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Sertse D, You FM, Klymiuk V, Haile JK, N'Diaye A, Pozniak CJ, Cloutier S, Kagale S. Historical Selection, Adaptation Signatures, and Ambiguity of Introgressions in Wheat. Int J Mol Sci 2023; 24:ijms24098390. [PMID: 37176097 PMCID: PMC10179502 DOI: 10.3390/ijms24098390] [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: 04/08/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Wheat was one of the crops domesticated in the Fertile Crescent region approximately 10,000 years ago. Despite undergoing recent polyploidization, hull-to-free-thresh transition events, and domestication bottlenecks, wheat is now grown in over 130 countries and accounts for a quarter of the world's cereal production. The main reason for its widespread success is its broad genetic diversity that allows it to thrive in different environments. To trace historical selection and hybridization signatures, genome scans were performed on two datasets: approximately 113K SNPs from 921 predominantly bread wheat accessions and approximately 110K SNPs from about 400 wheat accessions representing all ploidy levels. To identify environmental factors associated with the loci, a genome-environment association (GEA) was also performed. The genome scans on both datasets identified a highly differentiated region on chromosome 4A where accessions in the first dataset were dichotomized into a group (n = 691), comprising nearly all cultivars, wild emmer, and most landraces, and a second group (n = 230), dominated by landraces and spelt accessions. The grouping of cultivars is likely linked to their potential ancestor, bread wheat cv. Norin-10. The 4A region harbored important genes involved in adaptations to environmental conditions. The GEA detected loci associated with latitude and temperature. The genetic signatures detected in this study provide insight into the historical selection and hybridization events in the wheat genome that shaped its current genetic structure and facilitated its success in a wide spectrum of environmental conditions. The genome scans and GEA approaches applied in this study can help in screening the germplasm housed in gene banks for breeding, and for conservation purposes.
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Affiliation(s)
- Demissew Sertse
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Valentyna Klymiuk
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Jemanesh K Haile
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
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Li L, Han C, Yang J, Tian Z, Jiang R, Yang F, Jiao K, Qi M, Liu L, Zhang B, Niu J, Jiang Y, Li Y, Yin J. Comprehensive Transcriptome Analysis of Responses during Cold Stress in Wheat (Triticum aestivum L.). Genes (Basel) 2023; 14:genes14040844. [PMID: 37107602 PMCID: PMC10137996 DOI: 10.3390/genes14040844] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Wheat production is often impacted by pre-winter freezing damage and cold spells in later spring. To study the influences of cold stress on wheat seedlings, unstressed Jing 841 was sampled once at the seedling stage, followed by 4 °C stress treatment for 30 days and once every 10 days. A total of 12,926 differentially expressed genes (DEGs) were identified from the transcriptome. K-means cluster analysis found a group of genes related to the glutamate metabolism pathway, and many genes belonging to the bHLH, MYB, NAC, WRKY, and ERF transcription factor families were highly expressed. Starch and sucrose metabolism, glutathione metabolism, and plant hormone signal transduction pathways were found. Weighted Gene Co-Expression Network Analysis (WGCNA) identified several key genes involved in the development of seedlings under cold stress. The cluster tree diagram showed seven different modules marked with different colors. The blue module had the highest correlation coefficient for the samples treated with cold stress for 30 days, and most genes in this module were rich in glutathione metabolism (ko00480). A total of eight DEGs were validated using quantitative real-time PCR. Overall, this study provides new insights into the physiological metabolic pathways and gene changes in a cold stress transcriptome, and it has a potential significance for improving freezing tolerance in wheat.
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El Gaamouch F, Chen F, Ho L, Lin HY, Yuan C, Wong J, Wang J. Benefits of dietary polyphenols in Alzheimer's disease. Front Aging Neurosci 2022; 14:1019942. [PMID: 36583187 PMCID: PMC9792677 DOI: 10.3389/fnagi.2022.1019942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD) is an irreversible progressive neurodegenerative disease affecting approximately 50 million people worldwide. It is estimated to reach 152 million by the year 2050. AD is the fifth leading cause of death among Americans age 65 and older. In spite of the significant burden the disease imposes upon patients, their families, our society, and our healthcare system, there is currently no cure for AD. The existing approved therapies only temporarily alleviate some of the disease's symptoms, but are unable to modulate the onset and/or progression of the disease. Our failure in developing a cure for AD is attributable, in part, to the multifactorial complexity underlying AD pathophysiology. Nonetheless, the lack of successful pharmacological approaches has led to the consideration of alternative strategies that may help delay the onset and progression of AD. There is increasing recognition that certain dietary and nutrition factors may play important roles in protecting against select key AD pathologies. Consistent with this, select nutraceuticals and phytochemical compounds have demonstrated anti-amyloidogenic, antioxidative, anti-inflammatory, and neurotrophic properties and as such, could serve as lead candidates for further novel AD therapeutic developments. Here we summarize some of the more promising dietary phytochemicals, particularly polyphenols that have been shown to positively modulate some of the important AD pathogenesis aspects, such as reducing β-amyloid plaques and neurofibrillary tangles formation, AD-induced oxidative stress, neuroinflammation, and synapse loss. We also discuss the recent development of potential contribution of gut microbiome in dietary polyphenol function.
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Affiliation(s)
- Farida El Gaamouch
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Geriatric Research, Education and Clinical Center, James J Peters VA Medical Center, Research & Development, Bronx, NY, United States
| | - Fiona Chen
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Lap Ho
- Department of Genetics and Genomic sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Hsiao-Yun Lin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Geriatric Research, Education and Clinical Center, James J Peters VA Medical Center, Research & Development, Bronx, NY, United States
| | - Chongzhen Yuan
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Geriatric Research, Education and Clinical Center, James J Peters VA Medical Center, Research & Development, Bronx, NY, United States
| | - Jean Wong
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jun Wang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Geriatric Research, Education and Clinical Center, James J Peters VA Medical Center, Research & Development, Bronx, NY, United States,*Correspondence: Jun Wang,
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Li J, Zhou K, Wang Z, Zhou J, Deng X. 基于隐性核雄性不育系的杂交小麦制种技术研究进展、问题与展望. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Liu PG, Xu ZL, Zhu Y, Lin TB, Lv ZQ, Yang S, Wang JW, Hu WJ, Chen L, Wei J. Integrative Analyses of Transcriptomics and Metabolomics in Sex Differentiation of Mulberry Flowers. Front Mol Biosci 2022; 9:881090. [PMID: 35601834 PMCID: PMC9117626 DOI: 10.3389/fmolb.2022.881090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sex determination and sex differentiation of plants are important physiological processes of plant development. Mulberry (Morus indica L.) is an important economic tree being cultivated in sericulture countries, and mulberry leaf is commonly used for sericulture. The transcriptomic and metabolomic differences between the staminate flowers (SFs) and pistillate flowers (PFs) of mulberry were investigated by RNA sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Overall, we uncovered 4,230 genes and 209 metabolites are significantly differentially expressed between the SFs and PFs of mulberry. The combined transcriptomic and metabolomic analysis revealed these differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) are involved in flavonoid biosynthesis, galactose metabolism, plant–pathogen interaction, and starch and sucrose metabolism, and these detected DEGs and DEMs may be associated with sex differentiation of mulberry through the regulation of the enrichment pathways, such as the MAPK pathway, flavonoid biosynthesis, galactose metabolism, plant–pathogen interaction, and starch and sucrose metabolism. This study will provide a rich source for the analysis of the molecular mechanism of mulberry sex differentiation processes.
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Affiliation(s)
- Pei-Gang Liu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zi-Long Xu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yan Zhu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tian-Bao Lin
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhi-Qiang Lv
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sheng Yang
- Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Jin-Wang Wang
- Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Wen-Jun Hu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin Chen
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jia Wei
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Jia Wei,
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Zhu S, Fan R, Xiong X, Li J, Xiang L, Hong Y, Ye Y, Zhang X, Yu X, Chen Y. MeWRKY IIas, Subfamily Genes of WRKY Transcription Factors From Cassava, Play an Important Role in Disease Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:890555. [PMID: 35720572 PMCID: PMC9201764 DOI: 10.3389/fpls.2022.890555] [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: 03/06/2022] [Accepted: 05/02/2022] [Indexed: 05/20/2023]
Abstract
Cassava (Manihot esculenta Crantz) is an important tropical crop for food, fodder, and energy. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) occurs in all cassava growing regions and threatens global cassava production. WRKY transcription factor family plays the essential roles during plant growth, development, and abiotic or biotic stress. Particularly, previous studies have revealed the important role of the group IIa WRKY genes in plant disease resistance. However, a comprehensive analysis of group IIa subfamily in cassava is still missing. Here, we identified 102 WRKY members, which were classified into three groups, I, II, and III. Transient expression showed that six MeWRKY IIas were localized in the nucleus. MeWRKY IIas transcripts accumulated significantly in response to SA, JA, and Xam. Overexpression of MeWRKY27 and MeWRKY33 in Arabidopsis enhanced its resistance to Pst DC3000. In contrast, silencing of MeWRKY27 and MeWRKY33 in cassava enhanced its susceptibility to Xam. Co-expression network analysis showed that different downstream genes are regulated by different MeWRKY IIa members. The functional analysis of downstream genes will provide clues for clarifying molecular mechanism of cassava disease resistance. Collectively, our results suggest that MeWRKY IIas are regulated by SA, JA signaling, and coordinate response to Xam infection.
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Affiliation(s)
- Shousong Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Ruochen Fan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Xi Xiong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jianjun Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Li Xiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Yuhui Hong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yiwei Ye
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Xiaofei Zhang
- CGIAR Research Program on Roots Tubers and Bananas (RTB), International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Xiaohui Yu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Xiaohui Yu
| | - Yinhua Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Yinhua Chen
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Sun Y, Fu M, Ang Y, Zhu L, Wei L, He Y, Zeng H. Combined analysis of transcriptome and metabolome reveals that sugar, lipid, and phenylpropane metabolism are essential for male fertility in temperature-induced male sterile rice. FRONTIERS IN PLANT SCIENCE 2022; 13:945105. [PMID: 35968120 PMCID: PMC9370067 DOI: 10.3389/fpls.2022.945105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/28/2022] [Indexed: 05/16/2023]
Abstract
Photoperiod- and thermosensitive genic male sterility (PTGMS) rice is a vital germplasm resource consisting of two-line hybrid rice in which light and temperature strictly control their fertility changes. Variable environmental conditions present huge risks to the two-lines hybrid seed production. Explaining the regulatory mechanism of male fertility in rice PTGMS lines is an essential prerequisite to ensuring food security production. A group of near-isogenic lines (NILs) of a rice PTGMS line unique to this research group was used for this study. These lines have the same genetic background and regulate male fertility by responding to different temperature changes. Transcriptomic analysis revealed that 315 upregulated genes and 391 regulated genes regulated male fertility in response to temperature changes, and differentially expressed genes (DEGs) were mainly characterized in enrichment analysis as having roles in the metabolic pathways of sugar, lipid and phenylpropanoid. Electron microscopy analysis revealed that a lack of starch accumulation in sterile pollen grains induced by high temperature, with an abnormal exine development and a lack of inner pollen grains. Defective processes for sporopollenin synthesis, sporopollenin transport and pollen wall formation in sterile anthers were verified using qPCR. Targeted metabolomics analysis revealed that most lipids (phospholipids, sphingolipids and fatty acids) and flavonoids (flavones and flavanones) were upregulated in fertile anthers and involved in pollen wall development and male fertility formation, while lignin G units and C-type lignin were the major contributors to pollen wall development. The coding genes for trehalose 6-phosphate phosphatase, beta-1,3-glucanase, phospholipase D and 4-coumarate-CoA ligase are considered essential regulators in the process of male fertility formation. In conclusion, our results indicated that the expression of critical genes and accumulation of metabolites in the metabolism of sugar, lipid, and phenylpropanoid are essential for male fertility formation. The results provide new insights for addressing the negative effects of environmental variation on two-line hybrid rice production.
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Affiliation(s)
- Yujun Sun
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ming Fu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yina Ang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lan Zhu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Linan Wei
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ying He
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Ying He,
| | - Hanlai Zeng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hanlai Zeng,
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Yuan J, Shi G, Yang Y, Braynen J, Shi X, Wei X, Hao Z, Zhang X, Yuan Y, Tian B, Xie Z, Wei F. Non-homologous chromosome pairing during meiosis in haploid Brassica rapa. PLANT CELL REPORTS 2021; 40:2421-2434. [PMID: 34542669 DOI: 10.1007/s00299-021-02786-2] [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: 06/24/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Cytological observations of chromosome pairing showed that evolutionarily genome duplication might reshape non-homologous pairing during meiosis in haploid B. rapa. A vast number of flowering plants have evolutionarily undergone whole genome duplication (WGD) event. Typically, Brassica rapa is currently considered as an evolutionary mesohexaploid, which has more complicated genomic constitution among flowering plants. In this study, we demonstrated chromosome behaviors in haploid B. rapa to understand how meiosis proceeds in presence of a single homolog. The findings showed that a diploid-like chromosome pairing was generally adapted during meiosis in haploid B. rapa. Non-homologous chromosomes in haploid cells paired at a high-frequency at metaphase I, over 50% of examined meiocytes showed at least three pairs of bivalents then equally segregated at anaphase I during meiosis. The fluorescence immunostaining showed that the cytoskeletal configurations were mostly well-organized during meiosis. Moreover, the expressed genes identified at meiosis in floral development was rather similar between haploid and diploid B. rapa, especially the expression of known hallmark genes pivotal to chromosome synapsis and homologous recombination were mostly in haploid B. rapa. Whole-genome duplication evolutionarily homology of genomic segments might be an important reason for this phenomenon, which would reshape the first division course of meiosis and influence pollen development in plants.
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Affiliation(s)
- Jiachen Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Gongyao Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Janeen Braynen
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xinjie Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Zhuolin Hao
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Baoming Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Fang Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Zhang J, Li J, Ni Y, Jiang Y, Jiao Z, Li H, Wang T, Zhang P, Han M, Li L, Liu H, Li Q, Niu J. Key wheat GRF genes constraining wheat tillering of mutant dmc. PeerJ 2021; 9:e11235. [PMID: 33889451 PMCID: PMC8038642 DOI: 10.7717/peerj.11235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/17/2021] [Indexed: 11/29/2022] Open
Abstract
Tillering is a key agronomy trait for wheat (Triticum aestivum L.) production. Previously, we have reported a dwarf-monoculm wheat mutant (dmc) obtained from cultivar Guomai 301 (wild type, WT), and found growth regulating factors (GRFs) playing important roles in regulating wheat tillering. This study is to systematically investigate the roles of all the wheat GRFs (T. aestivum GRFs, TaGRFs) in regulating tillering, and screen out the key regulators. A total of 30 TaGRFs were identified and their physicochemical properties, gene structures, conserved domains, phylogenetic relationships and tissue expression profiles were analyzed. The expression levels of all the TaGRFs were significantly lower in dmc than those in WT at early tillering stage, and the abnormal expressions of TaGRF2-7(A, B, D), TaGRF5-7D, TaGRF10-6(A, B, D) and TaGRF11-2A were major causes constraining the tillering of dmc. The transcriptions of TaGRFs were significantly affected by exogenous indole acetic acid (IAA) and gibberellin acid (GA3) applications, which suggested that TaGRFs as well as IAA, GA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of GRF genes in wheat.
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Affiliation(s)
- Jing Zhang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Junchang Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu, Henan, China
| | - Yumei Jiang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zhixin Jiao
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Huijuan Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Ting Wang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Peipei Zhang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Mengyao Han
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Lei Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Hongjie Liu
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu, Henan, China
| | - Qiaoyun Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Jishan Niu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
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Kumar S, Mohapatra T. Dynamics of DNA Methylation and Its Functions in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:596236. [PMID: 34093600 PMCID: PMC8175986 DOI: 10.3389/fpls.2021.596236] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/19/2021] [Indexed: 05/20/2023]
Abstract
Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar, ; , orcid.org/0000-0002-7127-3079
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Zhang M, Liu J, Ma Q, Qin Y, Wang H, Chen P, Ma L, Fu X, Zhu L, Wei H, Yu S. Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line. BMC Genomics 2020. [PMID: 33228563 DOI: 10.1186/s12864-020-07250-7251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106. RESULTS Light and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (lUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition. CONCLUSIONS We propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton.
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Affiliation(s)
- Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Qiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Yuan Qin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China.
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Zhang M, Liu J, Ma Q, Qin Y, Wang H, Chen P, Ma L, Fu X, Zhu L, Wei H, Yu S. Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line. BMC Genomics 2020; 21:825. [PMID: 33228563 PMCID: PMC7685665 DOI: 10.1186/s12864-020-07250-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 11/18/2020] [Indexed: 01/17/2023] Open
Abstract
Background Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106. Results Light and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (lUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition. Conclusions We propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07250-1.
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Affiliation(s)
- Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Qiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Yuan Qin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, China.
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Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat. PLoS One 2020; 15:e0236186. [PMID: 32866164 PMCID: PMC7458298 DOI: 10.1371/journal.pone.0236186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
AIM To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes. METHODS AND FINDINGS 42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT). CONCLUSIONS Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.
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