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Kawanabe T, Ishikura S, Miyaji N, Sasaki T, Wu LM, Itabashi E, Takada S, Shimizu M, Takasaki-Yasuda T, Osabe K, Peacock WJ, Dennis ES, Fujimoto R. Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E6704-E6711. [PMID: 27791039 PMCID: PMC5087013 DOI: 10.1073/pnas.1613372113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Hybrid vigor or heterosis refers to the superior performance of F1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.
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Affiliation(s)
- Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Sonoko Ishikura
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Taku Sasaki
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Li Min Wu
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia
| | - Etsuko Itabashi
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Takada
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate, 024-0003, Japan
| | - Takeshi Takasaki-Yasuda
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - W James Peacock
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia;
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama, 332-0012 Japan
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A Multigenic Network of ARGONAUTE4 Clade Members Controls Early Megaspore Formation in Arabidopsis. Genetics 2016; 204:1045-1056. [PMID: 27591749 PMCID: PMC5105840 DOI: 10.1534/genetics.116.188151] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/17/2016] [Indexed: 01/01/2023] Open
Abstract
The development of gametophytes relies on the establishment of a haploid gametophytic generation that initiates with the specification of gametophytic precursors. The majority of flowering plants differentiate a single gametophytic precursor in the ovule: the megaspore mother cell. Here we show that, in addition to argonaute9 (ago9), mutations in other ARGONAUTE (AGO) genes such as ago4, ago6, and ago8, also show abnormal configurations containing supernumerary gametophytic precursors in Arabidopsis thaliana. Double homozygous ago4 ago9 individuals showed a suppressive effect on the frequency of ovules with multiple gametophytic precursors across three consecutive generations, indicating that genetic interactions result in compensatory mechanisms. Whereas overexpression of AGO6 in ago9 and ago4 ago9 confirms strong regulatory interactions among genes involved in RNA-directed DNA methylation, AGO8 is overexpressed in premeiotic ovules of ago4 ago9 individuals, suggesting that the regulation of this previously presumed pseudogene responds to the compensatory mechanism. The frequency of abnormal meiotic configurations found in ago4 ago9 individuals is dependent on their parental genotype, revealing a transgenerational effect. Our results indicate that members of the AGO4 clade cooperatively participate in preventing the abnormal specification of multiple premeiotic gametophytic precursors during early ovule development in A. thaliana.
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Zhang Q, Li Y, Xu T, Srivastava AK, Wang D, Zeng L, Yang L, He L, Zhang H, Zheng Z, Yang DL, Zhao C, Dong J, Gong Z, Liu R, Zhu JK. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism. Cell Discov 2016; 2:16027. [PMID: 27551435 PMCID: PMC4977722 DOI: 10.1038/celldisc.2016.27] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/09/2022] Open
Abstract
In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits.
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Affiliation(s)
- Qingzhu Zhang
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Yanqiang Li
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Tao Xu
- Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Ashish Kumar Srivastava
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Dong Wang
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Liang Zeng
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Lan Yang
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Li He
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Heng Zhang
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Zhimin Zheng
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Dong-Lei Yang
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Cheng Zhao
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers University , Piscataway, NJ, USA
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University , Beijing, China
| | - Renyi Liu
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
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Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R. Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC PLANT BIOLOGY 2016; 16:45. [PMID: 26882898 PMCID: PMC4756405 DOI: 10.1186/s12870-016-0734-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior performance compared to their parental inbred lines. Most commercial Chinese cabbage cultivars are F1 hybrids and their level of hybrid vigour is of critical importance and is a key selection criterion in the breeding system. RESULTS We have characterized the heterotic phenotype of one F1 hybrid cultivar of Chinese cabbage and its parental lines from early- to late-developmental stages of the plants. Hybrid cotyledons are larger than those of the parents at 4 days after sowing and biomass in the hybrid, determined by the fresh weight of leaves, is greater than that of the larger parent line by approximately 20% at 14 days after sowing. The final yield of the hybrid harvested at 63 days after sowing is 25% greater than the yield of the better parent. The larger leaves of the hybrid are a consequence of increased cell size and number of the photosynthetic palisade mesophyll cells and other leaf cells. The accumulation of plant hormones in the F1 was within the range of the parental levels at both 2 and 10 days after sowing. Two days after sowing, the expression levels of chloroplast-targeted genes in the cotyledon cells were upregulated in the F1 hybrid relative to their mid parent values. Shutdown of chlorophyll biosynthesis in the cotyledon by norflurazon prevented the increased leaf area in the F1 hybrid. CONCLUSIONS In the cotyledons of F1 hybrids, chloroplast-targeted genes were upregulated at 2 days after sowing. The increased activity levels of this group of genes suggested that their differential transcription levels could be important for establishing early heterosis but the increased transcription levels were transient. Inhibition of the photosynthetic process in the cotyledon reduced heterosis in later seedling stages. These observations suggest early developmental events in the germinating seedling of the hybrid may be important for later developmental vigour and yield advantage.
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Affiliation(s)
- Natsumi Saeki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Hua Ying
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
| | - Motoki Shimizu
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Mikiko Kojima
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - Hiroshi Abe
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, 305-0074, Japan.
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Makoto Kaji
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi, 987-0003, Japan.
| | | | - Hitoshi Sakakibara
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - W James Peacock
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Elizabeth S Dennis
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, 332-0012, Japan.
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55
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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56
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Fort A, Ryder P, McKeown PC, Wijnen C, Aarts MG, Sulpice R, Spillane C. Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2016; 209:590-9. [PMID: 26395035 DOI: 10.1111/nph.13650] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/05/2015] [Indexed: 05/10/2023]
Abstract
Heterosis is the phenomenon whereby hybrid offspring of genetically divergent parents display superior characteristics compared with their parents. Although hybridity and polyploidy can influence heterosis in hybrid plants, the differential contributions of hybridity vs polyploidy to heterosis effects remain unknown. To address this question, we investigated heterosis effects on rosette size and growth rate of 88 distinct F1 lines of Arabidopsis thaliana consisting of diploids, reciprocal triploids and tetraploids in isogenic and hybrid genetic contexts. 'Heterosis without hybridity' effects on plant size can be generated in genetically isogenic F1 triploid plants. Paternal genome excess F1 triploids display positive heterosis, whereas maternal genome excess F1 s display negative heterosis effects. Paternal genome dosage increases plant size in F1 hybrid triploid plants by, on average, 57% (in contrast with 35% increase displayed by F1 diploid hybrids). Such effects probably derive from differential seed size, as the growth rate of triploids was similar to diploids. Tetraploid plants display a lower growth rate compared with other ploidies, whereas hybrids display increased early stage growth rate. By disaggregating heterosis effects caused by hybridity vs genome dosage, we advance our understanding of heterosis in plants and facilitate novel paternal genome dosage-based strategies to enhance heterosis effects in crop plants.
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Affiliation(s)
- Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Cris Wijnen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Building 107, 6708, PB Wageningen, the Netherlands
| | - Mark G Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Building 107, 6708, PB Wageningen, the Netherlands
| | - Ronan Sulpice
- Systems Biology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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Cheng S, Yang J, Liao T, Zhu X, Suo Y, Zhang P, Wang J, Kang X. Transcriptomic changes following synthesis of a Populus full-sib diploid and allotriploid population with different heterozygosities driven by three types of 2n female gamete. PLANT MOLECULAR BIOLOGY 2015; 89:493-510. [PMID: 26419948 DOI: 10.1007/s11103-015-0384-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
Diploid gametes are usually applied to produce triploids of Populus [originating from first-division restitution (FDR), second-division restitution (SDR), and postmeiotic restitution (PMR) 2n eggs]. Three types of 2n gametes transmitted different parental heterozygosities in Populus. Failed spindle formation and no chromosomal separation to opposite poles during meiosis I mean that FDR 2n gametes carry nonsister chromatids that are potentially heterozygous. By contrast, SDR 2n gametes result from failed sister chromatid separation in meiosis II, and therefore, they carry sister chromatid that are potentially homozygous. Completely homozygous 2n gametes can arise from the PMR mechanism. The alteration of gene expression resulting from allopolyploidization is a prominent feature in plants. We compared gene expression in the full-sib progeny of three allotriploid Populus populations (triploid-F, triploid-S, and triploid-P) with that in its parent species, and their full-sib diploid F1 hybrid. Genome-wide expression level dominance was biased toward the maternal in the diploid F1 hybrid and three allotriploid populations, whereas our data indicated important, but different, effects of the transmission of different heterozygosity by 2n female gametes in the expression patterns of allopolyploids. Because of the higher level of heterozygosity, the triploids had higher rates of non-additive and transgressive expression patterns in the triploid-F than in triploid-S and triploid-P. Compared with diploid F1, about 30-fold more genes (251) were differently expressed in the triploid-F than in the triploid-S (9) and triploid-P (8), respectively. These findings indicate that hybridization and polyploidization have immediate and distinct effects on the large-scale patterns of gene expression, and different effects on the transmission of heterozygosity by three 2n female gametes.
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Affiliation(s)
- Shiping Cheng
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Pingdingshan University, Pingdingshan, 467000, Henan Province, People's Republic of China
| | - Jun Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Ting Liao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiaohu Zhu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- College of Forestry and Horticulture, Xinjiang Agricultural University, No. 311, East Nongda Road, Urumqi, 830052, People's Republic of China
| | - Yujing Suo
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Jun Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
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Eizadshenass S, Singh RS. Maternal effect and speciation: maternal effect contributes to the evolution of hybrid inviability between Drosophila simulans and Drosophila mauritiana. Genome 2015; 58:405-13. [PMID: 26436586 DOI: 10.1139/gen-2015-0053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Haldane's rule has been the basis of speciation research during the last 30 years. Most studies have focused on the nature of incompatibilities in the hybrid male, but not much attention has been given to the genetic basis of fertility and inviability in hybrid females. Hybridizations between Drosophila simulans and Drosophila mauritiana produce fertile females and sterile males. Here, we re-examined the level of fertility in reciprocal F1 females of these two species and looked for the presence of maternal effects. Our results show that the reciprocal F1 females of D. simulans and D. mauritiana hybridizations are fully fertile and in fact show a significant level of heterosis in the rate of oviposition but display reduced egg hatching in one direction. Reduced egg hatching was observed in the progenies of F1 hybrid females with D. mauritiana as mother, the same cross that showed a stronger negative effect on F1 male fertility. A review of the literature on the hybridizations in Lepidoptera also showed a maternal effect on inviability when reciprocal crosses produced asymmetric results. Our findings point to the importance of maternal effects in the evolution of embryo inviability and thus enhancing the process of speciation through the evolution of hybrid inviability.
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Affiliation(s)
- Sogol Eizadshenass
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.,Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Rama S Singh
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.,Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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60
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Cis-acting determinants of paramutation. Semin Cell Dev Biol 2015; 44:22-32. [DOI: 10.1016/j.semcdb.2015.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
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61
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Li Q, Li Y, Moose SP, Hudson ME. Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants. BMC PLANT BIOLOGY 2015; 15:168. [PMID: 26139102 PMCID: PMC4490736 DOI: 10.1186/s12870-015-0549-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/14/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Gene expression inheritance patterns in Arabidopsis hybrid plants were investigated for correlation with the presence of transposable elements (TEs) and small RNA profile. RESULTS The presence of TEs in a gene and the expression of small RNA matching a gene were both found to be associated with non-additive mRNA inheritance patterns in hybrids. Expression levels below mid-parent values in the hybrids were associated with low mRNA expression in parents, with the presence of small RNA from both strands, and with the presence of TEs. High-parent dominance of mRNA levels was found to be associated with high parental mRNA expression levels, the absence of TEs, and for some genes, with small RNA fragments that are predominantly from the sense strand. These small RNAs exhibit a broader size distribution than siRNA and reduced nucleotide end bias, which are consistent with an origin from degraded mRNA. Thus, increased as well as decreased gene expression in hybrids relative to the parental mean is associated with gene expression levels, TE presence and small RNA fragments with differing characteristics. CONCLUSIONS The data presented here is consistent with a role for differential mRNA decay kinetics as one mechanism contributing to high-parent dominance in gene expression. Our evidence is also consistent with trans repression by siRNA and TEs as the cause of low-parent dominance.
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Affiliation(s)
- Qing Li
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ying Li
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Stephen P Moose
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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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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Ronceret A, Vielle-Calzada JP. Meiosis, unreduced gametes, and parthenogenesis: implications for engineering clonal seed formation in crops. PLANT REPRODUCTION 2015; 28:91-102. [PMID: 25796397 DOI: 10.1007/s00497-015-0262-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/09/2015] [Indexed: 05/18/2023]
Abstract
Meiosis and unreduced gametes. Sexual flowering plants produce meiotically derived cells that give rise to the male and female haploid gametophytic phase. In the ovule, usually a single precursor (the megaspore mother cell) undergoes meiosis to form four haploid megaspores; however, numerous mutants result in the formation of unreduced gametes, sometimes showing female specificity, a phenomenon reminiscent of the initiation of gametophytic apomixis. Here, we review the developmental events that occur during female meiosis and megasporogenesis at the light of current possibilities to engineer unreduced gamete formation. We also provide an overview of the current understanding of mechanisms leading to parthenogenesis and discuss some of the conceptual implications for attempting the induction of clonal seed production in cultivated plants.
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Affiliation(s)
- Arnaud Ronceret
- Group of Reproductive Development and Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
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Wang J, Yao W, Zhu D, Xie W, Zhang Q. Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid. eLife 2015; 4:e04250. [PMID: 25821986 PMCID: PMC4415135 DOI: 10.7554/elife.03913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 03/30/2015] [Indexed: 12/16/2022] Open
Abstract
We performed a genetic analysis of sRNA abundance in flag leaf from an immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining 80,362 sRNA clusters, 22,263 sRNA cluster QTLs (scQTLs) were recovered for 20,249 of all the 50,139 sRNA cluster expression traits (sc-traits). The expression levels for most of s-traits from the same genes or the same sRNA clusters were slightly positively correlated. While genetic co-regulation between sRNAs from the same mother genes and between sRNAs and their mother genes was observed for a portion of the sRNAs, most of the sRNAs and their mother genes showed little co-regulation. Some sRNA biogenesis genes were located in distant-sQTL hotspots and showed correspondence with specific length classes of sRNAs suggesting their important roles in the regulation and biogenesis of the sRNAs. DOI:http://dx.doi.org/10.7554/eLife.03913.001 Genes within the DNA of a plant or animal contain instructions to make molecules called RNAs. Some RNA molecules can be decoded to make proteins, whereas others have different roles. A single gene often contains the instructions to make both protein-coding RNAs and non-coding RNAs. Molecules called small RNAs (or sRNAs) do not code for proteins. Instead, sRNAs can control protein-coding RNA molecules or chemically alter the DNA itself; this allows them to perform many different roles in living organisms. In plants, for example, these molecules affect how the plant grows, the shapes and structures it forms, and how likely it is to survive challenges such as drought and diseases. Often different plants of the same species have different amounts of sRNAs, but the reasons for this remain unclear. Now, Wang, Yao et al. have made use of a technique called ‘expression quantitative locus’ analysis to look at how sRNAs in rice plants are controlled by additional information encoded within DNA. The analysis identified over 53 million sRNA molecules from a population of rice plants. Many of these sRNAs varied in their abundance between different plants within the population. Wang, Yao et al. also found many thousands of individual instructions within the DNA of the rice that can either increase or reduce the abundance of their associated sRNA. Some of the abundant sRNAs were influenced by instructions within their own genes; some were influenced by instructions from other genes; and some were influenced by both. Wang, Yao et al. also found that the control of protein-coding RNAs was not necessarily related to the control of sRNAs encoded by the same gene. Further work is now needed to identify which specific DNA sequences regulate the abundance of sRNA molecules in plants and other organisms. DOI:http://dx.doi.org/10.7554/eLife.03913.002
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Affiliation(s)
- Jia Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wen Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dan Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Emmrich PMF, Roberts HE, Pancaldi V. A Boolean gene regulatory model of heterosis and speciation. BMC Evol Biol 2015; 15:24. [PMID: 25888139 PMCID: PMC4349475 DOI: 10.1186/s12862-015-0298-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 01/27/2015] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Modelling genetic phenomena affecting biological traits is important for the development of agriculture as it allows breeders to predict the potential of breeding for certain traits. One such phenomenon is heterosis or hybrid vigor: crossing individuals from genetically distinct populations often results in improvements in quantitative traits, such as growth rate, biomass production and stress resistance. Heterosis has become a very useful tool in global agriculture, but its genetic basis remains controversial and its effects hard to predict. We have taken a computational approach to studying heterosis, developing a simulation of evolution, independent reassortment of alleles and hybridization of Gene Regulatory Networks (GRNs) in a Boolean framework. These artificial regulatory networks exhibit topological properties that reflect those observed in biology, and fitness is measured as the ability of a network to respond to external inputs in a pre-defined way. RESULTS Our model reproduced common experimental observations on heterosis using only biologically justified parameters, such as mutation rates. Hybrid vigor was observed and its extent was seen to increase as parental populations diverged, up until a point of sudden collapse of hybrid fitness. Thus, the model also describes a process akin to speciation due to genetic incompatibility of the separated populations. We also reproduce, for the first time in a model, the fact that hybrid vigor cannot easily be fixed by within a breeding line, currently an important limitation of the use of hybrid crops. The simulation allowed us to study the effects of three standard models for the genetic basis of heterosis: dominance, over-dominance, and epistasis. CONCLUSION This study describes the most detailed simulation of heterosis using gene regulatory networks to date and reproduces several phenomena associated with heterosis for the first time in a model. The level of detail in our model allows us to suggest possible warning signs of the impending collapse of hybrid vigor in breeding. In addition, the simulation provides a framework that can be extended to study other aspects of heterosis and alternative evolutionary scenarios.
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Affiliation(s)
- Peter Martin Ferdinand Emmrich
- Department of Plant Sciences, University of Cambridge, CB2 3EA, Cambridge, UK.
- Current address: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Hannah Elizabeth Roberts
- Department of Plant Sciences, University of Cambridge, CB2 3EA, Cambridge, UK.
- Current address: The Nuffield Department of Clinical Medicine, Oxford University, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK.
| | - Vera Pancaldi
- Department of Plant Sciences, University of Cambridge, CB2 3EA, Cambridge, UK.
- Current address: Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernández Almagro, 3, Madrid, E-28029, Spain.
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Ng'oma E, Reichwald K, Dorn A, Wittig M, Balschun T, Franke A, Platzer M, Cellerino A. The age related markers lipofuscin and apoptosis show different genetic architecture by QTL mapping in short-lived Nothobranchius fish. Aging (Albany NY) 2015; 6:468-80. [PMID: 25093339 PMCID: PMC4100809 DOI: 10.18632/aging.100660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P<0.001) and apoptosis (P<0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F₁individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F₂ hybrids. Quantitative trait loci analysis of 287 F₂ fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P<0.001) with overdominance effect. Apoptotic cells revealed three significant- and two suggestive QTL explaining 19% of variance (P<0.001), showing additive and dominance effects, and two interacting loci. Our results show that lipofuscin and apoptosis are markers of different age-dependent biological processes controlled by different genetic mechanisms.
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Affiliation(s)
- Enoch Ng'oma
- Biology of Ageing, Leibniz Institute for Age Research - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Kathrin Reichwald
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Alexander Dorn
- Biology of Ageing, Leibniz Institute for Age Research - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Tobias Balschun
- Hufeland Klinikum Mühlhausen, Institut für Infektiologie und Pathobiologie, 99974 Mühlhausen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Allesandro Cellerino
- Biology of Ageing, Leibniz Institute for Age Research - Fritz Lipmann Institute, 07745 Jena, Germany. Neurobiology Laboratory, Scuola Normale Superiore, 56124 Pisa, Italy
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67
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Kornienko AV, Podvigina OA, Zhuzhzhalova TP, Fedulova TP, Bogomolov MA, Oshevnev VP, Butorina AK. High-priority research directions in genetics and the breeding of the sugar beet (Beta vulgaris L.) in the 21st century. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414110064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Thomas M, Pingault L, Poulet A, Duarte J, Throude M, Faure S, Pichon JP, Paux E, Probst AV, Tatout C. Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics 2014; 15:922. [PMID: 25342325 PMCID: PMC4223845 DOI: 10.1186/1471-2164-15-922] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plant and animal methyltransferases are key enzymes involved in DNA methylation at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in the hexaploid wheat Triticum aestivum (TaMET1). RESULTS Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7, indicating that group 2 homoeologous genes are predominant at the transcriptional level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous group 5 and 7, but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1. CONCLUSIONS We retraced the evolutionary history of MET1 genes in wheat, explaining the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.
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Affiliation(s)
- Mélanie Thomas
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Lise Pingault
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Axel Poulet
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Jorge Duarte
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Mickaël Throude
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Sébastien Faure
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Jean-Philippe Pichon
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Etienne Paux
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Aline Valeska Probst
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Christophe Tatout
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
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Feeney A, Nilsson E, Skinner MK. Epigenetics and transgenerational inheritance in domesticated farm animals. J Anim Sci Biotechnol 2014; 5:48. [PMID: 25810901 PMCID: PMC4373098 DOI: 10.1186/2049-1891-5-48] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/14/2014] [Indexed: 01/10/2023] Open
Abstract
Epigenetics provides a molecular mechanism of inheritance that is not solely dependent on DNA sequence and that can account for non-Mendelian inheritance patterns. Epigenetic changes underlie many normal developmental processes, and can lead to disease development as well. While epigenetic effects have been studied in well-characterized rodent models, less research has been done using agriculturally important domestic animal species. This review will present the results of current epigenetic research using farm animal models (cattle, pigs, sheep and chickens). Much of the work has focused on the epigenetic effects that environmental exposures to toxicants, nutrients and infectious agents has on either the exposed animals themselves or on their direct offspring. Only one porcine study examined epigenetic transgenerational effects; namely the effect diet micronutrients fed to male pigs has on liver DNA methylation and muscle mass in grand-offspring (F2 generation). Healthy viable offspring are very important in the farm and husbandry industry and epigenetic differences can be associated with production traits. Therefore further epigenetic research into domestic animal health and how exposure to toxicants or nutritional changes affects future generations is imperative.
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Affiliation(s)
- Amanda Feeney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, 99164-4236 Pullman, WA USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, 99164-4236 Pullman, WA USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, 99164-4236 Pullman, WA USA
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Groszmann M, Gonzalez-Bayon R, Greaves IK, Wang L, Huen AK, Peacock WJ, Dennis ES. Intraspecific Arabidopsis hybrids show different patterns of heterosis despite the close relatedness of the parental genomes. PLANT PHYSIOLOGY 2014; 166:265-80. [PMID: 25073707 PMCID: PMC4149712 DOI: 10.1104/pp.114.243998] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/24/2014] [Indexed: 05/03/2023]
Abstract
Heterosis is important for agriculture; however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development.
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Affiliation(s)
- Michael Groszmann
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
| | - Rebeca Gonzalez-Bayon
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
| | - Ian K Greaves
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
| | - Li Wang
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
| | - Amanda K Huen
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
| | - W James Peacock
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2600, Australia (M.G., R.G.-B., I.K.G., L.W., A.K.H., W.J.P., E.S.D.); andUniversity of Technology, Sydney, New South Wales 2007, Australia (E.S.D., W.J.P.)
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Kim KD, El Baidouri M, Jackson SA. Accessing epigenetic variation in the plant methylome. Brief Funct Genomics 2014; 13:318-27. [PMID: 24562692 DOI: 10.1093/bfgp/elu003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cytosine DNA methylation is the addition of a methyl group to the 5' position of a cytosine, which plays a crucial role in plant development and gene silencing. Genome-wide profiling of DNA methylation is now possible using various techniques and strategies. Using these technologies, we are beginning to elucidate the extent and impact of variation in DNA methylation between individuals and/or tissues. Here, we review the different techniques used to analyze the methylomes at the whole-genome level and their applications to better understand epigenetic variations in plants.
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Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A 2014; 111:2017-22. [PMID: 24449910 DOI: 10.1073/pnas.1323656111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hybridization in plants leads to transinteractions between the parental genomes and epigenomes that can result in changes to both 24 nt siRNA and cytosine methylation ((m)C) levels in the hybrid. In Arabidopsis the principle processes altering the hybrid methylome are Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM) in which the (m)C pattern of a genomic segment attains the same (m)C pattern of the corresponding segment on the other parental chromosome. We examined two loci that undergo TCM/TCdM in the Arabidopsis C24/Landsberg erecta (Ler) F1 hybrids, which show patterns of inheritance dependent on the properties of the particular donor and recipient chromosomal segments. At At1g64790 the TCM- and TCdM-derived (m)C patterns are maintained in the F2 generation but are transmitted in outcrosses or backcrosses only by the C24 genomic segment. At a region between and adjacent to At3g43340 and At3g43350, the originally unmethylated Ler genomic segment receives the C24 (m)C pattern in the F1, which is then maintained in backcross plants independent of the presence of the parental C24 segment. In backcrosses to an unmethylated Ler allele, the newly methylated F1 Ler segment may act as a TCM source in a process comparable to paramutation in maize. TCM-derived (m)C patterns are associated with reduced expression of both At3g43340 and At3g43350 in F1 and F2 plants, providing support for such events influencing the transcriptome. The inheritance of the F1 (m)C patterns and the segregation of other genetic and epigenetic determinants may contribute to the reduced hybrid vigor in the F2 and subsequent generations.
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Shi J, Dong A, Shen WH. Epigenetic regulation of rice flowering and reproduction. FRONTIERS IN PLANT SCIENCE 2014; 5:803. [PMID: 25674094 PMCID: PMC4309181 DOI: 10.3389/fpls.2014.00803] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/22/2014] [Indexed: 05/19/2023]
Abstract
Current understanding of the epigenetic regulator roles in plant growth and development has largely derived from studies in the dicotyledonous model plant Arabidopsis thaliana. Rice (Oryza sativa) is one of the most important food crops in the world and has more recently becoming a monocotyledonous model plant in functional genomics research. During the past few years, an increasing number of studies have reported the impact of DNA methylation, non-coding RNAs and histone modifications on transcription regulation, flowering time control, and reproduction in rice. Here, we review these studies to provide an updated complete view about chromatin modifiers characterized in rice and in particular on their roles in epigenetic regulation of flowering time, reproduction, and seed development.
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Affiliation(s)
- Jinlei Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
- *Correspondence: Wen-Hui Shen, CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg Cédex, France e-mail:
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