unstable in synthetic B. napus. The majority of miRNAs (67.2 %) were non-additively expressed in the synthesized Brassica allotetraploid, and 33.3 % of miRNAs were novel in the resynthesized B. napus. The percentage of miRNAs derived from transposable elements (TEs) also increased, indicating transposon activation and increased transposon-associated miRNA production in response to hybridization and polyploidization. The number of target genes for each miRNA in the synthesized Brassica allotetraploid was doubled relative to the parents, enhancing the complexity of gene expression regulation. The potential roles of miRNAs and their targets are discussed. Our data demonstrate generational changes in sRNAs and miRNAs in synthesized B. napus.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meili Xiao
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jiaming Yin
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Dongqing Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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Fowler NL, Levin DA. Critical factors in the establishment of allopolyploids. AMERICAN JOURNAL OF BOTANY 2016; 103:1236-1251. [PMID: 27370314 DOI: 10.3732/ajb.1500407] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/07/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The growth and spread of new polyploid populations have been explained in terms of fitness advantages over their diploid progenitors. However, a fitness advantage is not sufficient to insure the establishment of a polyploid; it must also overcome the obstacles of demographic stochasticity and minority disadvantage. Several studies have addressed the population dynamics of autopolyploids, but the present study is the first to consider allopolyploids, which are affected by more factors than autopolyploids. METHODS We constructed a population dynamic model of four types of plants (two parent species, hybrids, allopolyploids) that also included an explicit breeding system. KEY RESULTS The numbers of plants of each type were the most important factors determining whether the new allopolyploid would become established. More polyploid plants greatly increased the likelihood of polyploid persistence. More plants of the parent species and more hybrids resulted in more polyploids being produced. The model parameters with the most effect on polyploid establishment were potential population size (K), individual plant fecundity, and niche separation (α). The most important breeding system parameters were selfing rates, which mitigated minority disadvantage imposed by pollen limitation. CONCLUSIONS The importance of population sizes, and the parameters that controlled them, in overcoming demographic stochasticity parallels the well-recognized role of propagule pressure in determining the success of invasive species. We modeled the establishment of a new allopolyploid; analogous considerations would affect the establishment of a new autopolyploid. The critical role of population sizes in polyploid establishment should be more widely recognized.
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Affiliation(s)
- Norma L Fowler
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Donald A Levin
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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Husband BC, Baldwin SJ, Sabara HA. Direct vs. indirect effects of whole-genome duplication on prezygotic isolation in Chamerion angustifolium: Implications for rapid speciation. AMERICAN JOURNAL OF BOTANY 2016; 103:1259-1271. [PMID: 27440792 DOI: 10.3732/ajb.1600097] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The depiction of polyploid speciation as instantaneous implies that strong prezygotic and postzygotic isolation form as a direct result of whole-genome duplication. However, the direct vs. indirect contributions of genome duplication to phenotypic divergence and prezygotic isolation are rarely quantified across multiple reproductive barriers. METHODS We compared the phenotypic differences between diploid and both naturally occurring and synthesized tetraploids (neotetraploids) of the plant Chamerion angustifolium. Using this information and additional published values for this species, we compared the magnitude of isolation (ecological, flowering, pollinator, and gametic) between diploids and natural-occurring tetraploids to that between diploids and neotetraploids. KEY RESULTS Differences among ploidy cytotypes were observed for eight of 12 vegetative and reproductive traits measured. Neotetraploids resembled diploids but differed from natural tetraploids with respect to four traits, including flowering time and plant height. Diploid-neotetraploid (2x-4xneo) experimental arrays exhibited lower pollinator fidelity to cytotype and seed set compared with 2x-4xnat arrays. Based on these results and published evidence, reproductive isolation between diploids and neotetraploids across all four life stages averaged 0.48 and deviated significantly from that between diploids and natural tetraploids (RI = 0.96). CONCLUSIONS Genome duplication causes phenotypic shifts and contributes directly to prezygotic isolation for some barriers (gametic isolation) but cannot account for the cumulative isolation from diploids observed in natural tetraploids. Therefore, conditions for species formation through genome duplication are not necessarily instantaneous and selection to strengthen prezygotic barriers in young polyploids is critical for the establishment of polyploid species in sympatry.
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Affiliation(s)
- Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - Sarah J Baldwin
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - Holly A Sabara
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
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Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM. Molecular and systems approaches towards drought-tolerant canola crops. THE NEW PHYTOLOGIST 2016; 210:1169-1189. [PMID: 26879345 DOI: 10.1111/nph.13866] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
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Affiliation(s)
- Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - J Grey Monroe
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Florent Villiers
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
| | - Jack Mullen
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dianne Pater
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - Joel S Bader
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
| | - June M Kwak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
- Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
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Alexander-Webber D, Abbott RJ, Chapman MA. Morphological Convergence Between an Allopolyploid and One of its Parental Species Correlates with Biased Gene Expression and DNA Loss. J Hered 2016; 107:445-54. [DOI: 10.1093/jhered/esw035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/20/2016] [Indexed: 11/14/2022] Open
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40
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Gautam M, Dang Y, Ge X, Shao Y, Li Z. Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus. FRONTIERS IN PLANT SCIENCE 2016; 7:438. [PMID: 27148282 PMCID: PMC4828432 DOI: 10.3389/fpls.2016.00438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/21/2016] [Indexed: 05/24/2023]
Abstract
Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent.
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Affiliation(s)
- Mayank Gautam
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yanwei Dang
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yujiao Shao
- College of Chemistry and Life Science, Hubei University of EducationWuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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Springer NM, Lisch D, Li Q. Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. THE PLANT CELL 2016; 28:314-25. [PMID: 26869701 PMCID: PMC4790878 DOI: 10.1105/tpc.15.00911] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 05/02/2023]
Abstract
Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.
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Affiliation(s)
- Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
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42
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Zhang X, Liu T, Li X, Duan M, Wang J, Qiu Y, Wang H, Song J, Shen D. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables. Sci Rep 2016; 6:18618. [PMID: 26727246 PMCID: PMC4698638 DOI: 10.1038/srep18618] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops.
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Affiliation(s)
- Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Tongjin Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Mengmeng Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jinglei Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jiangping Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Di Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
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Gao L, Diarso M, Zhang A, Zhang H, Dong Y, Liu L, Lv Z, Liu B. Heritable alteration of DNA methylation induced by whole-chromosome aneuploidy in wheat. THE NEW PHYTOLOGIST 2016; 209:364-75. [PMID: 26295562 DOI: 10.1111/nph.13595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/03/2015] [Indexed: 05/05/2023]
Abstract
Aneuploidy causes changes in gene expression and phenotypes in all organisms studied. A previous study in the model plant Arabidopsis thaliana showed that aneuploidy-generated phenotypic changes can be inherited to euploid progenies and implicated an epigenetic underpinning of the heritable variations. Based on an analysis by amplified fragment length polymorphism and methylation-sensitive amplified fragment length polymorphism markers, we found that although genetic changes at the nucleotide sequence level were negligible, extensive changes in cytosine DNA methylation patterns occurred in all studied homeologous group 1 whole-chromosome aneuploid lines of common wheat (Triticum aestivum), with monosomic 1A showing the greatest amount of methylation changes. The changed methylation patterns were inherited by euploid progenies derived from the aneuploid parents. The aneuploidy-induced DNA methylation alterations and their heritability were verified at selected loci by bisulfite sequencing. Our data have provided empirical evidence supporting earlier suggestions that heritability of aneuploidy-generated, but aneuploidy-independent, phenotypic variations may have an epigenetic basis. That at least one type of aneuploidy - monosomic 1A - was able to cause significant epigenetic divergence of the aneuploid plants and their euploid progenies also lends support to recent suggestions that aneuploidy may have played an important and protracted role in polyploid genome evolution.
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Affiliation(s)
- Lihong Gao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Science, Changchun Normal University, Changchun, 130032, China
| | - Moussa Diarso
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yuzhu Dong
- School of Life Science, Changchun Normal University, Changchun, 130032, China
| | - Lixia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhenling Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Tanaka M, Tanaka H, Shitsukawa N, Kitagawa S, Takumi S, Murai K. Homoeologous copy-specific expression patterns of MADS-box genes for floral formation in allopolyploid wheat. Genes Genet Syst 2015; 90:217-29. [PMID: 26616759 DOI: 10.1266/ggs.15-00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The consensus model for floral organ formation in higher plants, the so-called ABCDE model, proposes that floral whorl-specific combinations of class A, B, C, D, and E genes specify floral organ identity. Class A, B, C, D and E genes encode MADS-box transcription factors; the single exception being the class A gene APETALA2. Bread wheat (Triticum aestivum) is a hexaploid species with a genome constitution AABBDD; the hexaploid originated from a cross between tetraploid T. turgidum (AABB) and diploid Aegilops tauschii (DD). Tetraploid wheat is thought to have originated from a cross between the diploid species T. urartu (AA) and Ae. speltoides (BB). Consequently, the hexaploid wheat genome contains triplicated homoeologous copies (homoeologs) of each gene derived from the different ancestral diploid species. In this study, we examined the expression patterns of homoeologs of class B, C and D MADS-box genes during floral development. For the class B gene wheat PISTILLATA2 (WPI2), the homoeologs from the A and D genomes were expressed, while expression of the B genome homoeolog was suppressed. For the class C gene wheat AGAMOUS1 (WAG1), the homoeologs on the A and B genomes were expressed, while expression of the D genome homoeolog was suppressed. For the class D gene wheat SEEDSTICK (WSTK), the B genome homoeolog was preferentially expressed. These differential patterns of homoeolog expression were consistently observed among different hexaploid wheat varieties and synthetic hexaploid wheat lines developed by artificial crosses between tetraploid wheat and Ae. tauschii. These results suggest that homoeolog-specific regulation of the floral MADS-box genes occurs in allopolyploid wheat.
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Affiliation(s)
- Miku Tanaka
- Department of Bioscience, Fukui Prefectural University
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45
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Chen X, Ge X, Wang J, Tan C, King GJ, Liu K. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. FRONTIERS IN PLANT SCIENCE 2015; 6:836. [PMID: 26500672 PMCID: PMC4598586 DOI: 10.3389/fpls.2015.00836] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/23/2015] [Indexed: 05/25/2023]
Abstract
Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 10(5)), 2.16% CHG (2.7 × 10(5)), and 1.68% CHH loci (1.05 × 10(5)) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as (5m)CG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss.
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Affiliation(s)
- Xun Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Chen Tan
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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46
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Covelo-Soto L, Leunda PM, Pérez-Figueroa A, Morán P. Genome-wide methylation study of diploid and triploid brown trout (Salmo trutta L.). Anim Genet 2015; 46:280-8. [PMID: 25917300 DOI: 10.1111/age.12287] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2015] [Indexed: 12/15/2022]
Abstract
The induction of triploidization in fish is a very common practice in aquaculture. Although triploidization has been applied successfully in many salmonid species, little is known about the epigenetic mechanisms implicated in the maintenance of the normal functions of the new polyploid genome. By means of methylation-sensitive amplified polymorphism (MSAP) techniques, genome-wide methylation changes associated with triploidization were assessed in DNA samples obtained from diploid and triploid siblings of brown trout (Salmo trutta). Simple comparative body measurements showed that the triploid trout used in the study were statistically bigger, however, not heavier than their diploid counterparts. The statistical analysis of the MSAP data showed no significant differences between diploid and triploid brown trout in respect to brain, gill, heart, liver, kidney or muscle samples. Nonetheless, local analysis pointed to the possibility of differences in connection with concrete loci. This is the first study that has investigated DNA methylation alterations associated with triploidization in brown trout. Our results set the basis for new studies to be undertaken and provide a new approach concerning triploidization effects of the salmonid genome while also contributing to the better understanding of the genome-wide methylation processes.
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Affiliation(s)
- L Covelo-Soto
- Dpto Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, Vigo, 36210, Spain
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Abstract
Allopolyploidy involves hybridization and duplication of divergent parental genomes and provides new avenues for gene expression. The expression levels of duplicated genes in polyploids can show deviation from parental additivity (the arithmetic average of the parental expression levels). Nonadditive expression has been widely observed in diverse polyploids and comprises at least three possible scenarios: (a) The total gene expression level in a polyploid is similar to that of one of its parents (expression-level dominance); (b) total gene expression is lower or higher than in both parents (transgressive expression); and (c) the relative contribution of the parental copies (homeologs) to the total gene expression is unequal (homeolog expression bias). Several factors may result in expression nonadditivity in polyploids, including maternal-paternal influence, gene dosage balance, cis- and/or trans-regulatory networks, and epigenetic regulation. As our understanding of nonadditive gene expression in polyploids remains limited, a new generation of investigators should explore additional phenomena (i.e., alternative splicing) and use other high-throughput "omics" technologies to measure the impact of nonadditive expression on phenotype, proteome, and metabolome.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525; , ,
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48
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Liu C, Yang X, Zhang H, Wang X, Zhang Z, Bian Y, Zhu B, Dong Y, Liu B. Genetic and epigenetic modifications to the BBAA component of common wheat during its evolutionary history at the hexaploid level. PLANT MOLECULAR BIOLOGY 2015; 88:53-64. [PMID: 25809554 DOI: 10.1007/s11103-015-0307-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/12/2015] [Indexed: 05/11/2023]
Abstract
The formation and evolution of common wheat (Triticum aestivum L., genome BBAADD) involves allopolyploidization events at two ploidy levels. Whether the two ploidy levels (tetraploidy and hexaploidy) have impacted the BBAA subgenomes differentially remains largely unknown. We have reported recently that extensive and distinct modifications of transcriptome expression occurred to the BBAA component of common wheat relative to the evolution of gene expression at the tetraploid level in Triticum turgidum. As a step further, here we analyzed the genetic and cytosine DNA methylation differences between an extracted tetraploid wheat (ETW) harboring genome BBAA that is highly similar to the BBAA subgenomes of common wheat, and a set of diverse T. turgidum collections, including both wild and cultivated genotypes. We found that while ETW had no significantly altered karyotype from T. turgidum, it diverged substantially from the later at both the nucleotide sequence level and in DNA methylation based on molecular marker assay of randomly sampled loci across the genome. In particular, ETW is globally less cytosine-methylated than T. turgidum, consistent with earlier observations of a generally higher transcriptome expression level in ETW than in T. turgidum. Together, our results suggest that genome evolution at the allohexaploid level has caused extensive genetic and DNA methylation modifications to the BBAA subgenomes of common wheat, which are distinctive from those accumulated at the tetraploid level in both wild and cultivated T. turgidum genotypes.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Inheritance and variation of Cytosine methylation in three populus allotriploid populations with different heterozygosity. PLoS One 2015; 10:e0126491. [PMID: 25901359 PMCID: PMC4406749 DOI: 10.1371/journal.pone.0126491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is an epigenetic mechanism with the potential to regulate gene expression and affect plant phenotypes. Both hybridization and genome doubling may affect the DNA methylation status of newly formed allopolyploid plants. Previous studies demonstrated that changes in cytosine methylation levels and patterns were different among individual hybrid plant, therefore, studies investigating the characteristics of variation in cytosine methylation status must be conducted at the population level to avoid sampling error. In the present study, an F1 hybrid diploid population and three allotriploid populations with different heterozygosity [originating from first-division restitution (FDR), second-division restitution (SDR), and post-meiotic restitution (PMR) 2n eggs of the same female parent] were used to investigate cytosine methylation inheritance and variation relative to their common parents using methylation-sensitive amplification polymorphism (MSAP). The variation in cytosine methylation in individuals in each population exhibited substantial differences, confirming the necessity of population epigenetics. The total methylation levels of the diploid population were significantly higher than in the parents, but those of the three allotriploid populations were significantly lower than in the parents, indicating that both hybridization and polyploidization contributed to cytosine methylation variation. The vast majority of methylated status could be inherited from the parents, and the average percentages of non-additive variation were 6.29, 3.27, 5.49 and 5.07% in the diploid, FDR, SDR and PMR progeny populations, respectively. This study lays a foundation for further research on population epigenetics in allopolyploids.
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Song Q, Chen ZJ. Epigenetic and developmental regulation in plant polyploids. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:101-9. [PMID: 25765928 PMCID: PMC4395545 DOI: 10.1016/j.pbi.2015.02.007] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape. The prevalence of polyploidy in the plant kingdom suggests it as an important evolutionary feature for plant speciation and crop domestication. Studies of natural and synthetic polyploids have revealed rapid and dynamic changes in genomic structure and gene expression after polyploid formation. Growing evidence suggests that epigenetic modifications can alter homoeologous gene expression and reprogram gene expression networks, which allows polyploids to establish new cytotypes, grow vigorously and promote adaptation in local environments. Sequence and gene expression changes in polyploids have been well documented and reviewed elsewhere. This review is focused on developmental regulation and epigenetic changes including DNA methylation and histone modifications in polyploids.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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