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June V, Song X, Chen ZJ. Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids. PLANT PHYSIOLOGY 2024; 195:1214-1228. [PMID: 38319651 PMCID: PMC11142339 DOI: 10.1093/plphys/kiae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024]
Abstract
The parent-of-origin effect on seeds can result from imprinting (unequal expression of paternal and maternal alleles) or combinational effects between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding factors, we produced cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in Arabidopsis (Arabidopsis thaliana) ecotypes Col-0 and C24. These CNS lines differed only in the nuclear genome (imprinting) or cytoplasm. The CNS reciprocal hybrids with the same cytoplasm displayed ∼20% seed size difference, whereas the seed size was similar between the reciprocal hybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection identified 104 maternally expressed genes (MEGs) and 90 paternally expressed genes (PEGs). These imprinted genes were involved in pectin catabolism and cell wall modification in the endosperm. Homeodomain Glabrous9 (HDG9), an epiallele and one of 11 cross-specific imprinted genes, affected seed size. In the embryo, there were a handful of imprinted genes in the CNS hybrids but only 1 was expressed at higher levels than in the endosperm. AT4G13495 was found to encode a long-noncoding RNA (lncRNA), but no obvious seed phenotype was observed in lncRNA knockout lines. Nuclear RNA Polymerase D1 (NRPD1), encoding the largest subunit of RNA Pol IV, was involved in the biogenesis of small interfering RNAs. Seed size and embryos were larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross, supporting a role of the maternal NRPD1 allele in seed development. Although limited ecotypes were tested, these results suggest that imprinting and the maternal NRPD1-mediated small RNA pathway play roles in seed size heterosis in plant hybrids.
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Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaoya Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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2
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Cao S, Chen ZJ. Transgenerational epigenetic inheritance during plant evolution and breeding. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00112-2. [PMID: 38806375 DOI: 10.1016/j.tplants.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024]
Abstract
Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of genetic changes are comprehensible, the basis for transgenerational inheritance of epigenetic variation is elusive. This review addresses contributions of external (environmental) and internal (genomic) factors to the establishment and maintenance of epigenetic memory during plant evolution, crop domestication, and modern breeding. Dynamic and pervasive changes in DNA methylation and chromatin modifications provide a diverse repertoire of epigenetic variation potentially for transgenerational inheritance. Elucidating and harnessing epigenetic inheritance will help us develop innovative breeding strategies and biotechnological tools to improve crop yield and resilience in the face of environmental challenges. Beyond plants, epigenetic principles are shared across sexually reproducing organisms including humans with relevance to medicine and public health.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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3
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Wang F, Han T, Jeffrey Chen Z. Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants. Commun Biol 2024; 7:579. [PMID: 38755402 PMCID: PMC11098820 DOI: 10.1038/s42003-024-06275-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tongwen Han
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Mishio M, Sudo E, Ozaki H, Oguchi R, Fujimoto R, Fujii N, Hikosaka K. Heterotic growth of hybrids of Arabidopsis thaliana is enhanced by elevated atmospheric CO 2. AMERICAN JOURNAL OF BOTANY 2024; 111:e16317. [PMID: 38634444 DOI: 10.1002/ajb2.16317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 04/19/2024]
Abstract
PREMISE With the global atmospheric CO2 concentration on the rise, developing crops that can thrive in elevated CO2 has become paramount. We investigated the potential of hybridization as a strategy for creating crops with improved growth in predicted elevated atmospheric CO2. METHODS We grew parent accessions and their F1 hybrids of Arabidopsis thaliana in ambient and elevated atmospheric CO2 and analyzed numerous growth traits to assess their productivity and underlying mechanisms. RESULTS The heterotic increase in total dry mass, relative growth rate and leaf net assimilation rate was significantly greater in elevated CO2 than in ambient CO2. The CO2 response of net assimilation rate was positively correlated with the CO2 response of leaf nitrogen productivity and with that of leaf traits such as leaf size and thickness, suggesting that hybridization-induced changes in leaf traits greatly affected the improved performance in elevated CO2. CONCLUSIONS Vegetative growth of hybrids seems to be enhanced in elevated CO2 due to improved photosynthetic nitrogen-use efficiency compared with parents. The results suggest that hybrid crops should be well-suited for future conditions, but hybrid weeds may also be more competitive.
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Affiliation(s)
- Masako Mishio
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
| | - Emi Sudo
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
| | - Hiroshi Ozaki
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
- Translational Research Support Section, National Cancer Center Hospital East, Kashiwa, 277-8577, Chiba, Japan
| | - Riichi Oguchi
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
- Graduate School of Science, Osaka Metropolitan University, 2000, Kisaichi, Katano, 576-0004, Osaka, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba, Sendai, 980-8577, Miyagi, Japan
| | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
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Gao Z, Su Y, Chang L, Jiao G, Ou Y, Yang M, Xu C, Liu P, Wang Z, Qi Z, Liu W, Sun L, He G, Deng XW, He H. Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:208-227. [PMID: 38326968 DOI: 10.1111/jipb.13620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.
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Affiliation(s)
- Zhaoxu Gao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yanning Su
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Le Chang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guanzhong Jiao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yang Ou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Mei Yang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Chao Xu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Pengtao Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zejia Wang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Wenwen Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guangming He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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Zhu J, Zou Z, Li D, Xiao W, Yu J, Chen B, Yang H. Comparative transcriptomes reveal different tolerance mechanisms to Streptococcus agalactiae in hybrid tilapia, nile tilapia, and blue tilapia. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109121. [PMID: 37802264 DOI: 10.1016/j.fsi.2023.109121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Tilapia is one of the most economically important freshwater fish farmed in China. Streptococcosis outbreaks have been extensively documented in farmed tilapia species. Hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂) exhibit greater disease resistance than Nile tilapia (O. niloticus) and blue tilapia (O. aureus). However, the molecular mechanism underlying the enhanced tolerance of hybrid tilapia is still poorly understood. In this study, comparative transcriptome analysis was performed to reveal the different tolerance mechanisms to Streptococcus agalactiae in the three tilapia lines. In total, 1982, 2355, and 2076 differentially expressed genes were identified at 48 h post-infection in hybrid tilapia, Nile tilapia, and blue tilapia, respectively. Functional enrichment analysis indicated that numerous metabolic and immune-related pathways were activated in all three tilapia lines. The differential expression of specific genes associated with phagosome, focal adhesion, cytokine-cytokine receptor interaction, and toll-like receptor signaling pathways contributed to the resistance of hybrid tilapia. Notably, immune response genes in hybrid tilapia, such as P38, TLR5, CXCR3, CXCL12, PSTPIP1, and TFR, were generally suppressed under normal conditions but selectively induced following pathogen challenge. These results expand our knowledge of the molecular mechanisms underlying S. agalactiae tolerance in hybrid tilapia and provide valuable insights for tilapia breeding programs.
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Affiliation(s)
- Jinglin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214128, China.
| | - Zhiying Zou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214128, China.
| | - Dayu Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Wei Xiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214128, China.
| | - Jie Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Binglin Chen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Hong Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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June V, Song X, Jeffrey Chen Z. Imprinting but not cytonuclear interactions affects parent-of-origin effect on seed size in Arabidopsis hybrids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557997. [PMID: 37745544 PMCID: PMC10516054 DOI: 10.1101/2023.09.15.557997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in the Arabidopsis thaliana ecotypes Col-0 and C24. These CNS lines differ only in the nuclear genome (imprinting) or in the cytoplasm. The CNS reciprocal hybrids with the same cytoplasm display a ~20% seed size difference as observed in the conventional hybrids. However, seed size is similar between the reciprocal cybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection have identified 104 maternally expressed genes (MEGs) and 90 paternally-expressed genes (PEGs). These imprinted genes are involved in pectin catabolism and cell wall modification in the endosperm. HDG9, an epiallele and one of 11 cross-specific imprinted genes, controls seed size. In the embryo, a handful of imprinted genes is found in the CNS hybrids but only one is expressed higher in the embryo than endosperm. AT4G13495 encodes a long-noncoding RNA (lncRNA), but no obvious seed phenotype is observed in the lncRNA knockout lines. NRPD1, encoding the largest subunit of RNA Pol IV, is involved in the biogenesis of small interfering RNAs. Seed size and embryo is larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross. In spite of limited ecotypes tested, these results suggest potential roles of imprinting and NRPD1-mediated small RNA pathway in seed size variation in hybrids.
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Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoya Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
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8
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June V, Xu D, Papoulas O, Boutz D, Marcotte EM, Chen ZJ. Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids. FRONTIERS IN PLANT SCIENCE 2023; 14:1252564. [PMID: 37780492 PMCID: PMC10538547 DOI: 10.3389/fpls.2023.1252564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Hybrid vigor or heterosis has been widely applied in agriculture and extensively studied using genetic and gene expression approaches. However, the biochemical mechanism underlying heterosis remains elusive. One theory suggests that a decrease in protein aggregation may occur in hybrids due to the presence of protein variants between parental alleles, but it has not been experimentally tested. Here, we report comparative analysis of soluble and insoluble proteomes in Arabidopsis intraspecific and interspecific hybrids or allotetraploids formed between A. thaliana and A. arenosa. Both allotetraploids and intraspecific hybrids displayed nonadditive expression (unequal to the sum of the two parents) of the proteins, most of which were involved in biotic and abiotic stress responses. In the allotetraploids, homoeolog-expression bias was not observed among all proteins examined but accounted for 17-20% of the nonadditively expressed proteins, consistent with the transcriptome results. Among expression-biased homoeologs, there were more A. thaliana-biased than A. arenosa-biased homoeologs. Analysis of the insoluble and soluble proteomes revealed more soluble proteins in the hybrids than their parents but not in the allotetraploids. Most proteins in ribosomal biosynthesis and in the thylakoid lumen, membrane, and stroma were in the soluble fractions, indicating a role of protein stability in photosynthetic activities for promoting growth. Thus, nonadditive expression of stress-responsive proteins and increased solubility of photosynthetic proteins may contribute to heterosis in Arabidopsis hybrids and allotetraploids and possibly hybrid crops.
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Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Dongqing Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ophelia Papoulas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Daniel Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
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9
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Yuan W, Beitel F, Srikant T, Bezrukov I, Schäfer S, Kraft R, Weigel D. Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids. Genome Biol 2023; 24:200. [PMID: 37667232 PMCID: PMC10478501 DOI: 10.1186/s13059-023-03043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative importance of both types of genetic interactions, we turn to hybrids, which provide a facile means for creating many novel allele combinations. RESULTS We focus on the interaction between alleles of the same locus, i.e., dominance, and perform a transcriptomic study involving 141 random crosses between different accessions of the plant model species Arabidopsis thaliana. Additivity is rare, consistently observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with F1 rosette size. Non-additive, dominant gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below the parental average. Unlike in the additive genes, regulatory rare-allele burden in the dominant gene set is strongly correlated with F1 rosette size, even though it only mildly covaries with the expression level of these genes. CONCLUSIONS Our study underscores under-dominance as the predominant gene action associated with emergence of rosette growth trajectories in the A. thaliana hybrid model. Our work lays the foundation for understanding molecular mechanisms and evolutionary forces that lead to dominance complementation of rare regulatory alleles.
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Affiliation(s)
- Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Fiona Beitel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Thanvi Srikant
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Sabine Schäfer
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Robin Kraft
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany.
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Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules 2023; 13:1110. [PMID: 37509146 PMCID: PMC10377273 DOI: 10.3390/biom13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.
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Affiliation(s)
- Harold Duruflé
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
- INRAE, ONF, BioForA, 45075 Orleans, France
| | - Thierry Balliau
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Nicolas Blanchet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Adeline Chaubet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Alexandra Duhnen
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Nicolas Pouilly
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Mélisande Blein-Nicolas
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Brigitte Mangin
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Maury
- INRAE, INP-ENSAT Toulouse, UMR AGIR, Université de Toulouse, 31000 Toulouse, France
| | | | - Michel Zivy
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
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Fu C, Ma C, Zhu M, Liu W, Ma X, Li J, Liao Y, Liu D, Gu X, Wang H, Wang F. Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:139-154. [PMID: 36995901 DOI: 10.1111/tpj.16217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.
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Affiliation(s)
- Chongyun Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Ce Ma
- Novogene Biotechnology Inc, Beijing, China
| | - Manshan Zhu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Jinhua Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Yilong Liao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs Beijing, China
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12
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Le QTN, Sugi N, Yamaguchi M, Hirayama T, Kobayashi M, Suzuki Y, Kusano M, Shiba H. Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis. Sci Rep 2023; 13:9529. [PMID: 37308530 DOI: 10.1038/s41598-023-36618-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F1 hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F1 hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F1 hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F1 hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.
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Affiliation(s)
- Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Thuyloi University, 175 Tay Son, Dong Da, Hanoi, Viet Nam
| | - Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masaaki Yamaguchi
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Touko Hirayama
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan
| | - Miyako Kusano
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Hiroshi Shiba
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan.
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ten-Nodai 1-1-1, Tsukuba, Ibaraki, Japan.
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13
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Zhu Q, Lv J, Wu Y, Peng M, Wu X, Li J, Wu T, Zhang X, Xu X, Wang Y, Feng Y. MdbZIP74 negatively regulates osmotic tolerance and adaptability to moderate drought conditions of apple plants. JOURNAL OF PLANT PHYSIOLOGY 2023; 283:153965. [PMID: 36898191 DOI: 10.1016/j.jplph.2023.153965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/15/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Drought is the most prominent threat to global agricultural production. The basic leucine zipper (bZIP) family is related to the response to a series of abiotic stress. In this case, apple calli and the seedlings of MdbZIP74-RNAi transgenic lines were obtained. Under osmotic stress and moderate drought conditions, the content of malondialdehyde, relative water content and other stress-related assays were measured. MdbZIP74 was found to negatively regulate the osmotic tolerance of apple callus. The growth of MdbZIP74-RNAi calli enhanced resistance without significant production loss. The silencing of MdbZIP74 contributes to redox balance and the adaptability of apple seedlings to moderate drought conditions. Four related differentially expressed genes in the biosynthesis of cytokinin and catabolic pathway were identified through a transcriptome analysis of MdbZIP74-RNAi seedlings under moderate drought conditions. MdLOG8 was further identified as the target of MdbZIP74 involved in the drought adaptability of apple plants using a dual experiment. Further confirmation showed MdLOG8 was maintained in the MdbZIP74-RNAi seedlings presumably acting as the growth regulator to enhance drought adaptability. It was concluded that the correct regulation of cytokinin level under moderate drought conditions maintains the redox balance and avoids the situation of plants surviving with the minimal resources.
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Affiliation(s)
- Qinyuan Zhu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jiahong Lv
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yue Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Mengqun Peng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinyi Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Feng
- College of Horticulture, China Agricultural University, Beijing, 100193, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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14
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Chen S, Yu Y, Wang X, Wang S, Zhang T, Zhou Y, He R, Meng N, Wang Y, Liu W, Liu Z, Liu J, Guo Q, Huang H, Sederoff RR, Wang G, Qu G, Chen S. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour 2023. [PMID: 36789493 DOI: 10.1111/1755-0998.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Many recent studies have provided significant insights into polyploid breeding, but limited research has been carried out on trees. The genomic information needed to understand growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to forests imposed by climate change. Populus alba 'Berolinensis,' also known "Yinzhong poplar," is a triploid poplar from northeast China. This hybrid triploid poplar is widely used as a landscape ornamental and in urban forestry owing to its adaptation to adverse environments and faster growth than its parental diploid. It is an artificially synthesized male allotriploid hybrid, with three haploid genomes of P. alba 'Berolinensis' originating from different poplar species, so it is attractive for studying polyploidy genomic mechanisms in heterosis. In this study, we focused on the allelic genomic interactions in P. alba 'Berolinensis,' and generated a high-quality chromosome-level genome assembly consisting of 19 allelic chromosomes. Its three haploid chromosome sets are polymorphic with an average of 25.73 nucleotide polymorphism sites per kilobase. We found that some stress-related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. The genome assembly has been deposited in our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genome-related resources will provide a critical foundation for the molecular breeding of P. alba 'Berolinensis' and help us uncover the allopolyploidization effects of heterosis and abiotic stress resistance and traits of polyploidy species in the future.
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Affiliation(s)
- Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruihan He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenxuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jinwen Liu
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
| | - Qiwen Guo
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R Sederoff
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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15
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Ma M, Zhong W, Zhang Q, Deng L, Wen J, Yi B, Tu J, Fu T, Zhao L, Shen J. Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid. FRONTIERS IN PLANT SCIENCE 2023; 14:1123729. [PMID: 36778699 PMCID: PMC9911877 DOI: 10.3389/fpls.2023.1123729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
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16
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Xie J, Wang W, Yang T, Zhang Q, Zhang Z, Zhu X, Li N, Zhi L, Ma X, Zhang S, Liu Y, Wang X, Li F, Zhao Y, Jia X, Zhou J, Jiang N, Li G, Liu M, Liu S, Li L, Zeng A, Du M, Zhang Z, Li J, Zhang Z, Li Z, Zhang H. Large-scale genomic and transcriptomic profiles of rice hybrids reveal a core mechanism underlying heterosis. Genome Biol 2022; 23:264. [PMID: 36550554 PMCID: PMC9773586 DOI: 10.1186/s13059-022-02822-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Heterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and 265 rice varieties from a mini-core collection. RESULTS Phenotypic analysis shows that heterosis is dependent on genetic backgrounds and environments. By genome-wide association study of 418 hybrids and their parents, we find that nonadditive QTLs are the main genetic contributors to heterosis. We show that nonadditive QTLs are more sensitive to the genetic background and environment than additive ones. Further simulations and experimental analysis support a novel mechanism, homo-insufficiency under insufficient background (HoIIB), underlying heterosis. We propose heterosis in most cases is not due to heterozygote advantage but homozygote disadvantage under the insufficient genetic background. CONCLUSION The HoIIB model elucidates that genetic background insufficiency is the intrinsic mechanism of background dependence, and also the core mechanism of nonadditive effects and heterosis. This model can explain most known hypotheses and phenomena about heterosis, and thus provides a novel theory for hybrid rice breeding in future.
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Affiliation(s)
- Jianyin Xie
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weiping Wang
- grid.496830.00000 0004 7648 0514State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Tao Yang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Quan Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhifang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoyang Zhu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ni Li
- grid.496830.00000 0004 7648 0514State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Linran Zhi
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoqian Ma
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Shuyang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yan Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xueqiang Wang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Fengmei Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China
| | - Yan Zhao
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xuewei Jia
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jieyu Zhou
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ningjia Jiang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| | - Gangling Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Miaosong Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Shijin Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lin Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - An Zeng
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| | - Mengke Du
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China
| | - Zhanying Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jinjie Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ziding Zhang
- grid.22935.3f0000 0004 0530 8290State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193 China
| | - Zichao Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China ,grid.22935.3f0000 0004 0530 8290State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193 China
| | - Hongliang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
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17
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Zhou T, Afzal R, Haroon M, Ma Y, Zhang H, Li L. Dominant complementation of biological pathways in maize hybrid lines is associated with heterosis. PLANTA 2022; 256:111. [PMID: 36352050 DOI: 10.1007/s00425-022-04028-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Allele-specific expressed genes (ASEGs) are widespread in maize hybrid lines and play important roles of complementation of biological pathways in heterosis. Heterosis (hybrid vigor) is an important phenomenon with both theoretical and practical value. However, our understanding of the genetic and molecular mechanisms behind heterosis is still limited. Here, we analyzed a comprehensive dataset of maize (Zea mays L.), including RNA-seq data from three hybrid-parent triplets (HPTs) and acetylated protein data from one HPT. The gene expression patterns exhibited extensive variation between the hybrids and their parents, and a substantial number of allele-specific expressed genes (ASEGs) were identified in the hybrids. Notably, ASEGs from different HPTs were significantly enriched in various conserved pathways. The parental alleles of ASEGs with fewer deleterious single-nucleotide polymorphisms were more likely to be expressed in hybrid lines than other parental alleles. ASEGs were mainly enriched in the functional gene ontology terms protein biosynthesis, photosynthesis, and metabolism. In addition, the ASEGs across the three HPTs were involved in key photosynthetic pathways and might enhance the photosynthetic efficiency of the hybrids. These findings suggest that ASEGs involved in complementary biological pathways in maize hybrids contribute to heterosis, shedding new light on the molecular mechanism of heterosis.
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Affiliation(s)
- Tao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rabail Afzal
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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18
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Lee SJ, Kang K, Lim JH, Paek NC. Natural alleles of CIRCADIAN CLOCK ASSOCIATED1 contribute to rice cultivation by fine-tuning flowering time. PLANT PHYSIOLOGY 2022; 190:640-656. [PMID: 35723564 PMCID: PMC9434239 DOI: 10.1093/plphys/kiac296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The timing of flowering is a crucial factor for successful grain production at a wide range of latitudes. Domestication of rice (Oryza sativa) included selection for natural alleles of flowering-time genes that allow rice plants to adapt to broad geographic areas. Here, we describe the role of natural alleles of CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) in cultivated rice based on analysis of single-nucleotide polymorphisms deposited in the International Rice Genebank Collection Information System database. Rice varieties harboring japonica-type OsCCA1 alleles (OsCCA1a haplotype) flowered earlier than those harboring indica-type OsCCA1 alleles (OsCCA1d haplotype). In the japonica cultivar "Dongjin", a T-DNA insertion in OsCCA1a resulted in late flowering under long-day and short-day conditions, indicating that OsCCA1 is a floral inducer. Reverse transcription quantitative PCR analysis showed that the loss of OsCCA1a function induces the expression of the floral repressors PSEUDO-RESPONSE REGULATOR 37 (OsPRR37) and Days to Heading 8 (DTH8), followed by repression of the Early heading date 1 (Ehd1)-Heading date 3a (Hd3a)-RICE FLOWERING LOCUS T 1 (RFT1) pathway. Binding affinity assays indicated that OsCCA1 binds to the promoter regions of OsPRR37 and DTH8. Naturally occurring OsCCA1 alleles are evolutionarily conserved in cultivated rice (O. sativa). Oryza rufipogon-I (Or-I) and Or-III type accessions, representing the ancestors of O. sativa indica and japonica, harbored indica- and japonica-type OsCCA1 alleles, respectively. Taken together, our results demonstrate that OsCCA1 is a likely domestication locus that has contributed to the geographic adaptation and expansion of cultivated rice.
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Affiliation(s)
| | | | - Jung-Hyun Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
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19
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Shahzad K, Zhang X, Zhang M, Guo L, Qi T, Tang H, Wang H, Mubeen I, Qiao X, Peng R, Wu J, Xing C. Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization. Funct Integr Genomics 2022; 22:757-768. [PMID: 35771309 DOI: 10.1007/s10142-022-00877-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybridization is useful to enhance the yield potential of agronomic crops in the world. Cotton has genome doubling due to the allotetraploid process and hybridization in coordination with duplicated genome can produce more yield and adaptability. Therefore, the expression of homoeologous gene pairs between hybrids and inbred parents is vital to characterize the genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (an average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.
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Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Iqra Mubeen
- Department of Biochemistry, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Renhai Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China. .,College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China.
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. .,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. .,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
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20
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Okubo K, Kaneko K. Heterosis of fitness and phenotypic variance in the evolution of a diploid gene regulatory network. PNAS NEXUS 2022; 1:pgac097. [PMID: 36741431 PMCID: PMC9896930 DOI: 10.1093/pnasnexus/pgac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/24/2022] [Indexed: 02/07/2023]
Abstract
Heterosis describes the phenomenon, whereby a hybrid population has higher fitness than an inbred population, which has previously been explained by either Mendelian dominance or overdominance under the general assumption of a simple genotype-phenotype relationship. However, recent studies have demonstrated that genes interact through a complex gene regulatory network (GRN). Furthermore, phenotypic variance is reportedly lower for heterozygotes, and the origin of such variance-related heterosis remains elusive. Therefore, a theoretical analysis linking heterosis to GRN evolution and stochastic gene expression dynamics is required. Here, we investigated heterosis related to fitness and phenotypic variance in a system with interacting genes by numerically evolving diploid GRNs. According to the results, the heterozygote population exhibited higher fitness than the homozygote population, indicating fitness-related heterosis resulting from evolution. In addition, the heterozygote population exhibited lower noise-related phenotypic variance in expression levels than the homozygous population, implying that the heterozygote population is more robust to noise. Furthermore, the distribution of the ratio of heterozygote phenotypic variance to homozygote phenotypic variance exhibited quantitative similarity with previous experimental results. By applying dominance and differential gene expression rather than only a single gene expression model, we confirmed the correlation between heterosis and differential gene expression. We explain our results by proposing that the convex high-fitness region is evolutionarily shaped in the genetic space to gain noise robustness under genetic mixing through sexual reproduction. These results provide new insights into the effects of GRNs on variance-related heterosis and differential gene expression.
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Affiliation(s)
- Kenji Okubo
- Research Center for Integrative Evolutionary Science, the Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa, 240-0193, Japan
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21
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Baldauf JA, Liu M, Vedder L, Yu P, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids. PLANT PHYSIOLOGY 2022; 189:1625-1638. [PMID: 35522211 PMCID: PMC9237695 DOI: 10.1093/plphys/kiac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The dominance model of heterosis explains the superior performance of F1-hybrids via the complementation of deleterious alleles by beneficial alleles in many genes. Genes active in one parent but inactive in the second lead to single-parent expression (SPE) complementation in maize (Zea mays L.) hybrids. In this study, SPE complementation resulted in approximately 700 additionally active genes in different tissues of genetically diverse maize hybrids on average. We established that the number of SPE genes is significantly associated with mid-parent heterosis (MPH) for all surveyed phenotypic traits. In addition, we highlighted that maternally (SPE_B) and paternally (SPE_X) active SPE genes enriched in gene co-expression modules are highly correlated within each SPE type but separated between these two SPE types. While SPE_B-enriched co-expression modules are positively correlated with phenotypic traits, SPE_X-enriched modules displayed a negative correlation. Gene ontology term enrichment analyses indicated that SPE_B patterns are associated with growth and development, whereas SPE_X patterns are enriched in defense and stress response. In summary, these results link the degree of phenotypic MPH to the prevalence of gene expression complementation observed by SPE, supporting the notion that hybrids benefit from SPE complementation via its role in coordinating maize development in fluctuating environments.
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Affiliation(s)
- Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | | | - Lucia Vedder
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Hans-Peter Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany
| | - Heiko Schoof
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210, USA
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22
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Koyro HW, Huchzermeyer B. From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity. PLANTS 2022; 11:plants11131654. [PMID: 35807605 PMCID: PMC9269222 DOI: 10.3390/plants11131654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022]
Abstract
Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.
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Affiliation(s)
- Hans-Werner Koyro
- Institute of Plantecology, Justus-Liebig-University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- Correspondence:
| | - Bernhard Huchzermeyer
- Institute of Botany, Leibniz Universitaet Hannover, Herrenhaeuser Str. 2, 30416 Hannover, Germany; or
- AK Biotechnology, VDI-BV-Hannover, Hanomagstr. 12, 30449 Hannover, Germany
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23
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Xu Z, Li E, Xue G, Zhang C, Yang Y, Ding Y. OsHUB2 inhibits function of OsTrx1 in heading date in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1670-1680. [PMID: 35395113 DOI: 10.1111/tpj.15763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/15/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Heading date is one of the most pivotal agronomic traits for rice (Oryza sativa) yield and adaptation. Little is known about the crosstalk between histone ubiquitination and histone methylation in rice heading date regulation. Here, we reported HISTONE MONOUBIQUITINATION 1 (OsHUB1) and OsHUB2 are involved in heading date regulation via the Hd1 and Ehd1 pathway. Loss of OsHUB1 and OsHUB2 function resulted in early heading under long-day and short-day photoperiods. The expression of Hd3a, RFT1, and Ehd1 was induced and the transcript levels of Hd1, Ghd7, OsCCA1, OsGI, OsFKF1, and OsTOC1 were reduced under long-day conditions, whereas RFT1 and Ehd1 expression was induced in oshub2 mutants under short-day conditions. OsHUB2 interacted with OsTrx1 and repressed the gene expression of OsTrx1. OsHUB2 directly bound to Ehd1 to ubiquitinate H2B at Ehd1, and H2B ubiquitination levels were reduced in oshub2-2 and oshub2-3 mutants. OsTrx1 were highly enriched at Ehd1, and H3K4me3 levels of Ehd1 were upregulated in oshub2-2. Mutations of OsTrx1 in the oshub2-2 background rescued the early-heading phenotype of oshub2-2. The increases in Ehd1 H3K4me3 levels and transcript levels in oshub2-2 mutants were attenuated in oshub2-2 ostrx1-2 double mutants. Together, our results (i) reveal that OsHUB2 represses the function of OsTrx1 and H3K4me3 levels at Ehd1 and (ii) suggest that OsHUB2-mediated H2B ubiquitination plays critical roles together with H3K4me3 in rice heading date regulation.
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Affiliation(s)
- Zuntao Xu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Enze Li
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Gan Xue
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Cheng Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Yachun Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yong Ding
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
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24
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Lee JS, Jahani M, Huang K, Mandel JR, Marek LF, Burke JM, Langlade NB, Owens GL, Rieseberg LH. Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower. J Adv Res 2022; 42:83-98. [PMID: 36513422 PMCID: PMC9788961 DOI: 10.1016/j.jare.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/01/2022] [Accepted: 04/16/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood. OBJECTIVES This study aimed to (1) elucidate the genetic and molecular mechanisms underlying heterosis in sunflower, and (2) determine how heterosis is maintained under different environments. METHODS Genome-wide association (GWA) analyses were employed to assess the effects of presence/absence variants (PAVs) and stop codons on 16 traits phenotyped in the sunflower association mapping population at three locations. To link the GWA results to transcriptomic variation, we sequenced the transcriptomes of two sunflower cultivars and their F1 hybrid (INEDI) under both control and drought conditions and analyzed patterns of gene expression and alternative splicing. RESULTS Thousands of PAVs were found to affect phenotypic variation using a relaxed significance threshold, and at most such loci the "absence" allele reduced values of heterotic traits, but not those of non-heterotic traits. This pattern was strengthened for PAVs that showed expression complementation in INEDI. Stop codons were much rarer than PAVs and less likely to reduce heterotic trait values. Hybrid expression patterns were enriched for the GO category, sensitivity to stimulus, but all genotypes responded to drought similarily - by up-regulating water stress response pathways and down-regulating metabolic pathways. Changes in alternative splicing were strongly negatively correlated with expression variation, implying that alternative splicing in this system largely acts to reinforce expression responses. CONCLUSION Our results imply that complementation of expression of PAVs in hybrids is a major contributor to heterosis in sunflower, consistent with the dominance model of heterosis. This mechanism can account for yield stability across different environments. Moreover, given the much larger numbers of PAVs in plant vs. animal genomes, it also offers an explanation for the stronger heterotic responses seen in the former.
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Affiliation(s)
- Joon Seon Lee
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer R. Mandel
- Department of Biological Sciences and Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Laura F. Marek
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens 30602, Georgia
| | | | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada,Corresponding author.
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25
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Liu W, Zhang Y, He H, He G, Deng XW. From hybrid genomes to heterotic trait output: Challenges and opportunities. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102193. [PMID: 35219140 DOI: 10.1016/j.pbi.2022.102193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Heterosis (or hybrid vigor) has been widely used in crop seed breeding to improve many key economic traits. Nevertheless, the genetic and molecular basis of this important phenomenon has long remained elusive, constraining its flexible and effective exploitation. Advanced genomic approaches are efficient in characterizing the mechanism of heterosis. Here, we review how the omics approaches, including genomic, transcriptomic, and population genetics methods such as genome-wide association studies, can reveal how hybrid genomes outperform parental genomes in plants. This information opens up opportunities for genomic exploration and manipulation of heterosis in crop breeding.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yilin Zhang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China.
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26
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Perrier A, Sánchez-Castro D, Willi Y. Environment dependence of the expression of mutational load and species' range limits. J Evol Biol 2022; 35:731-741. [PMID: 35290676 PMCID: PMC9314787 DOI: 10.1111/jeb.13997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 12/21/2022]
Abstract
Theoretical and empirical research on the causes of species’ range limits suggest the contribution of several intrinsic and extrinsic factors, with potentially complex interactions among them. An intrinsic factor proposed by recent theory is mutational load increasing towards range edges because of genetic drift. Furthermore, environmental quality may decline towards range edges and enhance the expression of load. Here, we tested whether the expression of mutational load associated with range limits in the North American plant Arabidopsis lyrata was enhanced under stressful environmental conditions by comparing the performance of within‐ versus between‐population crosses at common garden sites across the species’ distribution and beyond. Heterosis, reflecting the expression of load, increased with heightened estimates of genomic load and with environmental stress caused by warming, but the interaction was not significant. We conclude that range‐edge populations suffer from a twofold genetic Allee effect caused by increased mutational load and stress‐dependent load linked to general heterozygote deficiency, but there is no synergistic effect between them.
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Affiliation(s)
- Antoine Perrier
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | | | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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27
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Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂). FISHES 2022. [DOI: 10.3390/fishes7010043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hybrid tilapia were produced from hybridization of Nile tilapia (Oreochromis niloticus) and blue tilapia (O. aureus). Comparative transcriptome analysis was carried out on the liver of hybrid tilapia and their parents by RNA sequencing. A total of 2319 differentially expressed genes (DEGs) were identified. Trend co-expression analysis showed that non-additive gene expression accounted for 67.1% of all DEGs. Gene Ontology and KEGG enrichment analyses classified the respective DEGs. Gene functional enrichment analysis indicated that most up-regulated genes, such as FASN, ACSL1, ACSL3, ACSL6, ACACA, ELOVL6, G6PD, ENO1, GATM, and ME3, were involved in metabolism, including fatty acid biosynthesis, unsaturated fatty acid biosynthesis, glycolysis, pentose phosphate pathway, amino acid metabolism, pyruvate metabolism, and the tricarboxylic acid cycle. The expression levels of a gene related to ribosomal biosynthesis in eukaryotes, GSH-Px, and those associated with heat shock proteins (HSPs), such as HSPA5 and HSP70, were significantly down-regulated compared with the parent tilapia lineages. The results revealed that the metabolic pathway in hybrid tilapia was up-regulated, with significantly improved fatty acid metabolism and carbon metabolism, whereas ribosome biosynthesis in eukaryotes and basal defense response were significantly down-regulated. These findings provide new insights into our understanding of growth heterosis in hybrid tilapia.
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28
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Cao S, Wang L, Han T, Ye W, Liu Y, Sun Y, Moose SP, Song Q, Chen ZJ. Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize. Genome Biol 2022; 23:53. [PMID: 35139883 PMCID: PMC8827192 DOI: 10.1186/s13059-022-02614-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
Background Hybridization and backcrossing are commonly used in animal and plant breeding to induce heritable variation including epigenetic changes such as paramutation. However, the molecular basis for hybrid-induced epigenetic memory remains elusive. Results Here, we report that hybridization between the inbred parents B73 and Mo17 induces trans-acting hypermethylation and hypomethylation at thousands of loci; several hundreds (~ 3%) are transmitted through six backcrossing and three selfing generations. Notably, many transgenerational methylation patterns resemble epialleles of the nonrecurrent parent, despite > 99% of overall genomic loci are converted to the recurrent parent. These epialleles depend on 24-nt siRNAs, which are eliminated in the isogenic hybrid Mo17xB73:mop1-1 that is defective in siRNA biogenesis. This phenomenon resembles paramutation-like events and occurs in both intraspecific (Mo17xB73) and interspecific (W22xTeosinte) hybrid maize populations. Moreover, siRNA abundance and methylation levels of these epialleles can affect expression of their associated epigenes, many of which are related to stress responses. Conclusion Divergent siRNAs between the hybridizing parents can induce trans-acting epialleles in the hybrids, while the induced epigenetic status is maintained for transgenerational inheritance during backcross and hybrid breeding, which alters epigene expression to enhance growth and adaptation. These genetic and epigenetic principles may apply broadly from plants to animals. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02614-0.
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Affiliation(s)
- Shuai Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Longfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Tongwen Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yi Sun
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Stephen P Moose
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China.
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Birdseye D, de Boer LA, Bai H, Zhou P, Shen Z, Schmelz EA, Springer NM, Briggs SP. Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins. Proc Natl Acad Sci U S A 2021; 118:e2109332118. [PMID: 34782463 PMCID: PMC8617506 DOI: 10.1073/pnas.2109332118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
The use of hybrids is widespread in agriculture, yet the molecular basis for hybrid vigor (heterosis) remains obscure. To identify molecular components that may contribute to trait heterosis, we analyzed paired proteomic and transcriptomic data from seedling leaf and mature leaf blade tissues of maize hybrids and their inbred parents. Nuclear- and plastid-encoded subunits of complexes required for protein synthesis in the chloroplast and for the light reactions of photosynthesis were expressed above midparent and high-parent levels, respectively. Consistent with previous reports in Arabidopsis, ethylene biosynthetic enzymes were expressed below midparent levels in the hybrids, suggesting a conserved mechanism for heterosis between monocots and dicots. The ethylene biosynthesis mutant, acs2/acs6, largely phenocopied the hybrid proteome, indicating that a reduction in ethylene biosynthesis may mediate the differences between inbreds and their hybrids. To rank the relevance of expression differences to trait heterosis, we compared seedling leaf protein levels to the adult plant height of 15 hybrids. Hybrid/midparent expression ratios were most positively correlated with hybrid/midparent plant height ratios for the chloroplast ribosomal proteins. Our results show that increased expression of chloroplast ribosomal proteins in hybrid seedling leaves is mediated by reduced expression of ethylene biosynthetic enzymes and that the degree of their overexpression in seedlings can quantitatively predict adult trait heterosis.
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Affiliation(s)
- Devon Birdseye
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Laura A de Boer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Hua Bai
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Eric A Schmelz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Steven P Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
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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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Abstract
Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.
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Zhang Y, Cheng P, Wang J, Abdalmegeed D, Li Y, Wu M, Dai C, Wan S, Guan R, Pu H, Shen W. Nitric Oxide Is Associated With Heterosis of Salinity Tolerance in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2021; 12:649888. [PMID: 34122475 PMCID: PMC8194068 DOI: 10.3389/fpls.2021.649888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/13/2021] [Indexed: 06/01/2023]
Abstract
Heterosis is most frequently manifested as the superior performance of a hybrid than either of the parents, especially under stress conditions. Nitric oxide (NO) is a well-known gaseous signaling molecule that acts as a functional component during plant growth, development, and defense responses. In this study, the Brassica napus L. hybrid (F1, NJ4375 × MB1942) showed significant heterosis under salt stress, during both germination and post-germination periods. These phenotypes in the hybrid were in parallel with the better performance in redox homeostasis, including alleviation of reactive oxygen species accumulation and lipid peroxidation, and ion homeostasis, evaluated as a lower Na/K ratio in the leaves than parental lines. Meanwhile, stimulation of endogenous NO was more pronounced in hybrid plants, compared with parental lines, which might be mediated by nitrate reductase. Proteomic and biochemical analyses further revealed that protein abundance related to several metabolic processes, including chlorophyll biosynthesis, proline metabolism, and tricarboxylic acid cycle metabolism pathway, was greatly suppressed by salt stress in the two parental lines than in the hybrid. The above responses in hybrid plants were intensified by a NO-releasing compound, but abolished by a NO scavenger, both of which were matched with the changes in chlorophyll and proline contents. It was deduced that the above metabolic processes might play important roles in heterosis upon salt stress. Taken together, we proposed that heterosis derived from F1 hybridization in salt stress tolerance might be mediated by NO-dependent activation of defense responses and metabolic processes.
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Affiliation(s)
- Yihua Zhang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- Ministry of Agriculture’s Key Laboratory of Cotton and Rapeseed, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Pengfei Cheng
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dyaaaldin Abdalmegeed
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ying Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mangteng Wu
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Chen Dai
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Huiming Pu
- Ministry of Agriculture’s Key Laboratory of Cotton and Rapeseed, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Sarfraz Z, Iqbal MS, Geng X, Iqbal MS, Nazir MF, Ahmed H, He S, Jia Y, Pan Z, Sun G, Ahmad S, Wang Q, Qin H, Liu J, Liu H, Yang J, Ma Z, Xu D, Yang J, Zhang J, Li Z, Cai Z, Zhang X, Zhang X, Huang A, Yi X, Zhou G, Li L, Zhu H, Pang B, Wang L, Sun J, Du X. GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton ( Gossypium hirsutum L.) Across Multiple Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:565552. [PMID: 34093598 PMCID: PMC8173050 DOI: 10.3389/fpls.2021.565552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F1 hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F1 hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.
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Affiliation(s)
- Zareen Sarfraz
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Shahid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Sajid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Haris Ahmed
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, China
| | - Saghir Ahmad
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Qinglian Wang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Hongde Qin
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jinhai Liu
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | - Hui Liu
- Jing Hua Seed Industry Technologies Inc., Jingzhou, China
| | - Jun Yang
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Zhiying Ma
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Dongyong Xu
- Guoxin Rural Technical Service Association, Hebei, China
| | - Jinlong Yang
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | | | - Zhikun Li
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Zhongmin Cai
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | | | - Xin Zhang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Aifen Huang
- Sanyi Seed Industry of Changde in Hunan Inc., Changde, China
| | - Xianda Yi
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guanyin Zhou
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | - Lin Li
- Zhongli Company of Shandong, Shandong, China
| | - Haiyong Zhu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Baoyin Pang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
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A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs. Nat Commun 2021; 12:2317. [PMID: 33875651 PMCID: PMC8055661 DOI: 10.1038/s41467-021-22268-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/05/2021] [Indexed: 11/10/2022] Open
Abstract
Plant immunity frequently incurs growth penalties, which known as the trade-off between immunity and growth. Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits but rarely for disease resistance. Here, we report that the central circadian oscillator, CCA1, confers heterosis for bacterial defense in hybrids without growth vigor costs, and it even significantly enhances the growth heterosis of hybrids under pathogen infection. The genetic perturbation of CCA1 abrogated heterosis for both defense and growth in hybrids. Upon pathogen attack, the expression of CCA1 in F1 hybrids is precisely modulated at different time points during the day by its rhythmic histone modifications. Before dawn of the first infection day, epigenetic activation of CCA1 promotes an elevation of salicylic acid accumulation in hybrids, enabling heterosis for defense. During the middle of every infection day, diurnal epigenetic repression of CCA1 leads to rhythmically increased chlorophyll synthesis and starch metabolism in hybrids, effectively eliminating the immunity-growth heterosis trade-offs in hybrids. There is frequently a trade-off between plant immunity and growth. Here the authors show that the epigenetic control of CCA1, encoding a core component of the circadian oscillator, simultaneously promotes heterosis for both defense and growth in hybrids under pathogen invasion.
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35
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Ding Y, Zhang R, Zhu L, Wang M, Ma Y, Yuan D, Liu N, Hu H, Min L, Zhang X. An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid 'Huaza Mian H318', as revealed by genome-wide gene expression analysis. BMC Genomics 2021; 22:277. [PMID: 33865322 PMCID: PMC8052695 DOI: 10.1186/s12864-021-07580-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 04/04/2021] [Indexed: 12/15/2022] Open
Abstract
Background Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton. Results The elite cotton hybrid variety ‘Huaza Mian H318’ (H318) and its parental lines were used to explore the source of its yield heterosis. A four-year investigation of yield-related traits showed that the boll number of H318 showed higher stability than that of its two parents, both in suitable and unsuitable climate years. In addition, the hybrid H318 grew faster and showed higher fresh and dry weights than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differentially expressed genes (DEGs) between H318 and its parental lines, and 3490 extremely changed DEGs were screened out for later analysis. Most DEGs (3472/3490) were gathered between H318 and its paternal line (4–5), and only 64 DEGs were found between H318 and its maternal line (B0011), which implied that H318 displays more similar transcriptional patterns to its maternal parent at the seedling stage. GO and KEGG analyses showed that these DEGs were highly enriched in photosynthesis, lipid metabolic, carbohydrate metabolic and oxidation-reduction processes, and the expression level of these DEGs was significantly higher in H318 relative to its parental lines, which implied that photosynthesis, metabolism and stress resistances were enhanced in H318. Conclusion The enhanced photosynthesis, lipid and carbohydrate metabolic capabilities contribute to the heterosis of H318 at the seedling stage, and establishes a material foundation for subsequent higher boll-setting rates in complex field environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07580-8.
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Affiliation(s)
- Yuanhao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance. Proc Natl Acad Sci U S A 2021; 118:2023981118. [PMID: 33771925 DOI: 10.1073/pnas.2023981118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polyploidy is a prominent feature for genome evolution in many animals and all flowering plants. Plant polyploids often show enhanced fitness in diverse and extreme environments, but the molecular basis for this remains elusive. Soil salinity presents challenges for many plants including agricultural crops. Here we report that salt tolerance is enhanced in tetraploid rice through lower sodium uptake and correlates with epigenetic regulation of jasmonic acid (JA)-related genes. Polyploidy induces DNA hypomethylation and potentiates genomic loci coexistent with many stress-responsive genes, which are generally associated with proximal transposable elements (TEs). Under salt stress, the stress-responsive genes including those in the JA pathway are more rapidly induced and expressed at higher levels in tetraploid than in diploid rice, which is concurrent with increased jasmonoyl isoleucine (JA-Ile) content and JA signaling to confer stress tolerance. After stress, elevated expression of stress-responsive genes in tetraploid rice can induce hypermethylation and suppression of the TEs adjacent to stress-responsive genes. These induced responses are reproducible in a recurring round of salt stress and shared between two japonica tetraploid rice lines. The data collectively suggest a feedback relationship between polyploidy-induced hypomethylation in rapid and strong stress response and stress-induced hypermethylation to repress proximal TEs and/or TE-associated stress-responsive genes. This feedback regulation may provide a molecular basis for selection to enhance adaptation of polyploid plants and crops during evolution and domestication.
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37
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Sugi N, Le QTN, Kobayashi M, Kusano M, Shiba H. Integrated transcript and metabolite profiling reveals coordination between biomass size and nitrogen metabolism in Arabidopsis F 1 hybrids. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:67-75. [PMID: 34177326 PMCID: PMC8215461 DOI: 10.5511/plantbiotechnology.20.1126a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/26/2020] [Indexed: 05/24/2023]
Abstract
Heterosis refers to the improved agronomic performance of F1 hybrids relative to their parents. Although this phenomenon is widely employed to increase biomass, yield, and stress tolerance of plants, the underlying molecular mechanisms remain unclear. To dissect the metabolic fluctuations derived from genomic and/or environmental differences contributing to the improved biomass of F1 hybrids relative to their parents, we optimized the growth condition for Arabidopsis thaliana F1 hybrids and their parents. Modest but statistically significant increase in the biomass of F1 hybrids was observed. Plant samples grown under the optimized condition were also utilized for integrated omics analysis to capture specific changes in the F1 hybrids. Metabolite profiling of F1 hybrids and parent plants was performed using gas chromatography-mass spectrometry. Among the detected 237 metabolites, 2-oxoglutarate (2-OG) and malate levels were lower and the level of aspartate was higher in the F1 hybrids than in each parent. In addition, microarray analysis revealed that there were 44 up-regulated and 12 down-regulated genes with more than 1.5-fold changes in expression levels in the F1 hybrid compared to each parent. Gene ontology (GO) analyses indicated that genes up-regulated in the F1 hybrids were largely related to organic nitrogen (N) process. Quantitative PCR verified that glutamine synthetase 2 (AtGLN2) was upregulated in the F1 hybrids, while other genes encoding enzymes in the GS-GOGAT cycle showed no significant differences between the hybrid and parent lines. These results suggested the existence of metabolic regulation that coordinates biomass and N metabolism involving AtGLN2 in F1 hybrids.
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Affiliation(s)
- Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Kobayashi
- Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Miyako Kusano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
- Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Shiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
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38
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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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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Wang D, Mu Y, Hu X, Ma B, Wang Z, Zhu L, Xu J, Huang C, Pan Y. Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively. BMC PLANT BIOLOGY 2021; 21:34. [PMID: 33422018 PMCID: PMC7796551 DOI: 10.1186/s12870-020-02806-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/20/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids. RESULTS Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. CONCLUSIONS Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.
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Affiliation(s)
- Daoping Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yongying Mu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xiaojiao Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, People's Republic of China
| | - Bo Ma
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Zhibo Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Jiang Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Changling Huang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, People's Republic of China.
| | - Yinghong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, People's Republic of China.
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Cooper RD, Shaffer HB. Allele-specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense). Mol Ecol 2021; 30:987-1004. [PMID: 33338297 DOI: 10.1111/mec.15779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 01/26/2023]
Abstract
Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele-specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.
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Affiliation(s)
- Robert D Cooper
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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Mackay IJ, Cockram J, Howell P, Powell W. Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:26-34. [PMID: 32996672 PMCID: PMC7769232 DOI: 10.1111/pbi.13481] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 09/07/2020] [Accepted: 09/12/2020] [Indexed: 05/12/2023]
Abstract
Transgressive segregation and heterosis are the reasons that plant breeding works. Molecular explanations for both phenomena have been suggested and play a contributing role. However, it is often overlooked by molecular genetic researchers that transgressive segregation and heterosis are most simply explained by dispersion of favorable alleles. Therefore, advances in molecular biology will deliver the most impact on plant breeding when integrated with sources of heritable trait variation - and this will be best achieved within a quantitative genetics framework. An example of the power of quantitative approaches is the implementation of genomic selection, which has recently revolutionized animal breeding. Genomic selection is now being applied to both hybrid and inbred crops and is likely to be the major source of improvement in plant breeding practice over the next decade. Breeders' ability to efficiently apply genomic selection methodologies is due to recent technology advances in genotyping and sequencing. Furthermore, targeted integration of additional molecular data (such as gene expression, gene copy number and methylation status) into genomic prediction models may increase their performance. In this review, we discuss and contextualize a suite of established quantitative genetics themes relating to hybrid vigour, transgressive segregation and their central relevance to plant breeding, with the aim of informing crop researchers outside of the quantitative genetics discipline of their relevance and importance to crop improvement. Better understanding between molecular and quantitative disciplines will increase the potential for further improvements in plant breeding methodologies and so help underpin future food security.
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Affiliation(s)
- Ian J. Mackay
- SRUC (Scotland’s Rural College)EdinburghUK
- IMplant ConsultancyChelmsfordUK
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Li Z, Zhu A, Song Q, Chen HY, Harmon FG, Chen ZJ. Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis. THE PLANT CELL 2020; 32:3706-3722. [PMID: 33004616 PMCID: PMC7721322 DOI: 10.1105/tpc.20.00320] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 05/04/2023]
Abstract
Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.
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Affiliation(s)
- Zhi Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andan Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Helen Y Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Frank G Harmon
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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Zhang H, Zhao Y, Zhu JK. Thriving under Stress: How Plants Balance Growth and the Stress Response. Dev Cell 2020; 55:529-543. [DOI: 10.1016/j.devcel.2020.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/21/2020] [Accepted: 10/17/2020] [Indexed: 12/24/2022]
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Ahmadizadeh M, Chen JT, Hasanzadeh S, Ahmar S, Heidari P. Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa. J Genet Eng Biotechnol 2020; 18:62. [PMID: 33074438 PMCID: PMC7572930 DOI: 10.1186/s43141-020-00083-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022]
Abstract
Background Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous). Results The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice. Conclusion In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection.
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Affiliation(s)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, 811, Taiwan
| | - Soosan Hasanzadeh
- Department of Horticultural Sciences, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Sunny Ahmar
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Parviz Heidari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran.
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Inoue K, Takahagi K, Kouzai Y, Koda S, Shimizu M, Uehara-Yamaguchi Y, Nakayama R, Kita T, Onda Y, Nomura T, Matsui H, Nagaki K, Nishii R, Mochida K. Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy. NAR Genom Bioinform 2020; 2:lqaa067. [PMID: 33575616 PMCID: PMC7671347 DOI: 10.1093/nargab/lqaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/15/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative Brachypodium cytotypes, including the allotetraploid Brachypodium hybridum and its diploid progenitors Brachypodium distachyon and Brachypodium stacei. We also artificially induced an autotetraploid B. distachyon. We identified patterns of homoeolog expression bias (HEB) across Brachypodium cytotypes and time-dependent gain and loss of HEB in B. hybridum. Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in B. hybridum relative to B. distachyon and B. stacei, suggesting diurnal synchronization of homoeolog expression in B. hybridum. Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in Brachypodium, and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy.
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Affiliation(s)
- Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yusuke Kouzai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Risa Nakayama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshie Kita
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hidetoshi Matsui
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
| | - Ryuei Nishii
- School of Information and Data Science, Nagasaki University, Nagasaki, 852-8131, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
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Song Q, Ando A, Jiang N, Ikeda Y, Chen ZJ. Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biol 2020; 21:178. [PMID: 32698836 PMCID: PMC7375004 DOI: 10.1186/s13059-020-02094-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect. RESULTS To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER (DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization. CONCLUSIONS Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
| | - Ning Jiang
- Department of Biomedical Engineering, The University of Texas at Austin, 1 University Station C0800, Austin, TX, 78712, USA
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA.
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Yu K, Wang H, Liu X, Xu C, Li Z, Xu X, Liu J, Wang Z, Xu Y. Large-Scale Analysis of Combining Ability and Heterosis for Development of Hybrid Maize Breeding Strategies Using Diverse Germplasm Resources. FRONTIERS IN PLANT SCIENCE 2020; 11:660. [PMID: 32547580 PMCID: PMC7278714 DOI: 10.3389/fpls.2020.00660] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/28/2020] [Indexed: 05/14/2023]
Abstract
Understanding combining ability and heterosis among diverse maize germplasm resources is important for breeding hybrid maize (Zea mays L.). Using 28 temperate and 23 tropical maize inbreds that represent different ecotypes and worldwide diversity of maize germplasm, we first developed a large-scale multiple-hybrid population (MHP) with 724 hybrids, which could be divided into three subsets, 325 temperate diallel hybrids and 136 tropical diallel hybrids generated in Griffing IV, and 263 temperate by tropical hybrids generated in NCD II. All the parental lines and hybrids were evaluated for 11 traits in replicated tests across two locations and three years. Several widely used inbreds showed strong general combining ability (GCA), and their derived hybrids showed strong specific combining ability (SCA). Heterosis is a quantifiable, trait-dependent and environment-specific phenotype, and the response of parental lines and their hybrids to environments resulted in various levels of heterosis. For all the tested traits except plant height and hundred grain weight (HGW), NCD II (temperate × tropical) hybrids showed higher average heterosis than the temperate and tropical diallel hybrids, with higher hybrid performance for ear length, ear diameter, and HGW. Tropical maize germplasm can be used to improve the yield potential for temperate lines. Grain number per row and grain number per ear were two most important traits that determined yield heterosis, which can be used as direct selection criteria for yield heterosis. The hybrids from heterotic groups, Reid × SPT, Reid × LRC, SPT × PA, and Lancaster × LRC, contributed highly significant positive SCA effects and strong heterosis to yield-related traits, and the heterotic patterns identified in this study were potentially useful for commercial maize breeding. Heterosis was more significantly and positively correlated with SCA than GCA, indicating that SCA can be used in heterosis prediction to develop potential hybrids in commercial maize breeding. The results of the present study not only contribute to developing breeding strategies, but also improve targeted breeding efficiency by using both temperate and tropical maize to broaden genetic basis. Large sets of parental lines with available genotypic information can be shared and used in worldwide hybrid breeding programs through an open-source breeding strategy. Potential applications of the reported results in developing hybrid maize breeding strategies were also discussed.
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Affiliation(s)
- Kanchao Yu
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Hui Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaogang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiwei Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojie Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiacheng Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenhua Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- CIMMYT-China Tropical Maize Research Center, Foshan University, Foshan, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Mehraj H, Kawanabe T, Shimizu M, Miyaji N, Akter A, Dennis ES, Fujimoto R. In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F 1 Hybrid Population. PLANTS 2020; 9:plants9040414. [PMID: 32230994 PMCID: PMC7238264 DOI: 10.3390/plants9040414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 11/28/2022]
Abstract
Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F1 hybrid cultivars in many crops. A similar level of heterosis in all F1 individuals is expected as they are genetically identical. However, we found variation in rosette size in individual F1 plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big-sized F1 plants had 26.1% larger leaf area in the first and second leaves than medium-sized F1 plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big- and medium-sized F1 plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, and some lines had increased plant size at 14 or 21 days after sowing but not at all time points during development. Change of expression levels in stress-responsive genes among individual F1 plants could generate the variation in plant size of individual F1 plants in A. thaliana.
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Affiliation(s)
- Hasan Mehraj
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
| | - Takahiro Kawanabe
- School of Agriculture, Tokai University, Toroku, Higashi-ku, Kumamoto 862-8652, Japan
- Correspondence: (T.K.); (R.F.)
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita, Kitakami, Iwate 024-0003, Japan;
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
| | - Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
- Department of Horticulture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- University of Technology, Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
- Correspondence: (T.K.); (R.F.)
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