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Li X, Zheng J, Su J, Wang L, Luan L, Wang T, Bai F, Zhong Q, Gong Q. Myotubularin 2 interacts with SEC23A and negatively regulates autophagy at ER exit sites in arabidopsis. Autophagy 2024. [PMID: 39177202 DOI: 10.1080/15548627.2024.2394302] [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: 04/17/2024] [Revised: 08/11/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024] Open
Abstract
Starvation- or stress-induced phosphatidylinositol 3-phosphate (PtdIns3P/PI3P) production at the endoplasmic reticulum (ER) subdomains organizes phagophore assembly and autophagosome formation. Coat protein complex II (COPII) vesicles budding from ER exit site (ERES) also contribute to autophagosome formation. Whether any PtdIns3P phosphatase functions at ERES to inhibit macroautophagy/autophagy is unknown. Here we report Myotubularin 2 (MTM2) of Arabidopsis as a PtdIns3P phosphatase that localizes to ERES and negatively regulates autophagy. MTM2 binds PtdIns3P with its PH-GRAM domain in vitro and acts toward PtdIns3P in vivo. Transiently expressed MTM2 colocalizes with ATG14b, a subunit of the phosphatidylinositol 3-kinase (PtdIns3K) complex, and overexpression of MTM2 blocks autophagic flux and causes over-accumulation of ATG18a, ATG5, and ATG8a. The mtm2 mutant has higher levels of autophagy and is more tolerant to starvation, whereas MTM2 overexpression leads to reduced autophagy and sensitivity to starvation. The phenotypes of mtm2 are suppressed by ATG2 mutation, suggesting that MTM2 acts upstream of ATG2. Importantly, MTM2 does not affect the endosomal functions of PtdIns3P. Instead, MTM2 specifically colocalizes with COPII coat proteins and is cradled by the ERES-defining protein SEC16. MTM2 interacts with SEC23A with its phosphatase domain and inhibits COPII-mediated protein secretion. Finally, a role for MTM2 in salt stress response is uncovered. mtm2 resembles the halophyte Thellungiella salsuginea in its efficient vacuolar compartmentation of Na+, maintenance of chloroplast integrity, and timely regulation of autophagy-related genes. Our findings reveal a balance between PtdIns3P synthesis and turnover in autophagosome formation, and provide a new link between autophagy and COPII function.
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Affiliation(s)
- Xinjing Li
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Jing Zheng
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Jing Su
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, P. R. China
| | - Lin Luan
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Taotao Wang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, P. R. China
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
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2
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Lan L, Nègre N. Heterosis effect for larval performance of fall armyworm interstrain hybrids. INSECT SCIENCE 2024; 31:1296-1312. [PMID: 37969057 DOI: 10.1111/1744-7917.13295] [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: 04/13/2023] [Revised: 08/30/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Spodoptera frugiperda, also known as fall armyworm (FAW), is an invasive crop pest that can feed on a variety of host plants, posing a serious threat to food security. There are two sympatric strains of FAW that are morphologically identical but described with different food preferences: the "rice strain" (SfR) and the "corn strain" (SfC). A few genetic loci exist to identify these two strains. Mitochondrial and Z-chromosome-linked haplotypes are the most used, but the biggest part of the genome displays little polymorphism between strains that could explain their adaptation to different plants. We have previously observed consistent transcription differences between the strains in both laboratory and natural populations. Therefore, we wonder if there are effects from host-strain-associated loci, maternally or paternally inherited, on FAW performance that could explain the divergence between the two FAW strains. To test this hypothesis, we first produced two F1 hybrid generations (SfR ♀ × SfC ♂, SfC ♀ × SfR ♂). These reciprocal hybrids should be heterozygous for all chromosomes except for the maternally inherited mitochondrial and sexual W chromosomes. To evaluate whether plant preference is determined by these genetic loci, we cultivated the two hybrids and the two parental strains in triplicate on an artificial diet and recorded several phenotypic traits such as weight over time, survival rate, emerging rate, developmental time, and sex ratio. Then, the same performance experiment was carried out on corn plants. Surprisingly, on the artificial diet, the two hybrid genotypes were both more performant than the two parental strains in terms of survival rate, pupal emerging rate, and developmental time, whereas they were intermediate to the inbred parental strains in pupal weight. On the corn plant diet, both hybrid genotypes outperformed the two parental strains in larval weight. Although these asymmetrical results revealed that mitochondrial or sex-linked haplotypes alone cannot explain the performance differences, they suggested a heterosis effect in FAW. A reduction of the female number for the CR genotype and the decreased F1 offspring reproduction in both hybrids suggested the possibility of Haldane's rule, which might be explained by the dominance model.
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Affiliation(s)
- Laijiao Lan
- DGIMI, University of Montpellier, INRAE, Montpellier, France
| | - Nicolas Nègre
- DGIMI, University of Montpellier, INRAE, Montpellier, France
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3
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Zhao R, Li Y, Xu C, Zhang Z, Zhou Z, Zhou Y, Qi Z. Expression of heterosis in photosynthetic traits in F1 generation of sorghum ( Sorghum bicolor) hybrids and relationship with yield traits. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24135. [PMID: 39190770 DOI: 10.1071/fp24135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024]
Abstract
Heterosis is a crucial factor in enhancing crop yield, particularly in sorghum (Sorghum bicolor ). This research utilised six sorghum restorer lines, six sorghum sterile lines, and 36 hybrid combinations created through the NCII incomplete double-row hybridisation method. We evaluated the performance of F1 generation hybrids for leaf photosynthesis-related parameters, carbon metabolism-related enzymes, and their correlation with yield traits during the flowering stage. Results showed that hybrid sorghum exhibited significant high-parent heterosis in net photosynthetic rate (P n ), transpiration rate (T r ), stomatal conductance (G s ), apparent leaf meat conductance (AMC), ribulose-1,5-bisphosphate (RuBP) carboxylase, phosphoenolpyruvate (PEP) carboxylase, and sucrose phosphate synthase (SPS). Conversely, inter-cellular carbon dioxide concentration (C i ), instantaneous water uses efficiency (WUE), and sucrose synthase (SuSy) displayed mostly negative heterosis. Traits such as 1000-grain weight (TGW), grain weight per spike (GWPS), and dry matter content (DMC) exhibited significant high-parent heterosis, with TGW reaching the highest value of 82.54%. P n demonstrated positive correlations with T r , C i , G s , RuBP carboxylase, PEP carboxylase, GWPS, TGW, and DMC, suggesting that T r , C i , and G s could aid in identifying high-photosynthesis sorghum varieties. Concurrently, P n could help select carbon-efficient sorghum varieties due to its close relationship with yield. Overall, the F1 generation of sorghum hybrids displayed notable heterosis during anthesis. Combined with field performance, P n at athesis can serve as a valuable indicator for early prediction of the yield potential of the F1 generation of sorghum hybrids and for screening carbon-efficient sorghum varieties.
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Affiliation(s)
- Renjie Zhao
- College of Agriculture, Jilin Agricultural University, Changchun 130118, China
| | - Yueqiao Li
- Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Chen Xu
- Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Zhian Zhang
- College of Agriculture, Jilin Agricultural University, Changchun 130118, China
| | - Ziyang Zhou
- Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yihan Zhou
- Jilin Engineering Vocational College, Siping 136001, China
| | - Zexin Qi
- College of Agriculture, Jilin Agricultural University, Changchun 130118, China
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4
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Liu H, Liu Z, Qin A, Zhou Y, Sun S, Liu Y, Hu M, Yang J, Sun X. Mitochondrial ATP Synthase beta-Subunit Affects Plastid Retrograde Signaling in Arabidopsis. Int J Mol Sci 2024; 25:7829. [PMID: 39063070 PMCID: PMC11277312 DOI: 10.3390/ijms25147829] [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: 05/21/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Plastid retrograde signaling plays a key role in coordinating the expression of plastid genes and photosynthesis-associated nuclear genes (PhANGs). Although plastid retrograde signaling can be substantially compromised by mitochondrial dysfunction, it is not yet clear whether specific mitochondrial factors are required to regulate plastid retrograde signaling. Here, we show that mitochondrial ATP synthase beta-subunit mutants with decreased ATP synthase activity are impaired in plastid retrograde signaling in Arabidopsis thaliana. Transcriptome analysis revealed that the expression levels of PhANGs were significantly higher in the mutants affected in the AT5G08670 gene encoding the mitochondrial ATP synthase beta-subunit, compared to wild-type (WT) seedlings when treated with lincomycin (LIN) or norflurazon (NF). Further studies indicated that the expression of nuclear genes involved in chloroplast and mitochondrial retrograde signaling was affected in the AT5G08670 mutant seedlings treated with LIN. These changes might be linked to the modulation of some transcription factors (TFs), such as LHY (Late Elongated Hypocotyl), PIF (Phytochrome-Interacting Factors), MYB, WRKY, and AP2/ERF (Ethylene Responsive Factors). These findings suggest that the activity of mitochondrial ATP synthase significantly influences plastid retrograde signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (H.L.); (Z.L.); (A.Q.); (Y.Z.); (S.S.); (Y.L.); (M.H.); (J.Y.)
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5
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Steichen S, Deshpande A, Mosey M, Loob J, Douchi D, Knoshaug EP, Brown S, Nielsen R, Weissman J, Carrillo LR, Laurens LML. Central transcriptional regulator controls photosynthetic growth and carbon storage in response to high light. Nat Commun 2024; 15:4842. [PMID: 38844786 PMCID: PMC11156908 DOI: 10.1038/s41467-024-49090-7] [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: 12/08/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Carbon capture and biochemical storage are some of the primary drivers of photosynthetic yield and productivity. To elucidate the mechanisms governing carbon allocation, we designed a photosynthetic light response test system for genetic and metabolic carbon assimilation tracking, using microalgae as simplified plant models. The systems biology mapping of high light-responsive photophysiology and carbon utilization dynamics between two variants of the same Picochlorum celeri species, TG1 and TG2 elucidated metabolic bottlenecks and transport rates of intermediates using instationary 13C-fluxomics. Simultaneous global gene expression dynamics showed 73% of the annotated genes responding within one hour, elucidating a singular, diel-responsive transcription factor, closely related to the CCA1/LHY clock genes in plants, with significantly altered expression in TG2. Transgenic P. celeri TG1 cells expressing the TG2 CCA1/LHY gene, showed 15% increase in growth rates and 25% increase in storage carbohydrate content, supporting a coordinating regulatory function for a single transcription factor.
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Affiliation(s)
- Seth Steichen
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Arnav Deshpande
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Megan Mosey
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jessica Loob
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Damien Douchi
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Stuart Brown
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Robert Nielsen
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Joseph Weissman
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - L Ruby Carrillo
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Lieve M L Laurens
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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Dreisigacker S, Martini JWR, Cuevas J, Pérez-Rodríguez P, Lozano-Ramírez N, Huerta J, Singh P, Crespo-Herrera L, Bentley AR, Crossa J. Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools. THE PLANT GENOME 2024; 17:e20464. [PMID: 38764312 DOI: 10.1002/tpg2.20464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 05/21/2024]
Abstract
Bread wheat (Triticum aestivum L.) is a globally important food crop, which was domesticated about 8-10,000 years ago. Bread wheat is an allopolyploid, and it evolved from two hybridization events of three species. To widen the genetic base in breeding, bread wheat has been re-synthesized by crossing durum wheat (Triticum turgidum ssp. durum) and goat grass (Aegilops tauschii Coss), leading to so-called synthetic hexaploid wheat (SHW). We applied the quantitative genetics tools of "hybrid prediction"-originally developed for the prediction of wheat hybrids generated from different heterotic groups - to a situation of allopolyploidization. Our use-case predicts the phenotypes of SHW for three quantitatively inherited global wheat diseases, namely tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB). Our results revealed prediction abilities comparable to studies in 'traditional' elite or hybrid wheat. Prediction abilities were highest using a marker model and performing random cross-validation, predicting the performance of untested SHW (0.483 for SB to 0.730 for TS). When testing parents not necessarily used in SHW, combination prediction abilities were slightly lower (0.378 for SB to 0.718 for TS), yet still promising. Despite the limited phenotypic data, our results provide a general example for predictive models targeting an allopolyploidization event and a method that can guide the use of genetic resources available in gene banks.
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Affiliation(s)
| | | | - Jaime Cuevas
- Universidad Autónoma del Estado de Quintana Roo, Chetumal, México
| | | | | | - Julio Huerta
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Pawan Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | | | - Alison R Bentley
- Australian National University, Research School of Biology, Canberra, Australia
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
- Colegio de Postgraduados, Campus Montecillos, Texcoco, México
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7
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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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8
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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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9
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Kakoulidou I, Johannes F. DNA methylation remodeling in F1 hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:671-681. [PMID: 36752648 DOI: 10.1111/tpj.16137] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation patterns relative to their parents. To which extent these changes drive non-additive gene expression levels and phenotypic heterosis in F1 individuals is not fully resolved. Current mechanistic models propose that DNA methylation remodeling in hybrids is the result of epigenetic interactions between parental alleles via small interfering RNA (sRNA). These models have strong empirical support but are limited to genomic regions where the two parental lines differ in DNA methylation status. However, most remodeling events occur in parental regions with similar methylation patterns, and seem to be strongly conditioned by distally acting factors, even in isogenic hybrid systems. The molecular basis of these distal interactions is currently unknown, and will likely emerge as an active area of research in the future. Despite these gaps in our molecular understanding, parental DNA methylation states are statistically associated with heterosis, independent of genetic information, and may serve as biomarkers in crop breeding.
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Affiliation(s)
- Ioanna Kakoulidou
- Plant Epigenomics, Technical University of Munich, Emil-Ramman-Str. 4, 85354, Freising, Germany
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich, Emil-Ramman-Str. 4, 85354, Freising, Germany
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10
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [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: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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11
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Ren X, Chen L, Deng L, Zhao Q, Yao D, Li X, Cong W, Zang Z, Zhao D, Zhang M, Yang S, Zhang J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1364284. [PMID: 38444535 PMCID: PMC10913200 DOI: 10.3389/fpls.2024.1364284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.
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Affiliation(s)
- Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, South Subtropical Crops Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Lin Deng
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qiuzhu Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Weixuan Cong
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenyuan Zang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dingyi Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Miao Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
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12
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Ding H, Feng X, Yuan Y, Wang B, Wang Y, Zhang J. Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum. BMC Genomics 2024; 25:165. [PMID: 38336615 PMCID: PMC10854099 DOI: 10.1186/s12864-024-10073-z] [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: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.
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Affiliation(s)
- Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Xiaoxi Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuhao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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Li Y, Yan X, Cheng M, Wu Z, Zhang Q, Duan S, Zhou Y, Li H, Yang S, Cheng Y, Li W, Xu L, Li X, He R, Zhou Y, Yang C, Iqbal MZ, He J, Rong T, Tang Q. Genome dosage alteration caused by chromosome pyramiding and shuffling effects on karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:28. [PMID: 38252297 DOI: 10.1007/s00122-023-04540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE We developed an array of Zea-Tripsacum tri-hybrid allopolyploids with multiple ploidies. We unveiled that changes in genome dosage due to the chromosomes pyramiding and shuffling of three species effects karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. Polyploidy, or whole genome duplication, has played a major role in evolution and speciation. The genomic consequences of polyploidy have been extensively studied in many plants; however, the extent of chromosomal variation, genome dosage, phenotypic diversity, and heterosis in allopolyploids derived from multiple species remains largely unknown. To address this question, we synthesized an allohexaploid involving Zea mays, Tripsacum dactyloides, and Z. perennis by chromosomal pyramiding. Subsequently, an allooctoploid and an allopentaploid were obtained by hybridization of the allohexaploid with Z. perennis. Moreover, we constructed three populations with different ploidy by chromosomal shuffling (allopentaploid × Z. perennis, allohexaploid × Z. perennis, and allooctoploid × Z. perennis). We have observed 3 types of sexual reproductive modes and 2 types of asexual reproduction modes in the tri-species hybrids, including 2n gamete fusion (2n + n), haploid gamete fusion (n + n), polyspermy fertilization (n + n + n) or 2n gamete fusion (n + 2n), haploid gametophyte apomixis, and asexual reproduction. The tri-hybrids library presents extremely rich karyotype heterogeneity. Chromosomal compensation appears to exist between maize and Z. perennis. A rise in the ploidy of the trihybrids was linked to a higher frequency of chromosomal translocation. Variation in the degree of phenotypic diversity observed in different segregating populations suggested that genome dosage effects phenotypic manifestation. These findings not only broaden our understanding of the mechanisms of polyploid formation and reproductive diversity but also provide a novel insight into genome pyramiding and shuffling driven genome dosage effects and phenotypic diversity.
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Affiliation(s)
- Yingzheng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xu Yan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000, China
| | - Mingjun Cheng
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Zizhou Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000, China
| | - Qiyuan Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Saifei Duan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yong Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaxiong Li
- Neijiang Municipal Bureau of Agriculture and Rural Affairs, Neijiang, 641000, China
| | - Shipeng Yang
- Zigong Academy of Agricultural Sciences, Zigong, 643000, China
| | - Yulin Cheng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wansong Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lulu Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaofeng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ruyu He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunyan Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Guizhou Prataculture Institute, Guiyang, Guizhou, China
| | - Muhammad Zafar Iqbal
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianmei He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qilin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Wu Y, Guo Q, Long C, El-Kassaby YA, Sun Y, Li Y. Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L. Int J Mol Sci 2024; 25:1312. [PMID: 38279314 PMCID: PMC10816058 DOI: 10.3390/ijms25021312] [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: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Polyploid breeding techniques aid in the cultivation of new forestry cultivars, thus expanding the suite of strategies for the improvement of arboreal traits and innovation within the field of forestry. Compared to diploid Robinia pseudoacacia L. (black locust) 'D26-5①' (2×), its dwarfed homologous tetraploid 'D26-5②' (4×) variety has better application prospects in garden vegetation guardrails and urban landscape. However, the molecular mechanism of the generation and growth of this dwarf variety is still unclear. Here, plant growth and development as well as histological differences between the diploid and its autotetraploid were investigated. Levels of endogenous hormones at three different developmental stages (20, 40, and 70 days) of 2× and homologous 4× tissue culture plantlets were assessed, and it was found that the brassinosteroid (BR) contents of the former were significantly higher than the latter. Transcriptome sequencing data analysis of 2× and homologous 4× showed that differentially expressed genes (DEGs) were significantly enriched in plant hormone synthesis and signal transduction, sugar and starch metabolism, and the plant circadian rhythm pathway, which are closely related to plant growth and development. Therefore, these biological pathways may be important regulatory pathways leading to dwarfism and slow growth in tetraploids. Additionally, utilizing weighted gene coexpression network analysis (WGCNA), we identified three crucial differentially expressed genes (DEGs)-PRR5, CYP450, and SPA1-that potentially underlie the observed ploidy variation. This study provides a new reference for the molecular mechanism of dwarfism in dwarfed autotetraploid black locusts. Collectively, our results of metabolite analysis and comparative transcriptomics confirm that plant hormone signaling and the circadian rhythm pathway result in dwarfism in black locusts.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.W.)
| | - Qi Guo
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.W.)
| | - Cui Long
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.W.)
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada;
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.W.)
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.W.)
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15
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Seo JS, Kim SH, Shim JS, Um T, Oh N, Park T, Kim YS, Oh SJ, Kim JK. The rice NUCLEAR FACTOR-YA5 and MICRORNA169a module promotes nitrogen utilization during nitrogen deficiency. PLANT PHYSIOLOGY 2023; 194:491-510. [PMID: 37723121 PMCID: PMC10756765 DOI: 10.1093/plphys/kiad504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
Nitrogen (N) is essential for plant growth and development. Therefore, understanding its utilization is essential for improving crop productivity. However, much remains to be learned about plant N sensing and signaling. Here, rice (Oryza sativa) NUCLEAR FACTOR-YA5 (OsNF-YA5) expression was tightly regulated by N status and induced under N-deficient conditions. Overexpression (OE) of OsNF-YA5 in rice resulted in increased chlorophyll levels and delayed senescence compared to control plants under normal N conditions. Agronomic traits were significantly improved in OE plants and impaired in knockout mutants under N-deficient conditions. Using a dexamethasone-inducible system, we identified the putative targets of OsNF-YA5 that include amino acid, nitrate/peptide transporters, and NITRATE TRANSPORTER 1.1A (OsNRT1.1A), which functions as a key transporter in rice. OsNF-YA5 directly enhanced OsNRT1.1A expression and N uptake rate under N-deficient conditions. Besides, overexpression of OsNF-YA5 also enhanced the expression of GLUTAMINE SYNTHETASE 1/2 (GS1/2) and GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1/2 (GOGAT1/2), increasing free amino acid contents under N-deficient conditions. Osa-miR169a expression showed an opposite pattern with OsNF-YA5 depending on N status. Further analysis revealed that osa-miR169a negatively regulates OsNF-YA5 expression and N utilization, demonstrating that an OsNF-YA5/osa-miR169a module tightly regulates rice N utilization for adaptation to N status.
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Affiliation(s)
- Jun Sung Seo
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Sung Hwan Kim
- Crop Biotechnology Institute, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Jae Sung Shim
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Taeyoung Um
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Nuri Oh
- Crop Biotechnology Institute, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Taehyeon Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Youn Shic Kim
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Se-Jun Oh
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
| | - Ju-Kon Kim
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
- Crop Biotechnology Institute, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
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16
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Li M, Guo P, Nan N, Ma A, Liu W, Wang TJ, Yun DJ, Xu ZY. Plasma membrane-localized H +-ATPase OsAHA3 functions in saline-alkaline stress tolerance in rice. PLANT CELL REPORTS 2023; 43:9. [PMID: 38133824 DOI: 10.1007/s00299-023-03103-9] [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: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 12/23/2023]
Abstract
KEY MESSAGE A novel function of plasma membrane-localized H+-ATPase, OsAHA3, was identified in rice, which is involved in saline-alkaline tolerance and specifically responds to high pH during saline-alkaline stress. Saline-alkaline stress causes serious damage to crop production on irrigated land. Plants suffer more severe damage under saline-alkaline stress than under salinity stress alone. Plasma membrane-localized proton (H+) pump (H+-ATPase) is an important enzyme that controls plant growth and development by catalyzing H+ efflux and enabling effective charge balance. Many studies about the role of plasma membrane H+-ATPases in saline-alkaline stress tolerance have been reported in Arabidopsis, especially on the AtAHA2 (Arabidopsis thaliana H+-ATPase 2) gene; however, whether and how plasma membrane H+-ATPases play a role in saline-alkaline stress tolerance in rice remain unknown. Here, using the activation-tagged rice mutant pool, we found that the plasma membrane-localized H+-ATPase OsAHA3 (Oryza sativa autoinhibited H+-ATPase 3) is involved in saline-alkaline stress tolerance. Activation-tagged line 29 (AC29) was identified as a loss-of-function mutant of OsAHA3 and showed more severe growth retardation under saline-alkaline stress with high pH than under salinity stress. Moreover, osaha3 loss-of-function mutants generated by CRISPR/Cas9 system exhibited saline-alkaline stress sensitive phenotypes; staining of leaves with nitrotetrazolium blue chloride (NBT) and diaminobenzidine (DAB) revealed more reactive oxygen species (ROS) accumulation in osaha3 mutants. OsAHA3-overexpressing plants showed increased saline-alkaline stress tolerance than wild-type plants. Tissue-specific expression analysis revealed high expression level of OsAHA3 in leaf, sheath, glume, and panicle. Overall, our results revealed a novel function of plasma membrane-localized H+-ATPase, OsAHA3, which is involved in saline-alkaline stress tolerance and specifically responds to high pH.
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Affiliation(s)
- Mengting Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Nan Nan
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Ao Ma
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Wenxin Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Dae-Jin Yun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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17
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Lee S, Tri Le Q, Yang S, Hwang KY, Lee H. Arabidopsis ecotype Ct-1, with its altered nitrate sensing ability, exhibits enhanced growth under low nitrate conditions in comparison to Col-0. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111827. [PMID: 37586419 DOI: 10.1016/j.plantsci.2023.111827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
To address the urgent need for sustainable solutions to the increased use of nitrogen fertilizers in agriculture, it is imperative to acquire an in-depth comprehension of the intricate interplay between plants and nitrogen. In this context, our research aimed to elucidate the molecular mechanism behind NO3- sensing/signaling in plants, which can enhance nitrogen utilization efficiency. Previous reports have revealed that the density and quantity of root hairs exhibit responsive behavior to varying levels of NO3-, while the precise molecular mechanisms governing these changes remain elusive. To further investigate this phenomenon, we specifically selected the Ct-1 ecotype, which manifested a greater abundance of root hairs compared to the Col-0 ecotype under conditions of low NO3-. Our investigations unveiled that the dissimilarities in the amino acid sequence of NRT1.1, a transceptor responsible for regulating nitrate signaling and transport, accounted for the observed variation in root hair numbers. These results suggest that NRT1.1 represents a promising target for gene editing technology, offering potential applications in enhancing the efficiency of nitrogen utilization in agricultural crops.
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Affiliation(s)
- Seokjin Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Quang Tri Le
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Seonyoung Yang
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Hojoung Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea.
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Xue Z, Gao B, Chen G, Liu J, Ouyang W, Foda MF, Zhang Q, Zhang X, Zhang W, Guo M, Li X, Yi B. Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus. BMC Biol 2023; 21:241. [PMID: 37907908 PMCID: PMC10617162 DOI: 10.1186/s12915-023-01735-7] [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: 05/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Epigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression. Brassica napus is a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks. RESULTS In this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment in Brassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome in Brassica rapa, the An subgenome of Brassica napus displayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications. CONCLUSIONS Herein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes' rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes in Brassica napus.
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Affiliation(s)
- Zhifei Xue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jie Liu
- Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mohamed Frahat Foda
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Biochemistry, Faculty of Agriculture, Benha University, Toukh, 13736, Qalyubiyya, Egypt
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mingyue Guo
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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19
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Shekhawat PK, Goyal A, Akhatar J, Sharma S, Kaur N, Bharti B, Mittal M, Sardana VK, Chhuneja P, Banga SS, Atri C. Genetic analysis of the variation for mineral accumulation in the leaves and seeds of natural germplasm of Brassica rapa L. (AA) and the its derived forms extracted from an allotetraploid B.juncea L.(AABB). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108084. [PMID: 37832370 DOI: 10.1016/j.plaphy.2023.108084] [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: 06/18/2023] [Revised: 09/16/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Brassica rapa L. (2n = 20; AA) is a vegetable and oilseed crop that is grown all over the world. Its leaves, shoots, and seeds store significant amounts of minerals. We used inductively coupled plasma-optical emission spectroscopy (ICP-OES) to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines, of which 92 represented natural (NR) B. rapa and the remaining 103 were derived (DR) from a set of mother genotypes originally extracted from an allotetraploid B. juncea (2n = 36; AABB). The inbred lines differed for the composition of leaf and seed minerals. Leaf concentrations of N, K, Zn, and Se were higher in the DR subpanel as compared to NR subpanel, along with high seed accumulations of K and Se. DArT genotyping and genome wide association mapping led to the identification of SNPs associated with leaf and seed mineral compositions. Chromosomes A03, A05, and A10 harboured the most associated loci. Annotations of the regions adjacent to respective GWAS peaks allowed prediction of genes known for acquisition, transport, and accumulation of minerals and heavy metal detoxification. Transcriptome analysis revealed differential expression patterns of the predicted candidates, with most genes either down-regulated in derived genotypes relative to natural forms or their expression being comparable between the two. General downregulation may be a consequence of extracting B. rapa from allotetraploid B. juncea through genome resection. Some of the identified SNPs may be used as DNA markers for breeding programmes designed to modify the leaf and seed mineral compositions.
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Affiliation(s)
- Pooja Kanwar Shekhawat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - V K Sardana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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20
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Zhang Y, Chen G, Deng L, Gao B, Yang J, Ding C, Zhang Q, Ouyang W, Guo M, Wang W, Liu B, Zhang Q, Sung WK, Yan J, Li G, Li X. Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice. Nucleic Acids Res 2023; 51:9001-9018. [PMID: 37572350 PMCID: PMC10516653 DOI: 10.1093/nar/gkad658] [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: 10/12/2022] [Revised: 07/11/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023] Open
Abstract
Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness to the environment. Genome-wide characterization and comparison of rhythmic genes under different light conditions revealed delayed phase under constant darkness (DD) and reduced amplitude under constant light (LL) in rice. Interestingly, ChIP-seq and RNA-seq profiling of rhythmic genes exhibit synchronous circadian oscillation in H3K9ac modifications at their loci and long non-coding RNAs (lncRNAs) expression at proximal loci. To investigate how gene expression rhythm is regulated in rice, we profiled the open chromatin regions and transcription factor (TF) footprints by time-series ATAC-seq. Although open chromatin regions did not show circadian change, a significant number of TFs were identified to rhythmically associate with chromatin and drive gene expression in a time-dependent manner. Further transcriptional regulatory networks mapping uncovered significant correlation between core clock genes and transcription factors involved in light/temperature signaling. In situ Hi-C of ZT8-specific expressed genes displayed highly connected chromatin association at the same time, whereas this ZT8 chromatin connection network dissociates at ZT20, suggesting the circadian control of gene expression by dynamic spatial chromatin conformation. These findings together implicate the existence of a synchronization mechanism between circadian H3K9ac modifications, chromatin association of TF and gene expression, and provides insights into circadian dynamics of spatial chromatin conformation that associate with gene expression rhythms.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Cheng Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenxia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Beibei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wing-Kin Sung
- Department of Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jiapei Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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21
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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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22
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Yu J, Li P, Tu S, Feng N, Chang L, Niu Q. Integrated Analysis of the Transcriptome and Metabolome of Brassica rapa Revealed Regulatory Mechanism under Heat Stress. Int J Mol Sci 2023; 24:13993. [PMID: 37762295 PMCID: PMC10531312 DOI: 10.3390/ijms241813993] [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: 08/14/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Affected by global warming; heat stress is the main limiting factor for crop growth and development. Brassica rapa prefers cool weather, and heat stress has a significant negative impact on its growth, development, and metabolism. Understanding the regulatory patterns of heat-resistant and heat-sensitive varieties under heat stress can help deepen understanding of plant heat tolerance mechanisms. In this study, an integrative analysis of transcriptome and metabolome was performed on the heat-tolerant ('WYM') and heat-sensitive ('AJH') lines of Brassica rapa to reveal the regulatory networks correlated to heat tolerance and to identify key regulatory genes. Heat stress was applied to two Brassica rapa cultivars, and the leaves were analyzed at the transcriptional and metabolic levels. The results suggest that the heat shock protein (HSP) family, plant hormone transduction, chlorophyll degradation, photosynthetic pathway, and reactive oxygen species (ROS) metabolism play an outstanding role in the adaptation mechanism of plant heat tolerance. Our discovery lays the foundation for future breeding of horticultural crops for heat resistance.
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Affiliation(s)
| | | | | | | | | | - Qingliang Niu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (J.Y.); (P.L.); (S.T.); (N.F.) (L.C.)
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23
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Liu W, Ren D, Yang W, Xu M, Zhang Y, Wang X, He G, Deng XW. Genetic and molecular regulation of increased photosynthetic cell number contributes to leaf size heterosis in Arabidopsis. iScience 2023; 26:107366. [PMID: 37539024 PMCID: PMC10393828 DOI: 10.1016/j.isci.2023.107366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
Heterosis is an important genetic phenomenon that has been observed and widely utilized in agriculture. However, the genetic and molecular bases of heterosis are unclear. Through transcriptome-wide association studies (TWAS) and expression quantitative trait locus (eQTL) analysis to integrate genome, transcriptome, and heterotic phenotype of a half-sibling Arabidopsis hybrid population, we report that the genetic and molecular bases of variations in leaf growth heterosis can be explained by the varied expression levels of growth-regulating genes resulting from distinct sets of heterozygous eQTLs carried by the half-sibling hybrids. In F1 versus parent, the degree of up-regulated gene expression in the cell cycle pathway in the shoot apex and the photosynthesis pathway in true leaf positively correlates with true leaf area heterosis level, and this is affected by the accumulation of superior heterozygous eQTLs. This was further corroborated by the major contribution of increased photosynthetic cell number to leaf area heterosis.
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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
| | - Diqiu Ren
- 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
| | - Wenyi Yang
- 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
| | - Miqi Xu
- 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
| | - Yi 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
| | - Xingwei Wang
- 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
| | - 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, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
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24
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Albaqami M. The Splicing Factor SR45 Negatively Regulates Anthocyanin Accumulation under High-Light Stress in Arabidopsis thaliana. Life (Basel) 2023; 13:1386. [PMID: 37374167 DOI: 10.3390/life13061386] [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: 05/31/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
High-intensity light (HL) greatly induces the accumulation of anthocyanin, a fundamental compound in photoprotection and antioxidation. Many mechanisms regulating anthocyanin biosynthesis are well-characterized across developmental and environmental conditions; however, post-transcriptional regulation of its biosynthesis remains unclear. RNA splicing is one mechanism of post-transcriptional control and reprogramming in response to different developmental cues and stress conditions. The Arabidopsis splicing modulator SR45 regulates a number of developmental and environmental stress responses. Here, we investigated the role of SR45 and its isoforms in HL-induced anthocyanin accumulation. We found that the SR45 promoter contains light-responsive cis-elements, and that light stress significantly increases SR45 expression. Furthermore, we found that mutant plants lacking SR45 function (sr45) accumulate significantly more anthocyanin under HL. SR45 is alternatively spliced to produce two proteins, SR45.1 and SR45.2, which differ by seven amino acids. Intriguingly, these isoforms exhibited distinct functions, with only SR45.1 reversing anthocyanin accumulation in the sr45 plants. We also identified possible SR45 target genes that are involved in anthocyanin synthesis. Consistent with the antioxidant role of anthocyanin, we found that sr45 mutants and SR45.2 overexpression lines accumulate anthocyanin and better tolerate paraquat which induces oxidative stress. Collectively, our results reveal that the Arabidopsis splicing regulator SR45 inhibits anthocyanin accumulation under HL, which may negatively affect oxidative stress tolerance. This study illuminates splicing-level regulation of anthocyanin production in response to light stress and offers a possible target for genetic modification to increase plant stress tolerance.
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Affiliation(s)
- Mohammed Albaqami
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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25
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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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26
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Le QT, Truong HA, Nguyen DT, Yang S, Xiong L, Lee H. Enhanced growth performance of abi5 plants under high salt and nitrate is associated with reduced nitric oxide levels. JOURNAL OF PLANT PHYSIOLOGY 2023; 286:154000. [PMID: 37207503 DOI: 10.1016/j.jplph.2023.154000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/23/2023] [Accepted: 04/29/2023] [Indexed: 05/21/2023]
Abstract
Numerous environmental stresses have a significant impact on plant growth and development. By 2050, it is anticipated that high salinity will destroy more than fifty percent of the world's agricultural land. Understanding how plants react to the excessive use of nitrogen fertilizers and salt stress is crucial for enhancing crop yield. However, the effect of excessive nitrate treatment on plant development is disputed and poorly understood; so, we evaluated the effect of excessive nitrate supply and high salinity on abi5 plant growth performance. We demonstrated that abi5 plants are tolerant to the harmful environmental conditions of excessive nitrate and salt. abi5 plants have lower amounts of endogenous nitric oxide than Arabidopsis thaliana Columbia-0 plants due to their decreased nitrate reductase activity, caused by a decrease in the transcript level of NIA2, a gene encoding nitrate reductase. Nitric oxide appeared to have a critical role in reducing the salt stress tolerance of plants, which was diminished by an excess of nitrate. Discovering regulators such as ABI5 that can modulate nitrate reductase activity and comprehending the molecular activities of these regulators are crucial for the application of gene-editing techniques. This would result in the appropriate buildup of nitric oxide to increase the production of crops subjected to a variety of environmental stresses.
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Affiliation(s)
- Quang Tri Le
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Hai An Truong
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Dinh Thanh Nguyen
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Seonyoung Yang
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Kowloon Tang, Hong Kong, China
| | - Hojoung Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea.
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27
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Sun Z, Peng J, Lv Q, Ding J, Chen S, Duan M, He Q, Wu J, Tian Y, Yu D, Tan Y, Sheng X, Chen J, Sun X, Liu L, Peng R, Liu H, Zhou T, Xu N, Lou J, Yuan L, Wang B, Yuan D. Dissecting the genetic basis of heterosis in elite super-hybrid rice. PLANT PHYSIOLOGY 2023; 192:307-325. [PMID: 36755501 PMCID: PMC10152689 DOI: 10.1093/plphys/kiad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/06/2023] [Accepted: 01/18/2023] [Indexed: 05/03/2023]
Abstract
Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm-2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.
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Affiliation(s)
- Zhizhong Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | | | - Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Jia Ding
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Siyang Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Meijuan Duan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yan Tian
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Dong Yu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xiabing Sheng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jin Chen
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xuewu Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ling Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Rui Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Tianshun Zhou
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Na Xu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jianhang Lou
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Longping Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Bingbing Wang
- Biobin Data Sciences Co., Ltd., Changsha 410221, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
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28
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Feng Y, Ren Y, Zhang H, Heng Y, Wang Z, Wang Y. Halostachys caspica pathogenesis-related protein 10 acts as a cytokinin reservoir to regulate plant growth and development. FRONTIERS IN PLANT SCIENCE 2023; 14:1116985. [PMID: 37180382 PMCID: PMC10169677 DOI: 10.3389/fpls.2023.1116985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Pathogenesis-related class 10 (PR-10) proteins play a role in plant growth and development, but the underlying molecular mechanisms are unclear. Here, we isolated a salt-induced PR-10 gene from the halophyte Halostachys caspica and named it HcPR10. HcPR10 was constitutively expressed during development and HcPR10 localized to the nucleus and cytoplasm. HcPR10-mediated phenotypes including bolting, earlier flowering, increased branch number and siliques per plant are highly correlated with increased cytokinin levels in transgenic Arabidopsis. Meanwhile, increased levels of cytokinin in plants is temporally correlated with HcPR10 expression patterns. Although the expression of cytokinin biosynthesis genes validated was not upregulated, cytokinin-related genes including chloroplast-related genes, cytokinin metabolism and cytokinin responses genes and flowering-related genes were significantly upregulated in the transgenic Arabidopsis compared to the wild type by transcriptome deep sequencing. Analysis of the crystal structure of HcPR10 revealed a trans-zeatin riboside (a type of cytokinin) located deep in its cavity, with a conserved conformation and protein-ligand interactions, supporting HcRP10 acts as a cytokinin reservoir. Moreover, HcPR10 in Halostachys caspica predominantly accumulated in vascular tissue, the site of long-distance translocation of plant hormones. Collectively, we draw that HcPR10 as a cytokinin reservoir induces cytokinin-related signal transduction in plants, thereby promoting plant growth and development. These findings could provide intriguing insights into the role of HcPR10 proteins in phytohormone regulation in plants and advance our understanding of cytokinin-mediated plant development and could facilitate the breeding of transgenic crops with earlier mature, higher yielding agronomic traits.
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Affiliation(s)
- Yudan Feng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hua Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Youqiang Heng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yan Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Li R, Nie S, Zhang N, Tian M, Zhang L. Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage. PLANTS (BASEL, SWITZERLAND) 2023; 12:1195. [PMID: 36904055 PMCID: PMC10005390 DOI: 10.3390/plants12051195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815-10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796-5990 DEGs (female parent-vs-hybrid), and 2244-7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83-84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant-pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage.
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Wang L, Li J, Lin Y, Dang K, Wan J, Meng S, Qiu X, Wang Q, Mu L, Ding D, Luo H, Tang J. Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis. THE PLANT GENOME 2023; 16:e20293. [PMID: 36478177 DOI: 10.1002/tpg2.20293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/02/2022] [Indexed: 05/10/2023]
Abstract
Important traits related to maize (Zea mays L.) grain yield, such as kernel row number, ear length, kernel number per row, are determined during the development of female inflorescence. There is a significant positive correlation between yield component and the activity of inflorescence meristem (IM). To find the key stage of heterosis in the development of the ear, immature ears (from the IM stage until the end of the floral meristem [FM] stage) of Yudan888 and its parent lines were sampled to assay phenotype and for comparative transcriptomics analysis. The immature ear length of Yudan888 at the IM stage fitted an additive (mid-parental) model, but it showed high parental dominance at the spikelet-pair meristem (SPM) stage. Comparative analysis of transcriptomes suggested significant differences between additive and nonadditive expression patterns for different developmental stages. The number of distinct maternal or paternal genes (DMP) (genes expressed only in one parental line and their hybrid but silenced in another line) was greater than ABF1 (genes expressed in both parental lines but silenced in hybrid) at each stage. Gene Ontology (GO) enrichment suggested that the cell redox homeostasis genes with overdominance expression patterns in hybrids have an important contribution to heterosis. According to our research, an ear length heterosis network was established. The discovery of the inflection point for ear length heterosis allows us for inferring that the transition state of IM to SPM may be the starting point of ear length heterosis. These findings improved the understanding of maize ear length heterosis.
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Affiliation(s)
- Liangfa Wang
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- The Shennong Laboratory, Zhengzhou, 450002, China
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Wu Q, Bai X, Luo Y, Li L, Nie M, Liu C, Ye X, Zou L, Xiang D. Identification of the global diurnal rhythmic transcripts, transcription factors and time-of-day specific cis elements in Chenopodium quinoa. BMC PLANT BIOLOGY 2023; 23:96. [PMID: 36793005 PMCID: PMC9933291 DOI: 10.1186/s12870-023-04107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Photoperiod is an important environmental cue interacting with circadian clock pathway to optimize the local adaption and yield of crops. Quinoa (Chenopodium quinoa) in family Amaranthaceae has been known as superfood due to the nutritious elements. As quinoa was originated from the low-latitude Andes, most of the quinoa accessions are short-day type. Short-day type quinoa usually displays altered growth and yield status when introduced into higher latitude regions. Thus, deciphering the photoperiodic regulation on circadian clock pathway will help breed adaptable and high yielding quinoa cultivars. RESULTS In this study, we conducted RNA-seq analysis of the diurnally collected leaves of quinoa plants treated by short-day (SD) and long-day conditions (LD), respectively. We identified 19,818 (44% of global genes) rhythmic genes in quinoa using HAYSTACK analysis. We identified the putative circadian clock architecture and investigated the photoperiodic regulatory effects on the expression phase and amplitude of global rhythmic genes, core clock components and transcription factors. The global rhythmic transcripts were involved in time-of-day specific biological processes. A higher percentage of rhythmic genes had advanced phases and strengthened amplitudes when switched from LD to SD. The transcription factors of CO-like, DBB, EIL, ERF, NAC, TALE and WRKY families were sensitive to the day length changes. We speculated that those transcription factors may function as key mediators for the circadian clock output in quinoa. Besides, we identified 15 novel time-of-day specific motifs that may be key cis elements for rhythm-keeping in quinoa. CONCLUSIONS Collectively, this study lays a foundation for understanding the circadian clock pathway and provides useful molecular resources for adaptable elites breeding in quinoa.
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Affiliation(s)
- Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Xue Bai
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Yiming Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Li Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Mengping Nie
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengluo Road 2025, Longquanyi District, Chengdu, 610106 Sichuan China
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Li J, Wang L, Wan J, Dang K, Lin Y, Meng S, Qiu X, Wang Q, Zhao J, Mu L, Luo H, Ding D, Chen Z, Tang J. Dynamic patterns of gene expression and regulatory variation in the maize seed coat. BMC PLANT BIOLOGY 2023; 23:82. [PMID: 36750803 PMCID: PMC9903604 DOI: 10.1186/s12870-023-04078-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Seed size is an important factor contributing to maize yield, but its molecular mechanism remains unclear. The seed coat, which serves as one of the three components of the maize grain, determines seed size to a certain extent. The seed coat also shares the maternal genotype and is an ideal material for studying heterosis. RESULTS In this study, the self-pollinated seeds of the maize hybrid Yudan888 and its parental lines were continuously collected from 0 day after pollination (DAP) to 15 DAP for phenotyping, cytological observation and RNA-seq. The phenotypic data showed that 3 DAP and 8 DAP are the best time points to study maize seed coat heterosis. Cytological observations indicated that maize seed coat heterosis might be the result of the coordination between cell number and cell size. Furthermore, the RNA-seq results showed that the nonadditive genes changed significantly between 3 and 8 DAP. However, the number of genes expressed additively was not significantly different. Our findings suggest that seed coat heterosis in hybrid is the result of nonadditive expression caused by dynamic changes in genes at different time points during seed expansion and seed coat development. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that genes related to DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation contributed significantly to hybrid seed coat heterosis. CONCLUSION Maize seed coat phenotyping allowed us to infer that 3 DAP and 8 DAP are important time points in the study of seed coat heterosis. Our findings provide evidence for genes involved in DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation in hybrid with high or low parental expression as major contributors to hybrid seed coat heterosis.
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Affiliation(s)
- Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Liangfa Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan Lin
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiyue Wang
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Zehui Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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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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Fan XW, Sun JL, Cai Z, Zhang F, Li YZ, Palta JA. MeSWEET15a/b genes play a role in the resistance of cassava (Manihot esculenta Crantz) to water and salt stress by modulating sugar distribution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:394-405. [PMID: 36481708 DOI: 10.1016/j.plaphy.2022.11.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
The sugar transporter SWEET plays a role in plant growth, carbon allocation, and abiotic stress resistance. We examined the function of SWEET in cassava (Manihot esculenta Crantz) under water and salt stress. Bioinformatics, subcellular localization, yeast deficient complementation, and virus-induced gene silencing (VIGS) were used to examine the function of SWEET in cassava. Twenty-eight MeSWEETs genes were found based on the conserved domain MtN3/saliva of SWEET transporters, two MeSWEET15a/b of them were identified by phylogenetic analysis, which were located on the cell membrane. They transfer sucrose, fructose, glucose, and mannitol from culture media to yeast cells, predominately transferring sucrose via bleeding fluid saps in plant. Leaf sucrose content was increased in MeSWEET15a/b-silenced cassava plants, resulting in changes in carbon distribution, with an increase in starch accumulation in the leaves and a decrease in starch accumulation in the roots. The silencing of MeSWEET15a/b genes led to tolerance to water and salt stress, consistent with a high accumulation of osmolytes, and low lipid membrane peroxidation. Changes in sugar distribution increased the expression of MeTOR and MeE2Fa in pTRV2-MeSWEET15a and pTRV2-MeSWEET15b cassava leaves. MeSWEET15a/b acts as pivotal modulators of sugar distribution and tolerance to water and high salt stress in cassava.
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Affiliation(s)
- Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University; 100 Daxue Road, Nanning, Guangxi 530004, China.
| | - Jin-Liang Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University; 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Zheng Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University; 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Fan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University; 100 Daxue Road, Nanning, Guangxi 530004, China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University; 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Jairo A Palta
- CSIRO, Agriculture Flagship, Private Bag No. 5, Wembley, WA, 6913, Australia; School of Plant Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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Cha JY, Jeong SY, Ahn G, Shin GI, Ji MG, Lee SC, Khakurel D, Macoy DM, Lee YB, Kim MG, Lee SY, Yun DJ, Kim WY. The thiol-reductase activity of YUCCA6 enhances nickel heavy metal stress tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1007542. [PMID: 36237515 PMCID: PMC9551240 DOI: 10.3389/fpls.2022.1007542] [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: 07/30/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic activities cause the leaching of heavy metals into groundwater and their accumulation in soil. Excess levels of heavy metals cause toxicity in plants, inducing the production of reactive oxygen species (ROS) and possible death caused by the resulting oxidative stress. Heavy metal stresses repress auxin biosynthesis and transport, inhibiting plant growth. Here, we investigated whether nickel (Ni) heavy metal toxicity is reduced by exogenous auxin application and whether Ni stress tolerance in Arabidopsis thaliana is mediated by the bifunctional enzyme YUCCA6 (YUC6), which functions as an auxin biosynthetic enzyme and a thiol-reductase (TR). We found that an application of up to 1 µM exogenous indole-3-acetic acid (IAA) reduces Ni stress toxicity. yuc6-1D, a dominant mutant of YUC6 with high auxin levels, was more tolerant of Ni stress than wild-type (WT) plants, despite absorbing significantly more Ni. Treatments of WT plants with YUCASIN, a specific inhibitor of YUC-mediated auxin biosynthesis, increased Ni toxicity; however yuc6-1D was not affected by YUCASIN and remained tolerant of Ni stress. This suggests that rather than the elevated IAA levels in yuc6-1D, the TR activity of YUC6 might be critical for Ni stress tolerance. The loss of TR activity in YUC6 caused by the point-mutation of Cys85 abolished the YUC6-mediated Ni stress tolerance. We also found that the Ni stress-induced ROS accumulation was inhibited in yuc6-1D plants, which consequently also showed reduced oxidative damage. An enzymatic assay and transcriptional analysis revealed that the peroxidase activity and transcription of PEROXIREDOXIN Q were enhanced by Ni stress to a greater level in yuc6-1D than in the WT. These findings imply that despite the need to maintain endogenous IAA levels for basal Ni stress tolerance, the TR activity of YUC6, not the elevated IAA levels, plays the predominant role inNi stress tolerance by lowering Ni-induced oxidative stress.
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Affiliation(s)
- Joon-Yung Cha
- Research Institute of Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Gyeongik Ahn
- Research Institute of Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Myung Geun Ji
- Research Institute of Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Sang Cheol Lee
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Dhruba Khakurel
- Department of Biology, Graduate School of Gyeongsang National University, Jinju, South Korea
| | - Donah Mary Macoy
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Yong Bok Lee
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Woe-Yeon Kim
- Research Institute of Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
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Arabidopsis Ubiquitin-Conjugating Enzymes UBC4, UBC5, and UBC6 Have Major Functions in Sugar Metabolism and Leaf Senescence. Int J Mol Sci 2022; 23:ijms231911143. [PMID: 36232444 PMCID: PMC9569852 DOI: 10.3390/ijms231911143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
The ubiquitin-conjugating enzyme (E2) is required for protein ubiquitination. Arabidopsis has 37 E2s grouped into 14 subfamilies and the functions for many of them are unknown. We utilized genetic and biochemical methods to study the roles of Arabidopsis UBC4, UBC5, and UBC6 of the E2 subfamily IV. The Arabidopsis ubc4/5/6 triple mutant plants had higher levels of glucose, sucrose, and starch than the control plants, as well as a higher protein level of a key gluconeogenic enzyme, cytosolic fructose 1,6-bisphosphatase 1 (cyFBP). In an in vitro assay, the proteasome inhibitor MG132 inhibited the degradation of recombinant cyFBP whereas ATP promoted cyFBP degradation. In the quadruple mutant ubc4/5/6 cyfbp, the sugar levels returned to normal, suggesting that the increased sugar levels in the ubc4/5/6 mutant were due to an increased cyFBPase level. In addition, the ubc4/5/6 mutant plants showed early leaf senescence at late stages of plant development as well as accelerated leaf senescence using detached leaves. Further, the leaf senescence phenotype remained in the quadruple ubc4/5/6 cyfbp mutant. Our results suggest that UBC4/5/6 have two lines of important functions, in sugar metabolism through regulating the cyFBP protein level and in leaf senescence likely through a cyFBP-independent mechanism.
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Zhou J, Liu C, Chen Q, Liu L, Niu S, Chen R, Li K, Sun Y, Shi Y, Yang C, Shen S, Li Y, Xing J, Yuan H, Liu X, Fang C, Fernie AR, Luo J. Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1794-1810. [PMID: 35287184 DOI: 10.1007/s11427-021-2064-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation. However, the role of rhythmicity in altering the global aspects of metabolism is poorly characterized. Here, we subjected four rice (Oryza sativa) varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism. More than 40% of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions. Compared with the metabolome, the transcriptome was more strongly regulated by rhythm; however, the rhythm of metabolites had an obvious opposite trend between day and night. Through association analysis, the time delay of rhythmic transmission from the transcript to the metabolite level was ∼4 h under long-day conditions, although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism. The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network, whereas the correlation of some rhythmic metabolites, such as branched-chain amino acids (BCAAs), was significantly different intervariety. We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn. Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.
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Affiliation(s)
- Junjie Zhou
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Chengyuan Liu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Qiyu Chen
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Ling Liu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Shuying Niu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Ridong Chen
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Kang Li
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Yangyang Sun
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Yuheng Shi
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Xing
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Honglun Yuan
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 144776, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 570288, China.
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.
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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)
- Sang-Ji Lee
- 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
| | - Kiyoon Kang
- Division of Life Sciences, Incheon National University, Incheon 22012, South Korea
| | - 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
| | - Nam-Chon Paek
- 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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Mbebi AJ, Breitler JC, Bordeaux M, Sulpice R, McHale M, Tong H, Toniutti L, Castillo JA, Bertrand B, Nikoloski Z. A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3 GENES|GENOMES|GENETICS 2022; 12:6632664. [PMID: 35792875 PMCID: PMC9434219 DOI: 10.1093/g3journal/jkac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
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Affiliation(s)
- Alain J Mbebi
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
| | - Jean-Christophe Breitler
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Mélanie Bordeaux
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Ronan Sulpice
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Marcus McHale
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Hao Tong
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
| | - Lucile Toniutti
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Jonny Alonso Castillo
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Benoît Bertrand
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
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Description of an Arabica Coffee Ideotype for Agroforestry Cropping Systems: A Guideline for Breeding More Resilient New Varieties. PLANTS 2022; 11:plants11162133. [PMID: 36015436 PMCID: PMC9414076 DOI: 10.3390/plants11162133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations’ access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.
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Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L. Int J Mol Sci 2022; 23:ijms23158724. [PMID: 35955858 PMCID: PMC9369071 DOI: 10.3390/ijms23158724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 01/13/2023] Open
Abstract
Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs.
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43
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Dong Y, Hu G, Grover CE, Miller ER, Zhu S, Wendel JF. Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:872-887. [PMID: 35686631 PMCID: PMC9540634 DOI: 10.1111/tpj.15863] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.
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Affiliation(s)
- Yating Dong
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang455 000China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen518 120China
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Shuijin Zhu
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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Gong J, Tang Y, Liu Y, Sun R, Li Y, Ma J, Zhang S, Zhang F, Chen Z, Liao X, Sun H, Lu Z, Zhao C, Gao S. The Central Circadian Clock Protein TaCCA1 Regulates Seedling Growth and Spike Development in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:946213. [PMID: 35923880 PMCID: PMC9340162 DOI: 10.3389/fpls.2022.946213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 05/14/2023]
Abstract
The biological functions of the circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits, are poorly understood. In this study, we characterized the core clock gene CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns, which are positively regulated by rhythmic histone modifications including histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9Ac), and histone H3 lysine 36 trimethylation (H3K36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike, and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing [DNA affinity purification and sequencing (DAP-seq)] indicated that TaCCA1 preferentially binds to sequences similarly to "evening elements" (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization, and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photosynthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.
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Affiliation(s)
- Jie Gong
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yimiao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjie Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Renwei Sun
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhong Li
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinxiu Ma
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiangzheng Liao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zefu Lu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shiqing Gao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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46
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Zarattini M, Choaibi A, Magri S, Hermans C, Cannella D. The oxidized cellooligosaccharides confer thermotolerance in Arabidopsis by priming ethylene via heat shock factor A2. PHYSIOLOGIA PLANTARUM 2022; 174:e13737. [PMID: 35717612 DOI: 10.1111/ppl.13737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Global climate change, especially heatwaves and aridity, is a major threat to agricultural production and food security. This requires common efforts from the scientific community to find effective solutions to better understand and protect the plant's vulnerabilities to high temperatures. The current study demonstrates the potential of cellooligosaccharides (COS), which are native and oxidized signaling molecules released by lytic polysaccharide monooxygenases (LPMO) enzymes during cell wall degradation by microbial pathogens. The extracellular perception of COS leads to the activation of damage-triggered immunity, often protecting the plant against biotic stress. However, how these signaling molecules affect abiotic stress tolerance is poorly understood. Here, we show that native COS and oxidized COS (oxiCOS) perception increase the transcript levels of several HEAT SHOCK FACTORS (HSFs) and HEAT SHOCK PROTEINS (HSPs) genes in Arabidopsis plants. However, only oxiCOS treatment triggers ethylene priming and increases thermotolerance. Furthermore, the function of the transcription factor HSFA2 is required for these processes. Altogether, our results indicate that the perception of Damage-Associated Molecular Patterns (DAMPs) may improve tolerance to adverse abiotic conditions, like exposure to high temperatures.
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Affiliation(s)
- Marco Zarattini
- PhotoBiocatalysis Unit-Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, Brussels, Belgium
| | - Ali Choaibi
- PhotoBiocatalysis Unit-Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, Brussels, Belgium
| | - Silvia Magri
- PhotoBiocatalysis Unit-Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, Brussels, Belgium
| | - Christian Hermans
- PhotoBiocatalysis Unit-Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, Brussels, Belgium
| | - David Cannella
- PhotoBiocatalysis Unit-Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, Brussels, Belgium
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Fu J, Zhang Y, Yan T, Li Y, Jiang N, Zhou Y, Zhou Q, Qin P, Fu C, Lin H, Zhong J, Han X, Lin Z, Wang F, He H, Wang K, Yang Y. Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis. BMC PLANT BIOLOGY 2022; 22:314. [PMID: 35773646 PMCID: PMC9245205 DOI: 10.1186/s12870-022-03697-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/15/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND Heterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis of heterosis remains largely unclear. RESULTS Here, the transcriptomes of young panicles and leaves of the two widely grown two-line super hybrid rice varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ)) and their parents were analyzed by RNA-seq. Transcriptome profiling of the hybrids revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in two tissues, which were identified by comparing with their parents. GO, and KEGG enrichment analysis showed that the pathways significantly enriched in both tissues of two hybrids were all related to yield and resistance, like circadian rhythm (GO:0,007,623), response to water deprivation (GO:0,009,414), and photosynthetic genes (osa00196). Allele-specific expression genes (ASEGs) were also identified in hybrids. The ASEGs were most significantly enriched in ionotropic glutamate receptor signaling pathway, which was hypothesized to be potential amino acid sensors in plants. Moreover, the ASEGs were also differentially expressed between parents. The number of variations in ASEGs is higher than expected, especially for large effect variations. The DEGs and ASEGs are the potential reasons for the formation of heterosis in the two elite super hybrid rice. CONCLUSIONS Our results provide a comprehensive understanding of the heterosis of two-line super hybrid rice and facilitate the exploitation of heterosis in hybrid rice breeding with high yield heterosis.
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Affiliation(s)
- Jun Fu
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Yilin Zhang
- School of Advanced Agriculture 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
| | - Tianze Yan
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Yanfeng Li
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Nan Jiang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Yanbiao Zhou
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Qunfeng Zhou
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Peng Qin
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Chenjian Fu
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Haiyan Lin
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Jing Zhong
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Xue Han
- School of Advanced Agriculture 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
| | - Zechuan Lin
- School of Advanced Agriculture 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
| | - Fei Wang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hang He
- School of Advanced Agriculture 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.
| | - Kai Wang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China.
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Longping Hi-Tech (Sanya) Overseas Seed Industry R&D Co., Ltd, Sanya, 572099, China.
| | - Yuanzhu Yang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China.
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
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Chen S, Zhang Y, Zhang T, Zhan D, Pang Z, Zhao J, Zhang J. Comparative Transcriptomic, Anatomical and Phytohormone Analyses Provide New Insights Into Hormone-Mediated Tetraploid Dwarfing in Hybrid Sweetgum ( Liquidambar styraciflua × L. formosana). FRONTIERS IN PLANT SCIENCE 2022; 13:924044. [PMID: 35832220 PMCID: PMC9271929 DOI: 10.3389/fpls.2022.924044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Polyploid breeding is an effective approach to improve plant biomass and quality. Both fast growth and dwarf types of in vitro or ex vitro plants are produced after polyploidization. However, little is known regarding the dwarf type mechanism in polyploids grown in vitro. In this study, the morphological and cytological characteristics were measured in tetraploid and diploid hybrid sweetgum (Liquidambar styraciflua × L. formosana) with the same genetic background. RNA sequencing (RNA-Seq) was used to analyse shoot and root variations between tetraploid and diploid plants; important metabolites were validated. The results showed that the shoot and root lengths were significantly shorter in tetraploids than in diploids after 25 d of culture. Most tetraploid root cells were wider and more irregular, and the length of the meristematic zone was shorter, while tetraploid cells were significantly larger than diploid cells. Differentially expressed genes (DEGs) were significantly enriched in the plant growth and organ elongation pathways, such as plant hormone biosynthesis and signal transduction, sugar and starch metabolism, and cell cycles. Hormone biosynthesis and signal transduction genes, such as YUCCA, TAA1, GH3, SAUR, CPS, KO, KAO, GA20ox, GA3ox, BAS1 and CYCD3, which help to regulate organ elongation, were generally downregulated. The auxin, gibberellin, and brassinolide (BL) contents in roots and stems were significantly lower in tetraploids than in diploids, which may greatly contribute to slow growth in the roots and stems of tetraploid regenerated plants. Exogenous gibberellic acid (GA3) and indole-3-acetic acid (IAA), which induced plant cell elongation, could significantly promote growth in the stems and roots of tetraploids. In summary, comparative transcriptomics and metabolite analysis showed that the slow growth of regenerated tetraploid hybrid sweetgum was strongly related to auxin and gibberellin deficiency. Our findings provide insights into the molecular mechanisms that underlie dwarfism in allopolyploid hybrid sweetgum.
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Affiliation(s)
- Siyuan Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yan Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Ting Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Dingju Zhan
- Guangxi Bagui Forest and Flowers Seedlings Co., Ltd., Nanning, China
| | - Zhenwu Pang
- Guangxi Bagui Forest and Flowers Seedlings Co., Ltd., Nanning, China
| | - Jian Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jinfeng Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Transcriptome Profiling Identifies Candidate Genes Contributing to Male and Female Gamete Development in Synthetic Brassica Allohexaploids. PLANTS 2022; 11:plants11121556. [PMID: 35736707 PMCID: PMC9228180 DOI: 10.3390/plants11121556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Polyploidy plays a crucial role in plant evolution and speciation. The development of male and female gametes is essential to the reproductive capacity of polyploids, but their gene expression pattern has not been fully explored in newly established polyploids. The present study aimed to reveal a detailed atlas of gene expression for gamete development in newly synthetic Brassica allohexaploids that are not naturally existing species. Comparative transcriptome profiling between developing anthers (staged from meiosis to mature pollen) and ovules (staged from meiosis to mature embryo sac) was performed using RNA-Seq analysis. A total of 8676, 9775 and 4553 upregulated differentially expressed genes (DEGs) were identified for the development of both gametes, for male-only, and for female-only gamete development, respectively, in the synthetic Brassica allohexaploids. By combining gene ontology (GO) biological process analysis and data from the published literature, we identified 37 candidate genes for DNA double-strand break formation, synapsis and the crossover of homologous recombination during male and female meiosis and 51 candidate genes for tapetum development, sporopollenin biosynthesis and pollen wall development in male gamete development. Furthermore, 23 candidate genes for mitotic progression, nuclear positioning and cell specification and development were enriched in female gamete development. This study lays a good foundation for revealing the molecular regulation of genes related to male and female gamete development in Brassica allohexaploids and provides more resourceful genetic information on the reproductive biology of Brassica polyploid breeding.
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50
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Sun R, Gong J, Liu Y, Chen Z, Zhang F, Gao J, Cao J, Chen X, Zhang S, Zhao C, Gao S. Comprehensive molecular evaluation of the histone methyltransferase gene family and their important roles in two-line hybrid wheat. BMC PLANT BIOLOGY 2022; 22:290. [PMID: 35698040 PMCID: PMC9190116 DOI: 10.1186/s12870-022-03639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Histone methylation usually plays important roles in plant development through post-translational regulation and may provide a new visual field for heterosis. The histone methyltransferase gene family has been identified in various plants, but its members and functions in hybrid wheat related in heterosis is poorly studied. RESULTS In this study, 175 histone methyltransferase (HMT) genes were identified in wheat, including 152 histone lysine methyltransferase (HKMT) genes and 23 protein arginine methyltransferase (PRMT) genes. Gene structure analysis, physicochemical properties and subcellular localization predictions of the proteins, exhibited the adequate complexity of this gene family. As an allohexaploid species, the number of the genes (seven HKMTs orthologous groups and four PRMTs orthologous groups) in wheat were about three times than those in diploids and showed certain degrees of conservation, while only a small number of subfamilies such as ASH-like and Su-(var) subfamilies have expanded their members. Transcriptome analysis showed that HMT genes were mainly expressed in the reproductive organs. Expression analysis showed that some TaHMT genes with different trends in various hybrid combinations may be regulated by lncRNAs with similar expression trends. Pearson correlation analysis of the expression of TaHMT genes and two yield traits indicated that four DEGs may participate in the yield heterosis of two-line hybrid wheat. ChIP-qPCR results showed that the histone modifications (H3K4me3, H3K36me3 and H3K9ac) enriched in promoter regions of three TaCCA1 genes which are homologous to Arabidopsis heterosis-related CCA1/LHY genes. The higher expression levels of TaCCA1 in F1 than its parents are positive with these histone modifications. These results showed that histone modifications may play important roles in wheat heterosis. CONCLUSIONS Our study identified characteristics of the histone methyltransferase gene family and enhances the understanding of the evolution and function of these members in allohexaploid wheat. The causes of heterosis of two-line hybrid wheat were partially explained from the perspective of histone modifications.
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Affiliation(s)
- Renwei Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Jie Gong
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Yongjie Liu
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Jiangang Gao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Junmei Cao
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Xianchao Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
| | - Changping Zhao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
| | - Shiqing Gao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
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