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Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
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Duan T, Sicard A, Glémin S, Lascoux M. Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication. THE NEW PHYTOLOGIST 2023; 237:339-353. [PMID: 36254103 PMCID: PMC10099941 DOI: 10.1111/nph.18542] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
| | - Adrien Sicard
- Department of Plant BiologySwedish University of Agricultural Sciences750 07UppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
- UMR CNRS 6553 ECOBIOCampus Beaulieu, bât 14a, p.118, CS 7420535042RennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
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In Vitro Polyploid Induction of Highbush Blueberry through De Novo Shoot Organogenesis. PLANTS 2022; 11:plants11182349. [PMID: 36145750 PMCID: PMC9504489 DOI: 10.3390/plants11182349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022]
Abstract
Polyploid induction is of utmost importance in horticultural plants for the development of new varieties with desirable morphological and physiological traits. Polyploidy may occur naturally due to the formation of unreduced gametes or can be artificially induced by doubling the number of chromosomes in somatic cells. In this experiment, a protocol for in vitro polyploid induction of highbush blueberry (Vaccinium corymbosum L.) leaf tissues was studied by using different concentrations of colchicine and oryzalin. Oryzalin was found to be highly toxic to this species, while the adventitious shoot organogenesis media enriched with 25 and 250 µM colchicine was able to induce polyploidization, with significant differences among the treatments used. Higher concentrations of both antimitotic agents led to the browning and death of the leaf tissues. The polyploids obtained showed several morphological differences when compared with the diploid shoots. Flow cytometry analysis was used to confirm the ploidy level of the regenerated shoots, demonstrating that a total of 15 tetraploids and 34 mixoploids were obtained. The stomatal sizes (length and width) of the tetraploids were larger than those of the diploids, but a reduced stomatal density was observed as compared to the controls. These shoots will be acclimatized and grown until they reach the reproductive phase in order to test their potential appeal as new varieties or their use for breeding and genetic improvement.
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Carlson CH, Choi Y, Chan AP, Town CD, Smart LB. Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.). G3 (BETHESDA, MD.) 2022; 12:6472355. [PMID: 35100357 PMCID: PMC9210313 DOI: 10.1093/g3journal/jkab436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.
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Affiliation(s)
- Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Yongwook Choi
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Agnes P Chan
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | | | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
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He J, Yu Z, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of Chrysanthemum nankingense (Asteraceae). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030315. [PMID: 35161296 PMCID: PMC8839533 DOI: 10.3390/plants11030315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 05/09/2023]
Abstract
Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized C. nankingense autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-copia and Ty3-gypsy elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-copia and Ty3-gypsy were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.
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Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus. Int J Mol Sci 2021; 22:ijms22179246. [PMID: 34502153 PMCID: PMC8431428 DOI: 10.3390/ijms22179246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/12/2023] Open
Abstract
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.
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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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A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources. PLANTS 2021; 10:plants10050999. [PMID: 34067689 PMCID: PMC8156078 DOI: 10.3390/plants10050999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/03/2021] [Accepted: 05/12/2021] [Indexed: 01/11/2023]
Abstract
The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicagosativa-coerulea-falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, unreduced gametes combined with parthenogenesis (i.e., apomixis) would enable the cloning of plants through seeds, providing a unique opportunity for the selection of superior genotypes with permanently fixed heterosis. This reproductive strategy has never been detected in the genus Medicago, but features of apomixis, such as restitutional apomeiosis and haploid parthenogenesis, have been reported. By means of an original case study, we demonstrated that sexually tetraploidized plants maintain apomeiosis, but this trait is developmentally independent from parthenogenesis. Alfalfa meiotic mutants producing unreduced egg cells revealed a null or very low capacity for parthenogenesis. The overall achievements reached so far are reviewed and discussed along with the efforts and strategies made for exploiting reproductive mutants that express apomictic elements in alfalfa breeding programs. Although several studies have investigated the cytological mechanisms responsible for 2n gamete formation and the inheritance of this trait, only a very small number of molecular markers and candidate genes putatively linked to unreduced gamete formation have been identified. Furthermore, this scenario has remained almost unchanged over the last two decades. Here, we propose a reverse genetics approach, by exploiting the genomic and transcriptomic resources available in alfalfa. Through a comparison with 9 proteins belonging to Arabidopsis thaliana known for their involvement in 2n gamete production, we identified 47 orthologous genes and evaluated their expression in several tissues, paving the way for novel candidate gene characterization studies. An overall view on strategies suitable to fill the gap between well-established meiotic mutants and next-generation genomic resources is presented and discussed.
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Ardabili GS, Zakaria RA, Zare N, Namazi LG. Induction of Autotetraploidy in Bride Rose Poppy ( Papaver fugax Poir.) by Colchicine Treatment of Seeds and Seedlings. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Giti Sotoudeh Ardabili
- Department of Agronomy and Plant Breeding, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili
| | - Rasool Asghari Zakaria
- Department of Agronomy and Plant Breeding, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili
| | - Nasser Zare
- Department of Agronomy and Plant Breeding, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili
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Song L, Shi JY, Duan SF, Han DY, Li K, Zhang RP, He PY, Han PJ, Wang QM, Bai FY. Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature. Genome Res 2021; 31:622-634. [PMID: 33722936 PMCID: PMC8015850 DOI: 10.1101/gr.262055.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 02/12/2021] [Indexed: 11/25/2022]
Abstract
Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.
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Affiliation(s)
- Liang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Yu He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Yao H, Srivastava S, Swyers N, Han F, Doerge RW, Birchler JA. Inbreeding Depression in Genotypically Matched Diploid and Tetraploid Maize. Front Genet 2020; 11:564928. [PMID: 33329701 PMCID: PMC7734256 DOI: 10.3389/fgene.2020.564928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023] Open
Abstract
The genetic and molecular basis of heterosis has long been studied but without a consensus about mechanism. The opposite effect, inbreeding depression, results from repeated self-pollination and leads to a reduction in vigor. A popular explanation for this reaction is the homozygosis of recessive, slightly deleterious alleles upon inbreeding. However, extensive studies in alfalfa indicated that inbreeding between diploids and autotetraploids was similar despite the fact that homozygosis of alleles would be dramatically different. The availability of tetraploid lines of maize generated directly from various inbred lines provided the opportunity to examine this issue in detail in perfectly matched diploid and tetraploid hybrids and their parallel inbreeding regimes. Identical hybrids at the diploid and tetraploid levels were inbred in triplicate for seven generations. At the conclusion of this regime, F1 hybrids and selected representative generations (S1, S3, S5, S7) were characterized phenotypically in randomized blocks during the same field conditions. Quantitative measures of the multiple generations of inbreeding provided little evidence for a distinction in the decline of vigor between the diploids and the tetraploids. The results suggest that the homozygosis of completely recessive, slightly deleterious alleles is an inadequate hypothesis to explain inbreeding depression in general.
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Affiliation(s)
- Hong Yao
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Sanvesh Srivastava
- Department of Statistics and Actuarial Science, University of Iowa, Iowa City, IA, United States
| | - Nathan Swyers
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Fangpu Han
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Rebecca W Doerge
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, United States
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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Wu M, Ge Y, Xu C, Wang J. Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy. Genes (Basel) 2020; 11:genes11020187. [PMID: 32050732 PMCID: PMC7074301 DOI: 10.3390/genes11020187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/08/2020] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Polyploid plants are more often invasive species than their diploid counterparts. As the invasiveness of a species is often linked to its production of allelopathic compounds, we hypothesize that differences in invasive ability between cytotypes may be due to their different ability to synthesize allelopathic metabolites. We test this using two cytotypes of Solidago canadensis as the model and use integrated metabolome and transcriptome data to resolve the question. Metabolome analysis identified 122 metabolites about flavonoids, phenylpropanoids and terpenoids, of which 57 were differentially accumulated between the two cytotypes. Transcriptome analysis showed that many differentially expressed genes (DEGs) were enriched in ‘biosynthesis of secondary metabolites’, ‘plant hormone signal transduction’, and ‘MAPK signaling’, covering most steps of plant allelopathic metabolite synthesis. Importantly, the differentially accumulated flavonoids, phenylpropanoids and terpenoids were closely correlated with related DEGs. Furthermore, 30 miRNAs were found to be negatively associated with putative targets, and they were thought to be involved in target gene expression regulation. These miRNAs probably play a vital role in the regulation of metabolite synthesis in hexaploid S. canadensis. The two cytotypes of S. canadensis differ in the allelopathic metabolite synthesis and this difference is associated with regulation of expression of a range of genes. These results suggest that changes in gene expression may underlying the increased invasive potential of the polyploidy.
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Shahzad K, Zhang X, Guo L, Qi T, Tang H, Zhang M, Zhang B, Wang H, Qiao X, Feng J, Wu J, Xing C. Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton. BMC Genomics 2020; 21:140. [PMID: 32041531 PMCID: PMC7011360 DOI: 10.1186/s12864-020-6561-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
Background Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. Results Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.
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Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China.
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China.
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14
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Mao Y, Gabel A, Nakel T, Viehöver P, Baum T, Tekleyohans DG, Vo D, Grosse I, Groß-Hardt R. Selective egg cell polyspermy bypasses the triploid block. eLife 2020; 9:e52976. [PMID: 32027307 PMCID: PMC7004562 DOI: 10.7554/elife.52976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/22/2019] [Indexed: 01/21/2023] Open
Abstract
Polyploidization, the increase in genome copies, is considered a major driving force for speciation. We have recently provided the first direct in planta evidence for polyspermy induced polyploidization. Capitalizing on a novel sco1-based polyspermy assay, we here show that polyspermy can selectively polyploidize the egg cell, while rendering the genome size of the ploidy-sensitive central cell unaffected. This unprecedented result indicates that polyspermy can bypass the triploid block, which is an established postzygotic polyploidization barrier. In fact, we here show that most polyspermy-derived seeds are insensitive to the triploid block suppressor admetos. The robustness of polyspermy-derived plants is evidenced by the first transcript profiling of triparental plants and our observation that these idiosyncratic organisms segregate tetraploid offspring within a single generation. Polyspermy-derived triparental plants are thus comparable to triploids recovered from interploidy crosses. Our results expand current polyploidization concepts and have important implications for plant breeding.
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Affiliation(s)
- Yanbo Mao
- Centre for Biomolecular InteractionsUniversity of BremenBremenGermany
| | - Alexander Gabel
- Institute of Computer ScienceMartin Luther University Halle-WittenbergHalleGermany
| | - Thomas Nakel
- Centre for Biomolecular InteractionsUniversity of BremenBremenGermany
| | - Prisca Viehöver
- Faculty of BiologyBielefeld UniversityBielefeldGermany
- Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Thomas Baum
- Centre for Biomolecular InteractionsUniversity of BremenBremenGermany
| | | | - Dieu Vo
- Centre for Biomolecular InteractionsUniversity of BremenBremenGermany
| | - Ivo Grosse
- Institute of Computer ScienceMartin Luther University Halle-WittenbergHalleGermany
| | - Rita Groß-Hardt
- Centre for Biomolecular InteractionsUniversity of BremenBremenGermany
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15
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Van Drunen WE, Husband BC. Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms. THE NEW PHYTOLOGIST 2019; 224:1266-1277. [PMID: 31215649 DOI: 10.1111/nph.15999] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 05/10/2023]
Abstract
Clonal reproduction is thought to facilitate polyploid establishment in the angiosperms, but the evolutionary relationship between polyploidy and clonality has not been thoroughly tested. A perennial life history may confer many of the same advantages, and the relative importance of clonality versus perenniality is unknown. We used phylogenetic comparative analyses of 1751 species to examine associations between polyploidy, clonality, and life history. We test hypotheses of co-evolution by determining the sequence of trait development. Polyploidy is associated with both clonality and perenniality across species, and analyses show that clonality can be an important predictor of polyploidy beyond perenniality. Tests of directionality on our full dataset suggest that polyploidy is more likely to promote clonality or perenniality than vice versa, although there are significant differences in patterns of co-evolution among major angiosperm groups. Our results suggest that polyploidy and clonal reproduction are evolutionarily associated across the angiosperms, even when perenniality is considered, but we find little evidence at the whole-angiosperm level for the hypothesis that clonality promotes polyploidy. However, variation among different clades indicates that polyploidy and clonality are interacting in diverse ways, likely to be due to the variable roles of clonality in their evolutionary histories.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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16
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Washburn JD, McElfresh MJ, Birchler JA. Progressive heterosis in genetically defined tetraploid maize. J Genet Genomics 2019; 46:389-396. [PMID: 31444136 DOI: 10.1016/j.jgg.2019.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 01/24/2019] [Accepted: 02/20/2019] [Indexed: 12/30/2022]
Abstract
Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa, potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated field-based phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally, whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype, its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.
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Affiliation(s)
- Jacob D Washburn
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
| | - Mitchell J McElfresh
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA.
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17
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Ciska M, Hikida R, Masuda K, Moreno Díaz de la Espina S. Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2651-2664. [PMID: 30828723 PMCID: PMC6506774 DOI: 10.1093/jxb/erz102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/20/2019] [Indexed: 05/09/2023]
Abstract
Nuclear matrix constituent proteins (NMCPs), the structural components of the plant lamina, are considered to be the analogues of lamins in plants based on numerous structural and functional similarities. Current phylogenetic knowledge suggests that, in contrast to lamins, which are widely distributed in eukaryotes, NMCPs are taxonomically restricted to Streptophyta. At present, most information about NMCPs comes from angiosperms, and virtually no data are available from more ancestral groups. In angiosperms, the NMCP family comprises two phylogenetic groups, NMCP1 and NMCP2, which evolved from the NMCP1 and NMCP2 progenitor genes. Based on sequence conservation and the presence of NMCP-specific domains, we determined the structure and number of NMCP genes present in different Streptophyta clades. We analysed 91 species of embryophytes and report additional NMCP sequences from mosses, liverworts, clubmosses, horsetail, ferns, gymnosperms, and Charophyta algae. Our results confirm an origin of NMCPs in Charophyta (the earliest diverging group of Streptophyta), resolve the number and structure of NMCPs in the different clades, and propose the emergence of additional NMCP homologues by whole-genome duplication events. Immunofluorescence microscopy demonstrated localization of a basal NMCP from the moss Physcomitrella patens at the nuclear envelope, suggesting a functional conservation for basal and more evolved NMCPs.
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Affiliation(s)
- Malgorzata Ciska
- Cell and Molecular Biology Department, Centre of Biological Researches, CSIC, Ramiro de Maeztu, Madrid, Spain
| | - Riku Hikida
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo Japan
| | - Kiyoshi Masuda
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo Japan
| | - Susana Moreno Díaz de la Espina
- Cell and Molecular Biology Department, Centre of Biological Researches, CSIC, Ramiro de Maeztu, Madrid, Spain
- Correspondence:
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18
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Van Drunen WE, Husband BC. Whole-genome duplication decreases clonal stolon production and genet size in the wild strawberry Fragaria vesca. AMERICAN JOURNAL OF BOTANY 2018; 105:1712-1724. [PMID: 30248174 DOI: 10.1002/ajb2.1159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Clonal reproduction is often associated with polyploidy and is expected to influence polyploid establishment success, but the immediate effects of whole-genome duplication (WGD) on clonal reproduction in autopolyploids are unknown. METHODS We used synthesized neopolyploids to assess the direct effects of WGD on stolon and plantlet production in the wild strawberry Fragaria vesca by (1) comparing absolute clonal investment between diploids and neotetraploids under high and low resource conditions in the greenhouse and (2) determining realized clonal plantlet establishment and genet spatial structure using artificial field populations comprising both cytotypes. KEY RESULTS Neotetraploids produced fewer stolons and plantlets than diploids at slower weekly rates in the greenhouse when resources were high, resulting in lower total investment in clonal reproduction. Low resources led to smaller reductions in clonal biomass for neotetraploids and less pronounced differences between cytotypes. Comparisons between neotetraploids representing 13 independent WGD events and close diploid relatives revealed considerable variation in the response to polyploidization for some clonal traits. Field populations corroborated greenhouse results; neotetraploid genets were smaller than diploid genets, containing 28% fewer stolons and 46% fewer rooted plantlets. CONCLUSIONS WGD significantly decreases the clonal output of neotetraploid F. vesca, which is likely attributable to slower whole-plant growth of the neotetraploids than the diploids. In natural populations, smaller neotetraploid genets could decrease the probability of polyploid establishment in this species. However, variation between separate neopolyploid lines emphasizes that the response of clonal investment to WGD may not be uniform across polyploid origins.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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19
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Liu YJ, Gao SQ, Tang YM, Gong J, Zhang X, Wang YB, Zhang LP, Sun RW, Zhang Q, Chen ZB, Wang X, Guo CJ, Zhang SQ, Zhang FT, Gao JG, Sun H, Yang WB, Wang WW, Zhao CP. Transcriptome analysis of wheat seedling and spike tissues in the hybrid Jingmai 8 uncovered genes involved in heterosis. PLANTA 2018; 247:1307-1321. [PMID: 29504038 DOI: 10.1007/s00425-018-2848-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/12/2018] [Indexed: 05/23/2023]
Abstract
Transcriptome analysis was carried out for wheat seedlings and spikes from hybrid Jingmai 8 and both inbred lines to unravel mechanisms underlying heterosis. Heterosis, known as one of the most successful strategies for increasing crop yield, has been widely exploited in plant breeding systems. Despite its great importance, the molecular mechanism underlying heterosis remains elusive. In the present study, RNA sequencing (RNA-seq) was performed on the seedling and spike tissues of the wheat (Triticum aestivum) hybrid Jingmai 8 (JM8) and its homozygous parents to unravel the underlying mechanisms of wheat heterosis. In total, 1686 and 2334 genes were identified as differentially expressed genes (DEGs) between the hybrid and the two inbred lines in seedling and spike tissues, respectively. Gene Ontology analysis revealed that DEGs from seedling tissues were significantly enriched in processes involved in photosynthesis and carbon fixation, and the majority of these DEGs expressed at a higher level in JM8 compared to both inbred lines. In addition, cell wall biogenesis and protein biosynthesis-related pathways were also significantly represented. These results confirmed that a combination of different pathways could contribute to heterosis. The DEGs between the hybrid and the two inbred progenitors from the spike tissues were significantly enriched in biological processes related to transcription, RNA biosynthesis and molecular function categories related to transcription factor activities. Furthermore, transcription factors such as NAC, ERF, and TIF-IIA were highly expressed in the hybrid JM8. These results may provide valuable insights into the molecular mechanisms underlying wheat heterosis.
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Affiliation(s)
- Yong-Jie Liu
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shi-Qing Gao
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Yi-Miao Tang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jie Gong
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiao Zhang
- Hebei Normal University, Shijiazhuang, 050024, China
| | - Yong-Bo Wang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Li-Ping Zhang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ren-Wei Sun
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Beijing University of Agriculture, Beijing, 100036, China
| | - Quan Zhang
- Shandong Normal University, Jinan, 250014, China
| | - Zhao-Bo Chen
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiang Wang
- Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Sheng-Quan Zhang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Feng-Ting Zhang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian-Gang Gao
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hui Sun
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wei-Bing Yang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wei-Wei Wang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Chang-Ping Zhao
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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20
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Luo Q, Peng M, Zhang X, Lei P, Ji X, Chow W, Meng F, Sun G. Comparative mitochondrial proteomic, physiological, biochemical and ultrastructural profiling reveal factors underpinning salt tolerance in tetraploid black locust (Robinia pseudoacacia L.). BMC Genomics 2017; 18:648. [PMID: 28830360 PMCID: PMC5568289 DOI: 10.1186/s12864-017-4038-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/08/2017] [Indexed: 01/21/2023] Open
Abstract
Background Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia L.) is a polyploid plant and a pioneer tree species due to its wide ranging adaptability to adverse environments. To evaluate the ploidy-dependent differences in leaf mitochondria between diploid and tetraploid black locust under salinity stress, we conducted comparative proteomic, physiological, biochemical and ultrastructural profiling of mitochondria from leaves. Results Mitochondrial proteomic analysis was performed with 2-DE and MALDI-TOF-MS, and the ultrastructure of leaf mitochondria was observed by transmission electron microscopy. According to 2-DE analysis, 66 proteins that responded to salinity stress significantly were identified from diploid and/or tetraploid plants and classified into 9 functional categories. Assays of physiological characters indicated that tetraploids were more tolerant to salinity stress than diploids. The mitochondrial ultrastructure of diploids was damaged more severely under salinity stress than that of tetraploids. Conclusions Tetraploid black locust possessed more tolerance of, and ability to acclimate to, salinity stress than diploids, which may be attributable to the ability to maintain mitochondrial structure and to trigger different expression patterns of mitochondrial proteins during salinity stress. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4038-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiuxiang Luo
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Mu Peng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Xiuli Zhang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Pei Lei
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Ximei Ji
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Wahsoon Chow
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.,Division of Plant Science, Research School of Biology, The Australian National University, ACT, 2601, Australia
| | - Fanjuan Meng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Guanyu Sun
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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21
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Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids. PLoS Genet 2016; 12:e1006197. [PMID: 27467757 PMCID: PMC4965137 DOI: 10.1371/journal.pgen.1006197] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/24/2016] [Indexed: 12/31/2022] Open
Abstract
Heterosis has been widely used in agriculture, but the molecular mechanism for this remains largely elusive. In Arabidopsis hybrids and allopolyploids, increased photosynthetic and metabolic activities are linked to altered expression of circadian clock regulators, including CIRCADIAN CLOCK ASSOCIATED1 (CCA1). It is unknown whether a similar mechanism mediates heterosis in maize hybrids. Here we report that higher levels of carbon fixation and starch accumulation in the maize hybrids are associated with altered temporal gene expression. Two maize CCA1 homologs, ZmCCA1a and ZmCCA1b, are diurnally up-regulated in the hybrids. Expressing ZmCCA1 complements the cca1 mutant phenotype in Arabidopsis, and overexpressing ZmCCA1b disrupts circadian rhythms and biomass heterosis. Furthermore, overexpressing ZmCCA1b in maize reduced chlorophyll content and plant height. Reduced height stems from reduced node elongation but not total node number in both greenhouse and field conditions. Phenotypes are less severe in the field than in the greenhouse, suggesting that enhanced light and/or metabolic activities in the field can compensate for altered circadian regulation in growth vigor. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis reveals a temporal shift of ZmCCA1-binding targets to the early morning in the hybrids, suggesting that activation of morning-phased genes in the hybrids promotes photosynthesis and growth vigor. This temporal shift of ZmCCA1-binding targets correlated with nonadditive and additive gene expression in early and late stages of seedling development. These results could guide breeding better hybrid crops to meet the growing demand in food and bioenergy. All corn in the USA is grown as hybrids, which grow more vigorously and produce higher yield than their parents, a phenomenon known as heterosis. The molecular basis for heterosis remains elusive. Heterosis is predicted to arise from allelic interactions between parental genomes, leading to altered regulatory networks that promote the growth and fitness of hybrids. One such regulator is the circadian clock, which is functionally conserved in Arabidopsis and maize. Disrupting corn CCA1 expression reduces growth vigor. In corn hybrids, CCA1 proteins target thousands of output genes early in the morning, as if the hybrids wake up early to promote photosynthesis, starch metabolism and biomass accumulation. This early acting mechanism could guide breeding and selection of high-yield hybrids.
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22
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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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23
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Dahal D, Newton KJ, Mooney BP. Quantitative Proteomics of Zea mays Hybrids Exhibiting Different Levels of Heterosis. J Proteome Res 2016; 15:2445-54. [DOI: 10.1021/acs.jproteome.5b01120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Diwakar Dahal
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kathleen J. Newton
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Brian P. Mooney
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
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24
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Fasano C, Diretto G, Aversano R, D'Agostino N, Di Matteo A, Frusciante L, Giuliano G, Carputo D. Transcriptome and metabolome of synthetic Solanum autotetraploids reveal key genomic stress events following polyploidization. THE NEW PHYTOLOGIST 2016; 210:1382-94. [PMID: 26915816 DOI: 10.1111/nph.13878] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/06/2015] [Indexed: 05/19/2023]
Abstract
Polyploids are generally classified as autopolyploids, derived from a single species, and allopolyploids, arising from interspecific hybridization. The former represent ideal materials with which to study the consequences of genome doubling and ascertain whether there are molecular and functional rules operating following polyploidization events. To investigate whether the effects of autopolyploidization are common to different species, or if species-specific or stochastic events are prevalent, we performed a comprehensive transcriptomic and metabolomic characterization of diploids and autotetraploids of Solanum commersonii and Solanum bulbocastanum. Autopolyploidization remodelled the transcriptome and the metabolome of both species. In S. commersonii, differentially expressed genes (DEGs) were highly enriched in pericentromeric regions. Most changes were stochastic, suggesting a strong genotypic response. However, a set of robustly regulated transcripts and metabolites was also detected, including purine bases and nucleosides, which are likely to underlie a common response to polyploidization. We hypothesize that autopolyploidization results in nucleotide pool imbalance, which in turn triggers a genomic shock responsible for the stochastic events observed. The more extensive genomic stress and the higher number of stochastic events observed in S. commersonii with respect to S. bulbocastanum could be the result of the higher nucleoside depletion observed in this species.
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Affiliation(s)
- Carlo Fasano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome, 00123, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Nunzio D'Agostino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per l'orticoltura (CRA-ORT), via dei Cavalleggeri 25, Pontecagnano, Salerno, 84098, Italy
| | - Antonio Di Matteo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome, 00123, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
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Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation. G3-GENES GENOMES GENETICS 2016; 6:925-38. [PMID: 26858330 PMCID: PMC4825662 DOI: 10.1534/g3.115.026021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16) Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32) hybrids, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture.
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Gu AX, Zhao JJ, Li LM, Wang YH, Zhao YJ, Hua F, Xu YC, Shen SX. Analyses of phenotype and ARGOS and ASY1 expression in a ploidy Chinese cabbage series derived from one haploid. BREEDING SCIENCE 2016; 66:161-8. [PMID: 27162487 PMCID: PMC4784993 DOI: 10.1270/jsbbs.66.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 09/28/2015] [Indexed: 05/20/2023]
Abstract
The aim of this research was to improve our understanding of how ploidy level influences phenotype and gene expression in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Haploid plants (2n = 10) was induced by 0.2% colchicine to produce diploid (2n = 20) and tetraploid plants (2n = 40). The aneuploid (2n = 24) was also obtained by hybridization between diploid plants as the female and tetraploid plants. The ploidy levels of all plants were identified through chromosome counts and flow cytometry. Leaves and petals became larger as the ploidy level increased from haploid to diploid, and from aneuploid to tetraploid. Similarly, expression of ARGOS was regulated by genome size, increasing in parallel with the level of ploidy. Among the four ploidy types, expression was stronger in the floral buds than in the leaves. Expression by ASY1 also differed according to ploidy level, being highest in diploid plants, followed in order by tetraploids. Expression was similar between haploids and aneuploids at two stages-prior to and after meiosis-but was higher in the haploids during meiosis. When buds were compared within the same ploidy type at different stages, ASY1 expression was obviously higher during meiosis than either before or after. Our study demonstrated the generation and phenotype of a ploidy Chinese cabbage series derived from one haploid. Expression of genes ARGOS and ASY1 were modulated by genome size in this ploidy series, and the regulated patterns of the two genes was different.
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Affiliation(s)
- Ai Xia Gu
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Jian Jun Zhao
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Li Min Li
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Yan Hua Wang
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Yu Jing Zhao
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Fan Hua
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Yuan Chao Xu
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
| | - Shu Xing Shen
- College of Horticulture, Agricultural University of Hebei,
No. 289, Lingyusi Road, Baoding 071001,
China
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Wang T, Sui Z, Liu X, Li Y, Li H, Xing J, Song F, Zhang Y, Sun Q, Ni Z. Ectopic expression of a maize hybrid up-regulated gene, ErbB-3 binding Protein 1 (ZmEBP1), increases organ size by promoting cell proliferation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 243:23-34. [PMID: 26795148 DOI: 10.1016/j.plantsci.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 05/21/2023]
Abstract
The alteration of gene expression in hybrids may be an important factor promoting phenotypic variation and plasticity. To provide insight into the underlying molecular basis of maize heterosis in terms of the kernel number per ear, we established DGE profiles for the immature ears of maize hybrid Zong3/87-1 and its parental lines at the floral organ differentiation stage. Among 4,337 identified differentially expressed genes, 4,021 (92%) exhibited nonadditive expression patterns in the hybrid. Notably, the maize homolog of Arabidopsis EBP1, designated ZmEBP1, displayed an overdominant expression pattern in the Zong3/87-1 hybrid. Moreover, the results of qRT-PCR revealed that the ZmEBP1 gene was upregulated in the immature ears of the reciprocal hybrids Zong3/87-1 and 87-1/Zong3 at different developmental stages. Additionally, ectopic expression of ZmEBP1 in Arabidopsis increased organ size, which was mainly attributed to an increase in cell numbers, rather than cell size. Considering all of these findings together, we speculate that upregulation of ZmEBP1 in maize hybrids may accelerate cell proliferation and promote ear development.
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Affiliation(s)
- Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Yangyang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Hongjian Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Fangwei Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Yirong Zhang
- National Maize Improvement Centre of China, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China.
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del Pozo JC, Ramirez-Parra E. Whole genome duplications in plants: an overview from Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6991-7003. [PMID: 26417017 DOI: 10.1093/jxb/erv432] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Polyploidy is a common event in plants that involves the acquisition of more than two complete sets of chromosomes. Allopolyploidy originates from interspecies hybrids while autopolyploidy originates from intraspecies whole genome duplication (WGD) events. In spite of inconveniences derived from chromosomic rearrangement during polyploidization, natural plant polyploids species often exhibit improved growth vigour and adaptation to adverse environments, conferring evolutionary advantages. These advantages have also been incorporated into crop breeding programmes. Many tetraploid crops show increased stress tolerance, although the molecular mechanisms underlying these different adaptation abilities are poorly known. Understanding the physiological, cellular, and molecular mechanisms coupled to WGD, in both allo- and autopolyploidy, is a major challenge. Over the last few years, several studies, many of them in Arabidopsis, are shedding light on the basis of genetic, genomic, and epigenomic changes linked to WGD. In this review we summarize and discuss the latest advances made in Arabidopsis polyploidy, but also in other agronomic plant species.
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Affiliation(s)
- Juan Carlos del Pozo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Elena Ramirez-Parra
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
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29
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Li AL, Geng SF, Zhang LQ, Liu DC, Mao L. Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat. MOLECULAR PLANT 2015; 8:847-59. [PMID: 25747845 DOI: 10.1016/j.molp.2015.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/13/2015] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat.
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Affiliation(s)
- Ai-li Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai-Feng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lian-quan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Deng-cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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30
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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: 121] [Impact Index Per Article: 13.4] [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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31
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Tan FQ, Tu H, Liang WJ, Long JM, Wu XM, Zhang HY, Guo WW. Comparative metabolic and transcriptional analysis of a doubled diploid and its diploid citrus rootstock (C. junos cv. Ziyang xiangcheng) suggests its potential value for stress resistance improvement. BMC PLANT BIOLOGY 2015; 15:89. [PMID: 25848687 PMCID: PMC4374211 DOI: 10.1186/s12870-015-0450-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/05/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Polyploidy has often been considered to confer plants a better adaptation to environmental stresses. Tetraploid citrus rootstocks are expected to have stronger stress tolerance than diploid. Plenty of doubled diploid citrus plants were exploited from diploid species for citrus rootstock improvement. However, limited metabolic and molecular information related to tetraploidization is currently available at a systemic biological level. This study aimed to evaluate the occurrence and extent of metabolic and transcriptional changes induced by tetraploidization in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka), which is a special citrus germplasm native to China and widely used as an iron deficiency tolerant citrus rootstock. RESULTS Doubled diploid Ziyang xiangcheng has typical morphological and anatomical features such as shorter plant height, larger and thicker leaves, bigger stomata and lower stomatal density, compared to its diploid parent. GC-MS (Gas chromatography coupled to mass spectrometry) analysis revealed that tetraploidization has an activation effect on the accumulation of primary metabolites in leaves; many stress-related metabolites such as sucrose, proline and γ-aminobutyric acid (GABA) was remarkably up-regulated in doubled diploid. However, LC-QTOF-MS (Liquid chromatography quadrupole time-of-flight mass spectrometry) analysis demonstrated that tetraploidization has an inhibition effect on the accumulation of secondary metabolites in leaves; all the 33 flavones were down-regulated while all the 6 flavanones were up-regulated in 4x. By RNA-seq analysis, only 212 genes (0.8% of detected genes) are found significantly differentially expressed between 2x and 4x leaves. Notably, those genes were highly related to stress-response functions, including responses to salt stress, water and abscisic acid. Interestingly, the transcriptional divergence could not explain the metabolic changes, probably due to post-transcriptional regulation. CONCLUSION Taken together, tetraploidization induced considerable changes in leaf primary and secondary metabolite accumulation in Ziyang xiangcheng. However, the effect of tetraploidization on transcriptome is limited. Compared to diploid, higher expression level of stress related genes and higher content of stress related metabolites in doubled diploid could be beneficial for its stress tolerance.
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Affiliation(s)
- Feng-Quan Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hong Tu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wu-Jun Liang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hong-Yan Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
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32
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Wang H, Fang Y, Wang L, Zhu W, Ji H, Wang H, Xu S, Sima Y. Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling. Sci Rep 2015; 5:8750. [PMID: 25736158 PMCID: PMC4348626 DOI: 10.1038/srep08750] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/02/2015] [Indexed: 11/09/2022] Open
Abstract
Heterosis is a concern to all breeders, but the mechanism of heterosis remains unknown. In F1 organisms, genetic material is inherited from the two parents and theoretically, heterosis might be caused by differences in gene expression or modification. Differential gene expression was analyzed in hybrids and parents in Bombyx mori. The results showed that there were significant changes in gene expression in the fat body involving biological regulation, cellular and metabolic processes. Consistent trends in expression patterns covering different hybrid combinations were seen in 74 genes. Moreover, these differential gene expression patterns included overdominance, dominance, and additive effects. By correlating these patterns with economic traits, a potential relationship was found. Differential gene expression was seen in different cross combinations and in different sexes. In addition, a regulatory mechanism involving metabolism and ErbB signaling pathways was also found, suggesting that such a network might also be related to heterosis in Bombyx mori. Together, our data provide a comprehensive overview and useful resource for transcriptional analysis of heterosis of Bombyx mori.
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Affiliation(s)
- Hua Wang
- 1] Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China [2] Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yan Fang
- 1] Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China [2] Department of Immunology, Nankai University School of Medicine, Tianjin 300071, China
| | - Lipeng Wang
- Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Wenjuan Zhu
- Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Haipeng Ji
- Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Haiying Wang
- Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Shiqing Xu
- 1] Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China [2] National Engineering Laboratory for Modern Silk, Soochow University, Suzhou 215123, China
| | - Yanghu Sima
- 1] Department of Applied Biology, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China [2] National Engineering Laboratory for Modern Silk, Soochow University, Suzhou 215123, China
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33
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Leder EH, McCairns RJS, Leinonen T, Cano JM, Viitaniemi HM, Nikinmaa M, Primmer CR, Merilä J. The evolution and adaptive potential of transcriptional variation in sticklebacks--signatures of selection and widespread heritability. Mol Biol Evol 2015; 32:674-89. [PMID: 25429004 PMCID: PMC4327155 DOI: 10.1093/molbev/msu328] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Evidence implicating differential gene expression as a significant driver of evolutionary novelty continues to accumulate, but our understanding of the underlying sources of variation in expression, both environmental and genetic, is wanting. Heritability in particular may be underestimated when inferred from genetic mapping studies, the predominant "genetical genomics" approach to the study of expression variation. Such uncertainty represents a fundamental limitation to testing for adaptive evolution at the transcriptomic level. By studying the inheritance of expression levels in 10,495 genes (10,527 splice variants) in a threespine stickleback pedigree consisting of 563 individuals, half of which were subjected to a thermal treatment, we show that 74-98% of transcripts exhibit significant additive genetic variance. Dominance variance is also prevalent (41-99% of transcripts), and genetic sources of variation seem to play a more significant role in expression variance in the liver than a key environmental variable, temperature. Among-population comparisons suggest that the majority of differential expression in the liver is likely due to neutral divergence; however, we also show that signatures of directional selection may be more prevalent than those of stabilizing selection. This predominantly aligns with the neutral model of evolution for gene expression but also suggests that natural selection may still act on transcriptional variation in the wild. As genetic variation both within- and among-populations ultimately defines adaptive potential, these results indicate that broad adaptive potential may be found within the transcriptome.
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Affiliation(s)
- Erica H Leder
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - R J Scott McCairns
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Tuomas Leinonen
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - José M Cano
- Research Unit of Biodiversity (UO-CSIC-PA), University of Oviedo, Mieres, Spain
| | - Heidi M Viitaniemi
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Mikko Nikinmaa
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Craig R Primmer
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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del Pozo JC, Ramirez-Parra E. Deciphering the molecular bases for drought tolerance in Arabidopsis autotetraploids. PLANT, CELL & ENVIRONMENT 2014; 37:2722-37. [PMID: 24716850 DOI: 10.1111/pce.12344] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/29/2014] [Indexed: 05/21/2023]
Abstract
Whole genome duplication (autopolyploidy) is common in many plant species and often leads to better adaptation to adverse environmental conditions. However, little is known about the physiological and molecular mechanisms underlying these adaptations. Drought is one of the major environmental conditions limiting plant growth and development. Here, we report that, in Arabidopsis thaliana, tetraploidy promotes alterations in cell proliferation and organ size in a tissue-dependent manner. Furthermore, it potentiates plant tolerance to salt and drought stresses and decreases transpiration rate, likely through controlling stomata density and closure, abscisic acid (ABA) signalling and reactive oxygen species (ROS) homeostasis. Our transcriptomic analyses revealed that tetraploidy mainly regulates the expression of genes involved in redox homeostasis and ABA and stress response. Taken together, our data have shed light on the molecular basis associated with stress tolerance in autopolyploid plants.
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Affiliation(s)
- Juan C del Pozo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, 28223, Spain
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35
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Wu J, Shahid MQ, Guo H, Yin W, Chen Z, Wang L, Liu X, Lu Y. Comparative cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice. PLANT REPRODUCTION 2014; 27:181-96. [PMID: 25262386 DOI: 10.1007/s00497-014-0250-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 09/19/2014] [Indexed: 05/18/2023]
Abstract
Autotetraploid rice has greater genetic variation and higher vigor than diploid rice, but low pollen fertility is one of the major reasons for low yield of autotetraploid rice. Very little is known about the molecular mechanisms of low pollen fertility of autotetraploid rice. In this study, cytological observations and microarray analysis were used to assess the genetic variation during pollen development in autotetraploid and diploid rice. Many abnormal chromosome behaviors, such as mutivalents, lagged chromosomes, asynchronous cell division, and so on, were found during meiosis in autotetraploid. Microsporogenesis and microgametogenesis in autotetraploid rice was similar to diploid rice, but many different kinds of abnormalities, including microspores degeneration, multi-aperture, and abnormal cell walls, were found in autotetraploid rice. Compared with diploid rice, a total of 1,251 genes were differentially expressed in autotetraploid rice in pollen transcriptome, among them 1,011 and 240 genes were up-regulated and down-regulated, respectively. 124 and 6 genes were co-up-regulated and co-down-regulated during three pollen development stages, respectively. These results suggest that polyploidy induced up-regulation for most of the genes during pollen development. Quantitative RT-PCR was done to validate 12 differentially expressed genes selected from functional categories based on the gene ontology analysis. These stably expressed genes not only related to the pollen development genes, but also involved in cell metabolism, cell physiology, binding, catalytic activity, molecular transducer activity, and transcription regulator activity. The present study suggests that differential expression of some key genes may lead to complex gene regulation and abnormal pollen development in autotetraploid rice.
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Affiliation(s)
- Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
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Xu E, Fan G, Niu S, Zhao Z, Deng M, Dong Y. Transcriptome-wide profiling and expression analysis of diploid and autotetraploid Paulownia tomentosa × Paulownia fortunei under drought stress. PLoS One 2014; 9:e113313. [PMID: 25405758 PMCID: PMC4236183 DOI: 10.1371/journal.pone.0113313] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/22/2014] [Indexed: 12/23/2022] Open
Abstract
Paulownia is a fast-growing deciduous hardwood species native to China, which has high ecological and economic value. In an earlier study, we reported ploidy-dependent differences in Paulownia drought tolerance by the microscopic observations of the leaves. Autotetraploid Paulownia has a higher resistance to drought stress than their diploid relatives. In order to obtain genetic information on molecular mechanisms responses of Paulownia plants to drought, Illumina/Solexa Genome sequencing platform was used to de novo assemble the transcriptomes of leaves from diploid and autotetraploid Paulownia tomentosa × Paulownia fortunei seedlings (PTF2 and PTF4 respectively) grown under control conditions and under drought stress and obtained 98,671 nonredundant unigenes. A comparative transcriptome analysis revealed that hundreds of unigenes were predicted to be involved mainly in ROS-scavenging system, amino acid and carbohydrate metabolism, plant hormone biosynthesis and signal transduction, while these unigenes exhibited differential transcript alteration of the two accessions. This study provides a comprehensive map of how P. tomentosa × P. fortunei responds to drought stress at physiological and molecular levels, which may help in understanding the mechanisms involve in water-deficit response and will be useful for further study of drought tolerance in woody plants.
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Affiliation(s)
- Enkai Xu
- Institute of Paulownia, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- College of Forestry, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- College of Forestry, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- * E-mail:
| | - Suyan Niu
- Institute of Paulownia, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- College of Forestry, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- College of Forestry, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- College of Forestry, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
- College of Forestry, Henan Agricultural University, Jinshui Area, Zhengzhou, Henan, P.R. China
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Ding H, Qin C, Luo X, Li L, Chen Z, Liu H, Gao J, Lin H, Shen Y, Zhao M, Lübberstedt T, Zhang Z, Pan G. Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. Int J Mol Sci 2014; 15:13892-915. [PMID: 25116687 PMCID: PMC4159830 DOI: 10.3390/ijms150813892] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022] Open
Abstract
Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosis. To determine the parental contributions and their regulation during maize ear-development-genesis, we analyzed genome-wide digital gene expression profiles in two maize elite inbred lines (B73 and Mo17) and their F1 hybrid using deep sequencing technology. Our analysis revealed 17,128 genes expressed in these three genotypes and 22,789 genes expressed collectively in the present study. Approximately 38% of the genes were differentially expressed in early maize ear inflorescences from heterotic cross, including many transcription factor genes and some presence/absence variations (PAVs) genes, and exhibited multiple modes of gene action. These different genes showing differential expression patterns were mainly enriched in five cellular component categories (organelle, cell, cell part, organelle part and macromolecular complex), five molecular function categories (structural molecule activity, binding, transporter activity, nucleic acid binding transcription factor activity and catalytic activity), and eight biological process categories (cellular process, metabolic process, biological regulation, regulation of biological process, establishment of localization, cellular component organization or biogenesis, response to stimulus and localization). Additionally, a significant number of genes were expressed in only one inbred line or absent in both inbred lines. Comparison of the differences of modes of gene action between previous studies and the present study revealed only a small number of different genes had the same modes of gene action in both maize seedlings and ear inflorescences. This might be an indication that in different tissues or developmental stages, different global expression patterns prevail, which might nevertheless be related to heterosis. Our results support the hypotheses that multiple molecular mechanisms (dominance and overdominance modes) contribute to heterosis.
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Affiliation(s)
- Haiping Ding
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China; E-Mail:
| | - Xirong Luo
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China; E-Mail:
| | - Lujiang Li
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Zhe Chen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Jian Gao
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Maojun Zhao
- Life Science College, Sichuan Agricultural University, Ya’an 625014, China; E-Mail:
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; E-Mail:
| | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Authors to whom correspondence should be addressed; E-Mails: (Z.Z.); (G.P.); Tel.: +86-28-8629-0917 (G.P.); Fax: +86-28-8629-0916 (G.P.)
| | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Authors to whom correspondence should be addressed; E-Mails: (Z.Z.); (G.P.); Tel.: +86-28-8629-0917 (G.P.); Fax: +86-28-8629-0916 (G.P.)
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Birchler JA. Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 2014; 123:459-69. [DOI: 10.1007/s00412-014-0478-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
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Washburn JD, Birchler JA. Polyploids as a "model system" for the study of heterosis. PLANT REPRODUCTION 2014; 27:1-5. [PMID: 24202960 DOI: 10.1007/s00497-013-0237-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 10/28/2013] [Indexed: 06/02/2023]
Abstract
Heterosis research over the past century has focused primarily on diploid plants and animals. This is despite the fact that most heterotic organisms contain polyploid events in their recent and/or ancient past and various important crop species are heterotic polyploids. We present an argument for the study of heterosis within polyploid systems and give examples of how their study can improve current hypotheses and generate new ones. Polyploid systems allow experiments not possible in diploids but the insights gained must be incorporated into models to explain heterosis at all levels.
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Affiliation(s)
- Jacob D Washburn
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
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Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B. Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Mol Biol Evol 2014; 31:1066-76. [PMID: 24577842 PMCID: PMC3995341 DOI: 10.1093/molbev/msu085] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed “transcriptomic shock.” To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis-factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of “whole genome doubling” has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.
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Affiliation(s)
- Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Donoghue MT, Fort A, Clifton R, Zhang X, McKeown PC, Voigt-Zielinksi M, Borevitz JO, Spillane C. C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants. DNA Res 2013; 21:141-51. [PMID: 24212467 PMCID: PMC3989486 DOI: 10.1093/dnares/dst046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Triploid F1 hybrids generated via reciprocal interploidy crosses between genetically distinct parental plants can display parent-of-origin effects on gene expression or phenotypes. Reciprocal triploid F1 isogenic plants generated from interploidy crosses in the same genetic background allow investigation on parent-of-origin-specific (parental) genome-dosage effects without confounding effects of hybridity involving heterozygous mutations. Whole-genome transcriptome profiling was conducted on reciprocal F1 isogenic triploid (3x) seedlings of A. thaliana. The genetically identical reciprocal 3x genotypes had either an excess of maternally inherited 3x(m) or paternally inherited 3x(p) genomes. We identify a major parent-of-origin-dependent genome-dosage effect on transcript levels, whereby 602 genes exhibit differential expression between the reciprocal F1 triploids. In addition, using methylation-sensitive DNA tiling arrays, constitutive and polymorphic CG DNA methylation patterns at CCGG sites were analysed, which revealed that paternal-excess F1 triploid seedling C(m)CGG sites are overall hypermethylated. However, no correlation exists between C(m)CGG methylation polymorphisms and transcriptome dysregulation between the isogenic reciprocal F1 triploids. Overall, our study indicates that parental genome-dosage effects on the transcriptome levels occur in paternal-excess triploids, which are independent of C(m)CGG methylation polymorphisms. Such findings have implications for understanding parental effects and genome-dosage effects on gene expression and phenotypes in polyploid plants.
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Affiliation(s)
- Mark T.A. Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Rachel Clifton
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Xu Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - M.L. Voigt-Zielinksi
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Justin O. Borevitz
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
- To whom correspondence should be addressed: E-mail:
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Physiological and proteomic responses of diploid and tetraploid black locust (Robinia pseudoacacia L.) subjected to salt stress. Int J Mol Sci 2013; 14:20299-325. [PMID: 24129170 PMCID: PMC3821616 DOI: 10.3390/ijms141020299] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/31/2013] [Accepted: 09/09/2013] [Indexed: 12/16/2022] Open
Abstract
Tetraploid black locust (Robinia pseudoacacia L.) is adaptable to salt stress. Here, we compared morphological, physiological, ultrastructural, and proteomic traits of leaves in tetraploid black locust and its diploid relatives under salt stress. The results showed that diploid (2×) plants suffered from greater negative effects than those of tetraploid (4×) plants. After salt treatment, plant growth was inhibited, photosynthesis was reduced, reactive oxygen species, malondialdehyde content, and relative electrolyte leakage increased, and defense-related enzyme activities decreased in 2× compared to those in 4×. In addition, salt stress resulted in distorted chloroplasts, swollen thylakoid membranes, accumulation of plastoglobules, and increased starch grains in 2× compared to those in 4×. However, 4× developed diverse responses under salt stress. A comparative proteomic analysis revealed that 41 and 37 proteins were differentially expressed in 2× and 4×, respectively. These proteins were mainly involved in photosynthesis, stress and defense, energy, metabolism, transcription/translation, and transportation. Distinct patterns of protein changes between 2× and 4× were analyzed. Collectively, our results suggest that the plants showed significantly different responses to salt stress based on ploidy level of the plant. The 4× possessed a better salt protection mechanism than that of 2×, suggesting salt tolerance in the polyploid plant.
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Chen ZJ. Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet 2013; 14:471-82. [PMID: 23752794 DOI: 10.1038/nrg3503] [Citation(s) in RCA: 344] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Heterosis, also known as hybrid vigour, is widespread in plants and animals, but the molecular bases for this phenomenon remain elusive. Recent studies in hybrids and allopolyploids using transcriptomic, proteomic, metabolomic, epigenomic and systems biology approaches have provided new insights. Emerging genomic and epigenetic perspectives suggest that heterosis arises from allelic interactions between parental genomes, leading to altered programming of genes that promote the growth, stress tolerance and fitness of hybrids. For example, epigenetic modifications of key regulatory genes in hybrids and allopolyploids can alter complex regulatory networks of physiology and metabolism, thus modulating biomass and leading to heterosis. The conceptual advances could help to improve plant and animal productivity through the manipulation of heterosis.
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Affiliation(s)
- Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA.
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Tayalé A, Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 2013; 140:79-96. [PMID: 23751271 DOI: 10.1159/000351318] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative 'diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.
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Affiliation(s)
- A Tayalé
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Sanetomo R, Hosaka K. Pollen transcriptome analysis of Solanum tuberosum (2n = 4x = 48), S. demissum (2n = 6x = 72), and their reciprocal F1 hybrids. PLANT CELL REPORTS 2013; 32:623-636. [PMID: 23430172 DOI: 10.1007/s00299-013-1395-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/23/2013] [Accepted: 02/04/2013] [Indexed: 06/01/2023]
Abstract
Pollen mRNAs were different in reciprocal F 1 hybrids, which were probably caused by a cytoplasm-nuclear chromosomal genes interaction. We have found reciprocal differences in crossability between F1 hybrids of Solanum tuberosum (T) and a Mexican wild potato species S. demissum (D). When the reciprocal hybrids were crossed as pollen parents with S. demissum, a significantly higher berry-setting rate was obtained in TD compared with DT. In this study, we performed a whole-genome transcript analysis of the pollen mRNA using a high-throughput sequencer. We obtained 12.6 billion bases that were aligned into 13,020 transcripts with 9,366 loci. All possible genetic modes were observed between the parents and their progeny, where over-dominance and under-recessive types were relatively frequent (15.7 and 15.3 %, respectively). We found that 59.1 % of transcripts were more abundant in TD and over fourfold higher transcription levels were found in 66 TD transcripts and three DT transcripts. A higher proportion of over-dominance and a lower proportion of under-recessive transcription types were also observed in TD. The percentage contributions of multiple transcripts at the same locus varied greatly and were transcribed differently between species. In the new allelic combinations created by hybridization, approximately three-fourth of the transcripts had intermediate percentage contributions between the parents but no differential transcription patterns were apparent between the reciprocal hybrids. A broad spectrum of functionally different nuclear genes was over-represented in TD pollen, some of which were directly related to pollen behavior. Since TD and DT pollen had the same composition of nuclear genes, a cytoplasm-nuclear chromosomal genes interaction is suggested for the cause of transcriptional and phenotypic differences between reciprocal hybrids.
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Affiliation(s)
- Rena Sanetomo
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido, 082-0081, Japan
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Allario T, Brumos J, Colmenero-Flores JM, Iglesias DJ, Pina JA, Navarro L, Talon M, Ollitrault P, Morillon R. Tetraploid Rangpur lime rootstock increases drought tolerance via enhanced constitutive root abscisic acid production. PLANT, CELL & ENVIRONMENT 2013; 36:856-68. [PMID: 23050986 DOI: 10.1111/pce.12021] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Whole-genome duplication, or polyploidy, is common in many plant species and often leads to better adaptation to adverse environmental condition. However, little is known about the physiological and molecular determinants underlying adaptation. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological experiments to study root-shoot communication associated with gene expression studies in roots and leaves were performed. V/4xRL was much more tolerant to water deficit than V/2xRL. Gene expression analysis in leaves and roots showed that more genes related to the response to water stress were differentially expressed in V/2xRL than in V/4xRL. Prior to the stress, when comparing V/4xRL to V/2xRL, V/4xRL leaves had lower stomatal conductance and greater abscisic acid (ABA) content. In roots, ABA content was higher in V/4xRL and was associated to a greater expression of drought responsive genes, including CsNCED1, a pivotal regulatory gene of ABA biosynthesis. We conclude that tetraploidy modifies the expression of genes in Rangpur lime citrus roots to regulate long-distance ABA signalling and adaptation to stress.
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Affiliation(s)
- Thierry Allario
- Centre de Coopération Internationale en Recherche Agronomique pour Développement, UMR Amélioration Génétique et Adaptation des Plantes
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Reciprocal cross differences in Drosophila melanogaster longevity: an evidence for non-genomic effects in heterosis phenomenon? Biogerontology 2013; 14:153-63. [PMID: 23529279 DOI: 10.1007/s10522-013-9419-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/21/2013] [Indexed: 12/20/2022]
Abstract
Reciprocal cross effects (i.e., differences between reciprocal hybrids that are developed by reversing the strains from which the dam and the sire are taken) are commonly used as a measure of sex-linkage or maternal effects. However, the papers reporting parental effects on life span of experimental animals are scarce. In order to investigate the potential of parent-of-origin effects for the longevity of hybrids, we determined the life spans of the inbred lines of Drosophila melanogaster [Oregon-R (OR), Canton-S (CS) and Uman (Um)] that differ significantly in longevity, as well as the life span of the progeny from the reciprocal crosses among them. The hybridization caused the increase in both flies' mean and maximum life span mainly shifting the survival curves upward proportionally at all ages. This resulted in the reduction in the Gompertz intercept (frailty) whereas the Gompertz slope (the rate of aging) was predominantly unchanged. Better-parent heterosis was observed in hybrids between OR and Um inbred lines and the extent of heterosis was more pronounced in hybrids between CS and Um inbred lines if long-lived parent was used as the female parent, and short-lived parent was used as the male parent in the crossing scheme. Such discrepancy in life span between reciprocal crosses may indicate that non-chromosomal factors are significantly contributing to a heterotic response. Our data are in line with the previous reports suggesting the involvement of non-genomic factors, particularly epigenetic events attributed to hybridization, in the manifestation of heterosis.
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Madlung A. Polyploidy and its effect on evolutionary success: old questions revisited with new tools. Heredity (Edinb) 2013; 110:99-104. [PMID: 23149459 PMCID: PMC3554449 DOI: 10.1038/hdy.2012.79] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 11/09/2022] Open
Abstract
Polyploidy, the condition of possessing more than two complete genomes in a cell, has intrigued biologists for almost a century. Polyploidy is found in many plants and some animal species and today we know that polyploidy has had a role in the evolution of all angiosperms. Despite its widespread occurrence, the direct effect of polyploidy on evolutionary success of a species is still largely unknown. Over the years many attractive hypotheses have been proposed in an attempt to assign functionality to the increased content of a duplicated genome. Among these hypotheses are the proposal that genome doubling confers distinct advantages to a polyploid and that these advantages allow polyploids to thrive in environments that pose challenges to the polyploid's diploid progenitors. This article revisits these long-standing questions and explores how the integration of recent genomic developments with ecological, physiological and evolutionary perspectives has contributed to addressing unresolved problems about the role of polyploidy. Although unsatisfactory, the current conclusion has to be that despite significant progress, there still isn't enough information to unequivocally answer many unresolved questions about cause and effect of polyploidy on evolutionary success of a species. There is, however, reason to believe that the increasingly integrative approaches discussed here should allow us in the future to make more direct connections between the effects of polyploidy on the genome and the responses this condition elicits from the organism living in its natural environment.
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Affiliation(s)
- A Madlung
- Department of Biology, University of Puget Sound, Tacoma, WA 98416, USA.
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Aversano R, Caruso I, Aronne G, Micco VD, Scognamiglio N, Carputo D. Stochastic changes affect Solanum wild species following autopolyploidization. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:625-35. [PMID: 23307917 PMCID: PMC3542052 DOI: 10.1093/jxb/ers357] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Polyploidy is very common within angiosperms, and several studies are in progress to ascertain the effects of early polyploidization at the molecular, physiological, and phenotypic level. Extensive studies are available only in synthetic allopolyploids. By contrast, less is known about the consequences of autopolyploidization. The current study aimed to assess the occurrence and extent of genetic, epigenetic, and anatomical changes occurring after oryzaline-induced polyploidization of Solanum commersonii Dunal and Solanum bulbocastanum Dunal, two diploid (2n=2×=24) potato species widely used in breeding programmes. Microsatellite analysis showed no polymorphisms between synthetic tetraploids and diploid progenitors. By contrast, analysis of DNA methylation levels indicated that subtle alterations at CG and CHG sites were present in tetraploids of both species. However, no change occurred concurrently in all tetraploids analysed with respect to their diploid parent, revealing a stochastic trend in the changes observed. The morpho-anatomical consequences of polyploidization were studied in leaf main veins and stomata. With only a few exceptions, analyses showed no clear superiority of tetraploids in terms of leaf thickness and area, vessel number, lumen size and vessel wall thickness, stomata pore length and width, guard cell width, and stomatal density compared with their diploid progenitors. These results are consistent with the hypothesis that there are no traits systematically associated with autopolyploidy.
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Affiliation(s)
- Riccardo Aversano
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Immacolata Caruso
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Giovanna Aronne
- Department of Arboriculture, Botany and Plant Pathology, University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Veronica De Micco
- Department of Arboriculture, Botany and Plant Pathology, University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Nunzia Scognamiglio
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Domenico Carputo
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
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