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Ramlal A, Nautiyal A, Baweja P, Kumar Mahto R, Mehta S, Pujari Mallikarunja B, Vijayan R, Saluja S, Kumar V, Kumar Dhiman S, Lal SK, Raju D, Rajendran A. Harnessing heterosis and male sterility in soybean [ Glycine max (L.) Merrill]: A critical revisit. FRONTIERS IN PLANT SCIENCE 2022; 13:981768. [PMID: 36299790 PMCID: PMC9589222 DOI: 10.3389/fpls.2022.981768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Soybean is a predominantly self-pollinated crop. It is also one of the important oilseed legumes. Soybean is an excellent crop having industrial, traditional, culinary, feeding, and cultural roles. Genetic diversity in breeding programs is of prime importance as it ensures the success of any breeding by enhancing the outcomes and results of the plants. The phenomenon wherein the progeny exhibits greater biomass (yield) and a faster rate of development and fertility than its parents is referred to as heterosis. As of now, heterosis is mainly limited to the trait of seed yield and is considered the basis for the development of better (superior) varieties. Male sterility (MS) is extensively used for the production of seeds and the improvement of crops coupled with the traditional breeding programs and molecular technology. Therefore, deployment of MS and heterosis in breeding soybean could yield better outcomes. This review aims to focus on two aspects, namely, MS and heterosis in soybean with its scope for crop improvement.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
- DBC i4 Center, Deshbandhu College, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Sahil Mehta
- School of Agricultural Sciences, K. R. Mangalam University, Gurugram, Haryana, India
| | - Bingi Pujari Mallikarunja
- Division of Genetics, Regional Research Centre, ICAR-Indian Agricultural Research Institute (IARI), Dharwad, Karnataka, India
| | - Roshni Vijayan
- Regional Agricultural Research Station, Kerala Agricultural University, Pattambi, Kerala, India
| | - Shukla Saluja
- Department of Botany, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Vijay Kumar
- Department of Botany, Shivaji College, University of Delhi, New Delhi, India
| | - Sunil Kumar Dhiman
- Department of Botany, Kirori Mal College, University of Delhi, New Delhi, India
| | - S. K. Lal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Dhandapani Raju
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Ambika Rajendran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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Liu C, Huang R, Wang L, Liang G. Functional Identification of EjGIF1 in Arabidopsis and Preliminary Analysis of Its Regulatory Mechanisms in the Formation of Triploid Loquat Leaf Heterosis. FRONTIERS IN PLANT SCIENCE 2021; 11:612055. [PMID: 33510754 PMCID: PMC7835675 DOI: 10.3389/fpls.2020.612055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Although several results have been obtained in triploid loquat heterosis (i.e., leaf size of triploid loquat) studies in the past years, the underlying mechanisms of the heterosis are still largely unknown, especially the regulation effects of one specific gene on the corresponding morphology heterosis. In this study, we sought to further illustrate the regulatory mechanisms of one specific gene on the leaf size heterosis of triploid loquats. A leaf size development-related gene (EjGIF1) and its promoter were successfully cloned. Ectopic expression of EjGIF1 in Arabidopsis showed that the leaf size of transgenic plantlets was larger than that of WTs, and the transgenic plantlets had more leaves than WTs. Quantitative Reverse Transcription PCR (qRT-PCR) showed that the expression level of EjGIF1 showed an AHP expression pattern in most of the hybrids, and this was consistent with our previous phenotype observations. Structure analysis of EjGIF1 promoter showed that there were significantly more light-responsive elements than other elements. To further ascertain the regulatory mechanisms of EjGIF1 on triploid loquat heterosis, the methylation levels of EjGIF1 promoter in different ploidy loquats were analyzed by using bisulfite sequencing. Surprisingly, the total methylation levels of EjGIF1 promoter in triploid showed a decreasing trend compared with the mid-parent value (MPV), and this was also consistent with the qRT-PCR results of EjGIF1. Taken together, our results suggested that EjGIF1 played an important role in promoting leaf size development of loquat, and demethylation of EjGIF1 promoter in triploid loquats caused EjGIF1 to exhibit over-dominance expression pattern and then further to promote leaf heterosis formation. In conclusion, EjGIF1 played an important role in the formation of triploid loquat leaf size heterosis.
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Affiliation(s)
- Chao Liu
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Renwei Huang
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Lingli Wang
- Technical Advice Station of Economic Crop, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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Selva C, Riboni M, Baumann U, Würschum T, Whitford R, Tucker MR. Hybrid breeding in wheat: how shaping floral biology can offer new perspectives. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:675-694. [PMID: 32534601 DOI: 10.1071/fp19372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Hybrid breeding in wheat (Triticum aestivum L.) has the potential to deliver major yield increases. This is a requisite to guarantee food security for increasing population demands and to counterbalance the effects of extreme environmental conditions. Successful hybrid breeding in wheat relies on forced outcrossing while preventing self-pollination. To achieve this, research has been directed towards identifying and improving fertility control systems. To maximise cross-pollination and seed set, however, fertility control systems need to be complemented by breeding phenotypically distinct male and female lines. This review summarises existing and novel male sterility systems for wheat hybridisation. We also consider the genetic resources that can be used to alter wheat's floral development and spike morphology, with a focus on the genetic variation already available. Exploiting these resources can lead to enhanced outcrossing, a key requirement in the progress towards hybrid wheat breeding.
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Affiliation(s)
- Caterina Selva
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ryan Whitford
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
| | - Matthew R Tucker
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
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K. Srivastava R, Bollam S, Pujarula V, Pusuluri M, Singh RB, Potupureddi G, Gupta R. Exploitation of Heterosis in Pearl Millet: A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:E807. [PMID: 32605134 PMCID: PMC7412370 DOI: 10.3390/plants9070807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
| | | | | | | | | | | | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
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Han W, Xue Q, Li G, Yin J, Zhang H, Zhu Y, Xing W, Cao Y, Su Y, Wang K, Zou J. Genome-wide analysis of the role of DNA methylation in inbreeding depression of reproduction in Langshan chicken. Genomics 2020; 112:2677-2687. [PMID: 32057912 DOI: 10.1016/j.ygeno.2020.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 12/18/2022]
Abstract
Inbreeding depression of chicken reproduction is a major concern in the conservation of chicken genetic resources. To investigate the potential DNA methylation sites involved in the inbreeding depression of chicken reproduction, we carried out whole-genome bisulfite sequencing (WGBS) of hypothalamus and ovary tissues from the strongly and weakly inbred Langshan chickens, respectively. 5948 and 4593 differentially methylated regions (DMRs) were identified in the hypothalamus and ovary between the strongly and weakly inbred Langshan chickens, respectively. Large numbers of DMR-related genes (DMGs) were enriched in reproduction-related pathways. By combining the WGBS and transcriptome data, two DMRs in SRD5A1 and CDC27 genes were inferred as the most likely biomarkers of inbreeding depression of reproduction in Langshan chicken. Our study provides the first systematic investigation of the DNA methylation changes in strongly inbred chickens, and extends our understanding of the regulatory mechanisms underlying inbreeding depression in chicken reproduction.
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Affiliation(s)
- Wei Han
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Qian Xue
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Guohui Li
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Jianmei Yin
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Huiyong Zhang
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Yunfen Zhu
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Weijie Xing
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Yuxia Cao
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Yijun Su
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China
| | - Kehua Wang
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China.
| | - Jianmin Zou
- National Chickens Genetic Resources, Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China.
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7
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Berbel‐Filho WM, Garcia de Leaniz C, Morán P, Cable J, Lima SMQ, Consuegra S. Local parasite pressures and host genotype modulate epigenetic diversity in a mixed-mating fish. Ecol Evol 2019; 9:8736-8748. [PMID: 31410276 PMCID: PMC6686343 DOI: 10.1002/ece3.5426] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Parasite-mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of long-term self-fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the host's ability to respond to pathogens. DNA methylation represents a potential mechanism for generating additional adaptive variation under low genetic diversity. We compared genetic diversity (microsatellites and AFLPs), variation in DNA methylation (MS-AFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a predomintanly self-fertilizing fish, to analyze the potential adaptive value of DNA methylation in relation to genetic diversity and parasite loads. We found strong genetic population structuring, as well as differences in parasite loads and methylation levels among sampling sites and selfing lineages. Globally, the interaction between parasites and inbreeding with selfing lineages influenced DNA methylation, but parasites seemed more important in determining methylation levels at the local scale.
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Affiliation(s)
| | | | - Paloma Morán
- Facultad de BiologíaUniversity of Vigo. Campus Universitario Lagoas‐MarcosendeVigoSpain
| | - Joanne Cable
- School of BiosciencesCardiff UniversityCardiffUK
| | - Sergio M. Q. Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e ZoologiaUniversidade Federal do Rio Grande do NorteNatalBrazil
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8
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Venney CJ, Johansson ML, Heath DD. Inbreeding effects on gene-specific DNA methylation among tissues of Chinook salmon. Mol Ecol 2016; 25:4521-33. [PMID: 27480590 DOI: 10.1111/mec.13777] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/14/2023]
Abstract
Inbreeding depression is the loss of fitness resulting from the mating of genetically related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, although recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here, we use a targeted, multigene approach to assess methylation at 22 growth-, metabolic-, immune- and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, although methylation decreased with age in five genes, CK-1, IFN-ɣ, HNRNPL, hsc71 and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on ageing, environmental response and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically based inbreeding depression in vertebrates.
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Affiliation(s)
- Clare J Venney
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada.
| | - Mattias L Johansson
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada.,Department of Biological Sciences, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada
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9
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Kumar R, Chauhan PK, Khurana A. Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae. Funct Integr Genomics 2016; 16:513-28. [DOI: 10.1007/s10142-016-0502-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 12/17/2022]
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10
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Song Y, Ci D, Tian M, Zhang D. Stable methylation of a non-coding RNA gene regulates gene expression in response to abiotic stress in Populus simonii. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1477-92. [PMID: 26712827 DOI: 10.1093/jxb/erv543] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA methylation plays important roles in responses to environmental stimuli. However, in perennial plants, the roles of DNA methylation in stress-specific adaptions to different abiotic stresses remain unclear. Here, we present a systematic, comparative analysis of the methylome and gene expression in poplar under cold, osmotic, heat, and salt stress conditions from 3h to 24h. Comparison of the stress responses revealed different patterns of cytosine methylation in response to the four abiotic stresses. We isolated and sequenced 1376 stress-specific differentially methylated regions (SDMRs); annotation revealed that these SDMRs represent 1123 genes encoding proteins, 16 miRNA genes, and 17 long non-coding RNA (lncRNA) genes. The SDMR162 region, consisting of Psi-MIR396e and PsiLNCRNA00268512, is regulated by epigenetic pathways and we speculate that PsiLNCRNA00268512 regulates miR396e levels by acting as a target mimic. The ratios of methylated cytosine declined to ~35.1% after 1 month of recovery from abiotic stress and to ~15.3% after 6 months. Among methylated miRNA genes, only expression of the methylation-regulated gene MIRNA6445a showed long-term stability. Our data provide a strong basis for future work and improve our understanding of the effect of epigenetic regulation of non-coding RNA expression, which will enable in-depth functional analysis.
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Affiliation(s)
- Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Dong Ci
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Min Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
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11
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Han P, Lu X, Mi F, Dong J, Xue C, Li J, Han B, Zhang X. Proteomic analysis of heterosis in the leaves of sorghum-sudangrass hybrids. Acta Biochim Biophys Sin (Shanghai) 2016; 48:161-73. [PMID: 26792642 DOI: 10.1093/abbs/gmv126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/08/2015] [Indexed: 01/15/2023] Open
Abstract
Sorghum-sudangrass hybrids are widely used for forage and silage in the animal husbandry industry due to their hardiness. The heterozygous first generation of sorghum-sudangrass hybrids displays performance superior to their homozygous, parental inbred lines. In order to study the molecular details underlying its heterosis, the leaves of sorghum-sudangrass hybrids and their parents were compared using mass spectrometry-based proteomics. Results showed that among the 996 proteins that were identified, 32 proteins showed 'additive accumulation expression patterns', indicating that the protein abundance in sorghum-sudangrass hybrids showed no significant difference from the average of their parents. Additionally, 74 proteins showed 'nonadditive accumulation expression patterns' (the proteins abundance in the hybrids showed significant difference from the average of their parents). Both additive and nonadditive proteins were mainly involved in photosynthesis and carbohydrate metabolism. More upregulated additive and nonadditive proteins were in the hybrids than in their parents, suggesting that additive and nonadditive proteins are essential to the vigor of sorghum-sudangrass hybrids. The nonadditive proteins were enriched in photosynthesis, carbohydrate metabolism, and protein oligomerization, but the additive proteins were not enriched in any pathway, which indicated that the nonadditive proteins could be greater contributors to heterosis than additive proteins. Furthermore, the highly activated photosynthetic pathway in nonadditive proteins implies that photosynthesis in hybrids is heightened to assimilate more organic matter, resulting in an increased yield. Our results provide a proof-of-concept that reveals the molecular components of heterosis in sorghum-sudangrass hybrid leaves and serves as an important step for future genetic manipulation of specific proteins to improve the performance of hybrids.
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Affiliation(s)
- Pingan Han
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Xiaoping Lu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Fugui Mi
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Jing Dong
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Chunlei Xue
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Jianke Li
- Chinese Academy of Agricultural Science, Institute of Apicultural Research, Beijing 100093, China
| | - Bin Han
- Chinese Academy of Agricultural Science, Institute of Apicultural Research, Beijing 100093, China
| | - Xiaoyu Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
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12
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Liu TJ, Sun LF, Shan XH, Wu Y, Su SZ, Li SP, Liu HK, Han JY, Yuan YP. Analysis of DNA methylation patterns and levels in maize hybrids and their parents. GENETICS AND MOLECULAR RESEARCH : GMR 2014. [PMID: 25366740 DOI: 10.1007/s10535-015-0490-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.
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Affiliation(s)
- T J Liu
- College of Plant Science, Jilin University, Changchun, China
| | - L F Sun
- College of Plant Science, Jilin University, Changchun, China
| | - X H Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Y Wu
- College of Plant Science, Jilin University, Changchun, China
| | - S Z Su
- College of Plant Science, Jilin University, Changchun, China
| | - S P Li
- College of Plant Science, Jilin University, Changchun, China
| | - H K Liu
- College of Plant Science, Jilin University, Changchun, China
| | - J Y Han
- College of Plant Science, Jilin University, Changchun, China
| | - Y P Yuan
- College of Plant Science, Jilin University, Changchun, China
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13
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Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. J Appl Genet 2014; 56:1-13. [PMID: 25027629 DOI: 10.1007/s13353-014-0231-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/09/2023]
Abstract
Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
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Affiliation(s)
- Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China,
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14
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Gao M, Huang Q, Chu Y, Ding C, Zhang B, Su X. Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides. BMC Genet 2014; 15 Suppl 1:S8. [PMID: 25080097 PMCID: PMC4118634 DOI: 10.1186/1471-2156-15-s1-s8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Plants with heterosis/hybrid vigor perform better than their parents in many traits. However, the biological mechanisms underlying heterosis remain unclear. To investigate the significance of DNA methylation to heterosis, a comprehensive analysis of whole-genome DNA methylome profiles of Populus deltoides cl.'55/65' and '10/17' parental lines and their intraspecific F1 hybrids lines was performed using methylated DNA immunoprecipitation (MeDIP) and high-throughput sequencing. Results Here, a total of 486.27 million reads were mapped to the reference genome of Populus trichocarpa, with an average unique mapping rate of 57.8%. The parents with similar genetic background had distinct DNA methylation levels. F1 hybrids with hybrid vigor possessed non-additive DNA methylation level (their levels were higher than mid-parent values). The DNA methylation levels in promoter and repetitive sequences and transposable element of better-parent F1 hybrids and parents and lower-parent F1 hybrids were different. Compared with the maternal parent, better-parent F1 hybrids had fewer hypermethylated genes and more hypomethylated ones. Compared with the paternal parent and lower-parent L1, better-parent F1 hybrids had more hypermethylated genes and fewer hypomethylated ones. The differentially methylated genes between better-parent F1 hybrids, the parents and lower-parent F1 hybrids were enriched in the categories metabolic processes, response to stress, binding, and catalytic activity, development, and involved in hormone biosynthesis, signaling pathway. Conclusions The methylation patterns of the parents both partially and dynamically passed onto their hybrids, and F1 hybrids has a non-additive mathylation level. A multidimensional process is involved in the formation of heterosis.
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15
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Shen H, He H, Li J, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W, Deng XW. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. THE PLANT CELL 2012; 24:875-92. [PMID: 22438023 PMCID: PMC3336129 DOI: 10.1105/tpc.111.094870] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/25/2012] [Accepted: 03/03/2012] [Indexed: 05/18/2023]
Abstract
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs, implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to methylome remodeling were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes circadian clock associated1 and late elongated hypocotyl. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA enhancer1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in heterosis.
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Affiliation(s)
- Huaishun Shen
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Hang He
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Wei Chen
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuncheng Wang
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Lan Guo
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiyu Peng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Guangming He
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Shangwei Zhong
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Yijun Qi
- National Institute of Biological Sciences, Beijing 102206, China
| | - William Terzaghi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Address correspondence to
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16
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Kumar M, Bijo AJ, Baghel RS, Reddy CRK, Jha B. Selenium and spermine alleviate cadmium induced toxicity in the red seaweed Gracilaria dura by regulating antioxidants and DNA methylation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 51:129-38. [PMID: 22153249 DOI: 10.1016/j.plaphy.2011.10.016] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/24/2011] [Indexed: 05/20/2023]
Abstract
The protective role of exogenously supplied selenium (Se) and polyamines (PAs) such as putrescine (Put) and spermine (Spm) in detoxifying the cadmium (Cd) induced toxicity was studied in the marine red alga Gracilaria dura in laboratory conditions. The Cd exposure (0.4 mM) impede the growth of alga while triggering the reactive oxygen species (ROS viz. O(2)(•-) and H(2)O(2)) generation, inhibition of antioxidant system, and enhancing the lipoxygenase (LOX) activity, malondialdehyde (MDA) level and demethylation of DNA. Additions of Se (50 μM) and/or Spm (1 mM) to the culture medium in contrast to Put, efficiently ameliorated the Cd toxicity by decreasing the accumulation of ROS and MDA contents, while restoring or enhancing the level of enzymatic and nonenzymatic antioxidants and their redox ratio, phycobiliproteins and phytochelatins, over the controls. The isoforms of antioxidant enzymes namely superoxide dismutase (Mn-SOD, ~150 kDa; Fe-SOD ~120 kDa), glutathione peroxidase (GSH-Px, ~120 and 140 kDa), glutathione reductase (GR, ~110 kDa) regulated differentially to Se and/or Spm supplementation. Furthermore, it has also resulted in enhanced levels of endogenous PAs (specially free and bound insoluble Put and Spm) and n-6 PUFAs (C20-3, n-6 and C20-4, n-6). This is for the first time wherein Se and Spm were found to regulate the stabilization of DNA methylation by reducing the events of cytosine demethylation in a mechanism to alleviate the Cd stress in marine alga. The present findings reveal that both Se and Spm play a crucial role in controlling the Cd induced oxidative stress in G. dura.
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Affiliation(s)
- Manoj Kumar
- Discipline of Marine Biotechnology and Ecology, Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial Research, Gijubhai Badheka Marg, Bhavnagar 364021, India
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17
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Li A, Fang MD, Song WQ, Chen CB, Qi LW, Wang CG. Gene expression profiles of two intraspecific Larix lines and their reciprocal hybrids. Mol Biol Rep 2011; 39:3773-84. [PMID: 21750915 DOI: 10.1007/s11033-011-1154-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 06/30/2011] [Indexed: 12/17/2022]
Abstract
Heterosis has been widely explored in Larix breeding for more than a century, but the molecular mechanisms underlying this phenomenon remain elusive. In the present study, the genome-wide transcript profiles from two Larix genotypes and their reciprocal hybrids were analyzed using Arabidopsis 70-mer oligonucleotide microarrays. Despite sharing the same two parental lines, one of the hybrids showed obvious heterosis, while the other did not. In total, 1,171 genes were differentially expressed between the heterotic hybrid and its parents, of which 133 genes were nonadditive expression. The number of differentially expressed genes between the non-heterotic hybrid and the parents was 939, but only 54 of these genes were nonadditive expression. Further, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses indicated that most of these differentially expressed genes in the heterotic hybrid were associated with several important biological functions such as physiological processes, responses to stimulus, and starch and sucrose metabolism. The reliability of the microarray data was further validated by the Real-time quantitative RT-PCR. A high Pearson linear correlation coefficient value was detected (r = 0.759, P < 0.01). In conclusion, the gene expression profile in the Larix heterotic hybrid was significantly different from that obtained from the non-heterotic hybrid, and more nonadditive differentially expressed genes were detected in the heterotic hybrid, implying that nonadditive effects may be closely associated with the formation of heterosis in the intraspecific Larix hybridization.
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Affiliation(s)
- Ai Li
- College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
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