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Zhang X, Yang X, Zhang Q, Wang J, Zeng T, Xi Y, Shen Q. Genome-wide identification and comparative analysis of YABBY transcription factors in oil tea and tea tree. 3 Biotech 2024; 14:113. [PMID: 38515867 PMCID: PMC10951194 DOI: 10.1007/s13205-024-03940-9] [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: 10/14/2023] [Accepted: 01/26/2024] [Indexed: 03/23/2024] Open
Abstract
The plant-specific transcription factor gene family, YABBY, plays an important role in plant development and stress response. Although YABBY genes have been identified in numerous species, a comprehensive characterization of YABBYs in tea tree and oil tea has been lacking. In this study, ten and three YABBY genes were identified in Camellia sinensis and C. oleifera, respectively. YABBY proteins could be divided into five subfamilies. Most YABBY genes in the same clade had similar structures and conserved motifs. Protein evolutionary analysis revealed that FIL/YAB3 displayed high conservation in all positions, followed by INO, YAB2, YAB5, and CRC. Specific site analysis suggested that the YABBY family was polyphyletic during the evolution. Compared to C. oleifera, two segmentally duplicated gene pairs were formed in C. sinensis during recent WGD events generated 30.69 and 45.08 Mya, respectively. Cis-acting element indicated that most YABBY genes contain box4, ARE, and MYB elements. A total of 120 SSR loci were found within CsYABBYs, consisting of six types, while 48 SSR loci were identified within CoYABBY, consisting of three types. Transcriptome results revealed that CRC and INO clades were specifically expressed in floral organs. The expression of CsYABBY10 and CsYABBY5 was significantly up-regulated under drought and salt treatments, respectively, as confirmed by qRT-PCR. CoYABBY genes were more susceptible to salt stress, as CoYABBY3 increased by about 15-fold. Furthermore, functional differentiation may have occurred in duplicated genes. These discoveries provide important information for further research on YABBYs in tea tree and oil tea. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03940-9.
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Affiliation(s)
- Xiaoqin Zhang
- Guizhou Tea Research Institute, Guiyang, 550006 China
| | - Xianfeng Yang
- College of Tea Sciences, Guizhou University, Guiyang, 550025 China
| | - Qinqin Zhang
- Guizhou Normal University, Guiyang, 550001 China
| | - Jialun Wang
- Guizhou Tea Research Institute, Guiyang, 550006 China
| | - Tingting Zeng
- Guizhou Tea Research Institute, Guiyang, 550006 China
| | - Yanan Xi
- Guizhou Tea Research Institute, Guiyang, 550006 China
| | - Qiang Shen
- Guizhou Tea Research Institute, Guiyang, 550006 China
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2
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Yu Z, Huang X, Wen S, Cao H, Wang N, Shen S, Ding M. Alternative Splicing under Cold Stress in Paper Mulberry. PLANTS (BASEL, SWITZERLAND) 2023; 12:3950. [PMID: 38068587 PMCID: PMC10707748 DOI: 10.3390/plants12233950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 05/19/2024]
Abstract
The paper mulberry is a commonly found tree species with a long history of cultivation. It also serves as a crucial case study for understanding how woody plants adapt to low temperatures. Under cold treatment, we observed a substantial number of alternative splicing (AS) genes, showcasing the intricate landscape of AS events. We have detected all seven types of AS events, with the alternative 3' splice site (A3) having the most. We observed that many genes that underwent differential AS were significantly enriched in starch and sucrose metabolism and circadian rhythm pathways. Moreover, a considerable proportion of differentially spliced genes (DSGs) also showed differential expression, with 20.38% and 25.65% under 12 h and 24 h cold treatments, respectively. This suggests a coordinated regulation between gene AS and expression, playing a pivotal role in the paper mulberry's adaptation to cold stress. We further investigated the regulatory mechanisms of AS, identifying 41 serine/arginine-rich (SR) splicing factors, among which 11 showed differential expression under cold treatment, while 29 underwent alternative splicing. Additionally, genes undergoing AS displayed significantly higher DNA methylation levels under cold stress, while normal splicing (non-AS) genes exhibited relatively lower methylation levels. These findings suggest that methylation may play an important role in governing gene AS. Finally, our research will provide useful information on the role of AS in the cold acclimation tolerance of the paper mulberry.
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Affiliation(s)
- Zhipeng Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Xia Huang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Shuhan Wen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Haijuan Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Nan Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Shihua Shen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
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3
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Yang M, Zhou M, Shu M, Han Z, Ma R, Chen Y, Zheng T, Chen H. The Blinin Accumulation Promoted by CbMYB32 Involved in Conyza blinii Resistance to Nocturnal Low Temperature. Int J Mol Sci 2023; 24:ijms24087143. [PMID: 37108302 PMCID: PMC10139108 DOI: 10.3390/ijms24087143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Blinin, a unique terpenoid from Conyza blinii (C. blinii), benefits our health even though this is not its primary function. Physiological and ecological studies have found that the great secondary metabolites participate in important biological processes and relate to species evolution, environmental adaptation, and so on. Moreover, our previous studies have shown that the metabolism and accumulation of blinin has a close correspondence with nocturnal low temperature (NLT). To find out the transcriptional regulation linker in the crosstalk between blinin and NLT, RNA-seq, comparative analysis, and co-expression network were performed. The results indicated that CbMYB32 is located in a nucleus without independent transcriptional activation activity and is probably involved in the metabolism of blinin. Furthermore, we compared the silence and overexpression of CbMYB32 with wild C. blinii. Compared with the overexpression and the wildtype, the CbMYB32 silence line lost more than half of the blinin and detected more peroxide under NLT. Finally, as a characteristic secret of C. blinii, it is reasonable to infer that blinin participates in the NLT adaptation mechanism and has contributed to the systematic evolution of C. blinii.
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Affiliation(s)
- Ming Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Min Zhou
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Mengdan Shu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhengqi Han
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Ruiqi Ma
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Yuting Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Tianrun Zheng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
- Traditional Chinese Medicine Planting Institute, Chongqing Academy of Chinese Materia Medica, Chongqing College of Traditional Chinese Medicine, Chongqing 402760, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
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Mazhar HSUD, Shafiq M, Ali H, Ashfaq M, Anwar A, Tabassum J, Ali Q, Jilani G, Awais M, Sahu R, Javed MA. Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum). Genes (Basel) 2023; 14:genes14040824. [PMID: 37107580 PMCID: PMC10137784 DOI: 10.3390/genes14040824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.
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Zhao S, Zhang Y, Tan M, Jiao J, Zhang C, Wu P, Feng K, Li L. Identification of YABBY Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera. PLANTS (BASEL, SWITZERLAND) 2023; 12:380. [PMID: 36679092 PMCID: PMC9866709 DOI: 10.3390/plants12020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
The plant-specific transcription factor family YABBY plays important roles in plant responses to biotic and abiotic stresses. Although the function of YABBY has been identified in many species, systematic analysis in lotus (Nelumbo nucifera) is still relatively lacking. The present study aimed to characterize all of the YABBY genes in lotus and obtain better insights into NnYABBYs in response to salt stress by depending on ABA signaling. Here, we identified nine YABBY genes by searching the whole lotus genome based on the conserved YABBY domain. Further analysis showed that these members were distributed on six different chromosomes and named from YABBY1 to YABBY9, which were divided into five subgroups, including YAB1, YAB2, YAB5, INO, and CRC. The analysis of cis-elements in promotors revealed that NnYABBYs could be involved in plant hormone signaling and plant responses to abiotic stresses. Quantitative real-time PCR (qRT-PCR) showed that NnYABBYs could be up-regulated or down-regulated by ABA, fluridone, and salt treatment. Subcellular localization indicated that NnYABBY4, NnYABBY5, and NnYABBY6 were mainly localized in the cell membrane and cytoplasm. In addition, the intrinsic trans-activity of NnYABBY was tested by a Y2H assay, which revealed that NnYABBY4, NnYABBY5, and NnYABBY6 are deprived of such a property. This study provided a theoretical basis and reference for the functional research of YABBY for the molecular breeding of lotus.
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Affiliation(s)
- Shuping Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Yao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Mengying Tan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jiao Jiao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Chuyan Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Peng Wu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Kai Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Chen QJ, Zhang LP, Song SR, Wang L, Xu WP, Zhang CX, Wang SP, Liu HF, Ma C. vvi-miPEP172b and vvi-miPEP3635b increase cold tolerance of grapevine by regulating the corresponding MIRNA genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111450. [PMID: 36075277 DOI: 10.1016/j.plantsci.2022.111450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
As a kind of small molecular weight proteins, many peptides have been discovered, including peptides encoded by pri-miRNA (miPEPs). Similar as traditional phytohormone or signaling molecular, these peptides participate in numerous plant growth processes. MicroRNAs (miRNAs) play an important regulatory role in plant stress response. While the roles of miPEPs in response to abiotic stress has not been studied now. In this study, to explore whether miPEPs could contribute to low temperature (4ºC) tolerance of plants, the expression pattern of 23 different vvi-MIRs were analyzed by qRT-PCR in 'Thompson Seedless' (Vitis vinifera) plantlets under cold stress (4ºC) firstly, and vvi-MIR172b and vvi-MIR3635b which showed an elevated expression levels were selected to identify miPEPs. Through transient expression, one small open reading frame (sORF) in each of the two pri-miRNAs could increase the expression of corresponding vvi-MIR, and the amino acid sequences of sORFs were named vvi-miPEP172b and vvi-miPEP3635b, respectively. The synthetic vvi-miPEP172b and vvi-miPEP3635b were applied to the grape plantlets, and the tissue culture plantlets exhibited a higher cold tolerance compared with the control groups. These results revealed the effective roles of miPEPs in plant cold stress resistance for the first time, providing a theoretical basis for the future application of miPEPs to agricultural production.
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Affiliation(s)
- Qiu-Ju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Li-Peng Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Shi-Ren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Ping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cai-Xi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Ping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai-Feng Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Soorni J, Kazemitabar SK, Kahrizi D, Dehestani A, Bagheri N, Kiss A, Kovács PG, Papp I, Mirmazloum I. Biochemical and Transcriptional Responses in Cold-Acclimated and Non-Acclimated Contrasting Camelina Biotypes under Freezing Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:3178. [PMID: 36432910 PMCID: PMC9693809 DOI: 10.3390/plants11223178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Cold-acclimated and non-acclimated contrasting Camelina (Camelina sativa L.) biotypes were investigated for changes in stress-associated biomarkers, including antioxidant enzyme activity, lipid peroxidation, protein, and proline content. In addition, a well-known freezing tolerance pathway participant known as C-repeat/DRE-binding factors (CBFs), an inducer of CBF expression (ICE1), and a cold-regulated (COR6.6) genes of the ICE-CBF-COR pathway were studied at the transcriptional level on the doubled-haploid (DH) lines. Freezing stress had significant effects on all studied parameters. The cold-acclimated DH34 (a freezing-tolerant line) showed an overall better performance under freezing stress than non-acclimated plants. The non-cold-acclimated DH08 (a frost-sensitive line) showed the highest electrolyte leakage after freezing stress. The highest activity of antioxidant enzymes (glutathione peroxidase, superoxide dismutase, and catalase) was also detected in non-acclimated plants, whereas the cold-acclimated plants showed lower enzyme activities upon stress treatment. Cold acclimation had a significantly positive effect on the total protein and proline content of stressed plants. The qRT-PCR analysis revealed significant differences in the expression and cold-inducibility of CsCBF1-3, CsICE1, and CsCOR6.6 genes among the samples of different treatments. The highest expression of all CBF genes was recorded in the non-acclimated frost-tolerant biotype after freezing stress. Interestingly a significantly higher expression of COR6.6 was detected in cold-acclimated samples of both frost-sensitive and -tolerant biotypes after freezing stress. The presented results provide more insights into freezing tolerance mechanisms in the Camelina plant from both a biochemical point of view and the expression of the associated genes.
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Affiliation(s)
- Jahad Soorni
- Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 68984, Iran
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari 68984, Iran
| | - Seyed Kamal Kazemitabar
- Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 68984, Iran
| | - Danial Kahrizi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Razi University, Kermanshah 67144, Iran
| | - Ali Dehestani
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari 68984, Iran
| | - Nadali Bagheri
- Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 68984, Iran
| | - Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro-, Food- and Environmental Science, Debrecen University, H-4032 Debrecen, Hungary
| | - Péter Gergő Kovács
- Department of Agronomy, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary
| | - István Papp
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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Li M, Yu Q, Xu J, Sun H, Cheng Q, Xie Y, Wang C, Li P, Chen C, Zheng Y. Effect of different organic acid additives on the fermentation quality and bacterial community of paper mulberry ( Broussonetia papyrifera) silage. Front Microbiol 2022; 13:1038549. [PMID: 36386675 PMCID: PMC9665874 DOI: 10.3389/fmicb.2022.1038549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023] Open
Abstract
To investigate the effects of different organic acid additives and their concentrations on the fermentation quality and bacterial community of paper mulberry silage, paper mulberry was left untreated (control) or was treated with ethylenediaminetetraacetic acid (EDTA), propionic acid (PA) or citric acid (CA), the amount of each additive was 2 g.kg-1 FM, 5 g.kg-1 FM and g.kg-1 FM. All groups were ensiled for 3, 7, 15, 30 and 60 days. Compared to the control, adding EDTA reduced protein breakdown, preserved more water-soluble carbohydrates of the silages (WSCs, 24.74 g.kg-1 DM), and high concentrations of EDTA inhibited the activity of undesirable microorganisms. Adding PA increased the abundance of Lactiplantibacillus and decreased the abundance of Enterococcus, and it caused a rapid decrease in the pH of the silage at an early stage (from 6.50 to 5.31) while altering the microbiota, and low concentrations of PA resulted in high LA (66.22 g.kg-1 DM) concentration and low PA (9.92 g.kg-1 DM) concentration at 60 days of ensiling. Different concentrations of additives altered the microbial community of paper mulberry to different degrees. High concentrations of PA and CA can increase the abundance of Lactiplantibacillus. High concentrations of CA resulted in a rapid decrease in silage pH at an early stage and higher WSC concentration. These results suggest that EDTA, PA and CA can be used as additives to improve the quality of paper mulberry silage.
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Affiliation(s)
- Mengxin Li
- College of Animal Science, Guizhou University, Guiyang, China
| | - Qiang Yu
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jinyi Xu
- College of Animal Science, Guizhou University, Guiyang, China
| | - Hong Sun
- College of Animal Science, Guizhou University, Guiyang, China
| | - Qiming Cheng
- College of Animal Science, Guizhou University, Guiyang, China
| | - Yixiao Xie
- College of Animal Science, Guizhou University, Guiyang, China
| | - Chunmei Wang
- Key Laboratory of Animal Genetics, Breeding & Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China
| | - Ping Li
- College of Animal Science, Guizhou University, Guiyang, China
| | - Chao Chen
- College of Animal Science, Guizhou University, Guiyang, China
- Key Laboratory of Animal Genetics, Breeding & Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China
| | - Yulong Zheng
- College of Animal Science, Guizhou University, Guiyang, China
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9
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Dong B, Zheng Z, Zhong S, Ye Y, Wang Y, Yang L, Xiao Z, Fang Q, Zhao H. Integrated Transcriptome and Metabolome Analysis of Color Change and Low-Temperature Response during Flowering of Prunus mume. Int J Mol Sci 2022; 23:12831. [PMID: 36361622 PMCID: PMC9658476 DOI: 10.3390/ijms232112831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 10/07/2023] Open
Abstract
In China, Prunus mume is a famous flowering tree that has been cultivated for 3000 years. P. mume grows in tropical and subtropical regions, and most varieties lack cold resistance; thus, it is necessary to study the low-temperature response mechanism of P. mume to expand the scope of its cultivation. We used the integrated transcriptomic and metabolomic analysis of a cold-resistant variety of P. mume 'Meiren', to identify key genes and metabolites associated with low temperatures during flowering. The 'Meiren' cultivar responded in a timely manner to temperature by way of a low-temperature signal transduction pathway. After experiencing low temperatures, the petals fade and wilt, resulting in low ornamental value. At the same time, in the cold response pathway, the activities of related transcription factors up- or downregulate genes and metabolites related to low temperature-induced proteins, osmotic regulators, protective enzyme systems, and biosynthesis and metabolism of sugars and acids. Our findings promote research on the adaptation of P. mume to low temperatures during wintering and early flowering for domestication and breeding.
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Affiliation(s)
- Bin Dong
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Zifei Zheng
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Shiwei Zhong
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Yong Ye
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yiguang Wang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Liyuan Yang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Zheng Xiao
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Qiu Fang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Hongbo Zhao
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
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10
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Ni ZQ, Jin J, Ye Y, Luo WW, Zheng YN, Tong ZK, Lv YQ, Ye JH, Wu LY. Integrative Transcriptomic and Phytohormonal Analyses Provide Insights into the Cold Injury Recovery Mechanisms of Tea Leaves. PLANTS (BASEL, SWITZERLAND) 2022; 11:2751. [PMID: 36297775 PMCID: PMC9610371 DOI: 10.3390/plants11202751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 06/16/2023]
Abstract
Tea plant is susceptible to low temperature, while the cold injury recovery mechanisms of tea leaves are still unclear. Windbreak has an effective and gradient range of protecting tea plants. Tea plants with increasing cold damage degree have varying recovery status accordingly, which are the ideal objects for investigating the cold injury recovery mechanisms of tea leaves. Here, we investigated the transcriptome and phytohormone profiles of tea leaves with different cold injury degrees in recovery (adjacent to the windbreak), and the levels of chlorophylls, malondialdehyde, major phytohormones as well as the activities of peroxidase (POD) and superoxide dismutase (SOD) were also measured. The results showed the content of total chlorophylls and the activity of POD in mature tea leaves gradually decreased with the distance to windbreak, while SOD showed the opposite. The major phytohormones were highly accumulated in the moderately cold-injured tea leaves. The biosynthesis of abscisic acid (ABA) was enhanced in the moderate cold damaged tea leaves, suggesting that ABA plays an important role in the cold response and resistance of tea plants. The transcriptomic result showed that the samples in different rows were well discriminated, and the pathways of plant-pathogen interaction and flavonoid biosynthesis were enriched based on KEGG analysis. WRKY, GRAS and NAC were the top classes of transcription factors differentially expressed in the different cold-injured tea leaves. Thus, windbreak is effective to protect adjacent tea plants from cold wave, and phytohormones importantly participate in the cold injury recovery of tea leaves.
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Affiliation(s)
- Zhi-Qi Ni
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Jing Jin
- Zhejiang Agricultural Technical Extension Center, 29 Fengqi East Road, Hangzhou 310020, China
| | - Ying Ye
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Wen-Wen Luo
- Jinhua Department of Economic Specialty Technology Promotion, 828 Shuanglong South Road, Jinhua 321000, China
| | - Ya-Nan Zheng
- Jinhua Department of Economic Specialty Technology Promotion, 828 Shuanglong South Road, Jinhua 321000, China
| | - Zheng-Kun Tong
- Lanxi Chishan Lake Green Farm Co., Ltd., Lanxi 321100, China
| | - Yi-Qing Lv
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Jian-Hui Ye
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Liang-Yu Wu
- College of Horticulture, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China
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11
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Shen C, Li Q, An Y, Zhou Y, Zhang Y, He F, Chen L, Liu C, Mao W, Wang X, Liang H, Yin W, Xia X. The transcription factor GNC optimizes nitrogen use efficiency and growth by up-regulating the expression of nitrate uptake and assimilation genes in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4778-4792. [PMID: 35526197 DOI: 10.1093/jxb/erac190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plants have evolved complex mechanisms to cope with the fluctuating environmental availability of nitrogen. However, potential genes modulating plant responses to nitrate are yet to be characterized. Here, a poplar GATA transcription factor gene PdGNC (GATA nitrate-inducible carbon-metabolism-involved) was found to be strongly induced by low nitrate. Overexpressing PdGNC in poplar clone 717-1B4 (P. tremula × alba) significantly improved nitrate uptake, remobilization, and assimilation with higher nitrogen use efficiency (NUE) and faster growth, particularly under low nitrate conditions. Conversely, CRISPR/Cas9-mediated poplar mutant gnc exhibited decreased nitrate uptake, relocation, and assimilation, combined with lower NUE and slower growth. Assays with yeast one-hybrid, electrophoretic mobility shift, and a dual-luciferase reporter showed that PdGNC directly activated the promoters of nitrogen pathway genes PdNRT2.4b, PdNR, PdNiR, and PdGS2, leading to a significant increase in nitrate utilization in poplar. As expected, the enhanced NUE promoted growth under low nitrate availability. Taken together, our data show that PdGNC plays an important role in the regulation of NUE and growth in poplar by improving nitrate acquisition, remobilization, and assimilation, and provide a promising strategy for molecular breeding to improve productivity under nitrogen limitation in trees.
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Affiliation(s)
- Chao Shen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Qing Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Yi An
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Yangyan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Yue Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Fang He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Lingyun Chen
- Hangzhou Lifeng Seed Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Chao Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Wei Mao
- Salver Academy of Botany, Rizhao, Shandong 276800, China
| | - Xiaofei Wang
- Salver Academy of Botany, Rizhao, Shandong 276800, China
| | - Haiying Liang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Weilun Yin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
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12
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Jiang M, Li X, Yuan Y, Zhang G, Pang J, Ren J, Wang J, Yang M. Integrated physiological and transcriptomic analyses reveal the molecular mechanism behind the response to cultivation in Quercus mongolica. FRONTIERS IN PLANT SCIENCE 2022; 13:947696. [PMID: 36003809 PMCID: PMC9393570 DOI: 10.3389/fpls.2022.947696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Quercus mongolica, a common tree species for building and landscaping in northern China, has great commercial and ecological value. The seedlings of Q. mongolica grow poorly and develop chlorosis when introduced from high-altitude mountains to low-altitude plains. Effective cultivation measures are key to improving the quality of seedlings. To investigate the complex responses of Q. mongolica to different cultivation measures, we compared the adaptability of 3-year-old Q. mongolica seedlings to pruning (P), irrigation (W), and fertilization [F (nitro compound fertilizer with 16N-16P-16K)]. Physiological measurements and transcriptome sequencing were performed on leaves collected under the P treatments (control, cutting, removal of all lateral branches, and removal of base branches to one-third of seedling height), the W treatments (0, 1, 2, 3, 4, or 5 times in sequence), and the F treatments (0, 2, 4, and 6 g/plant). Analyses of the physiological data showed that P was more effective than W or F for activating intracellular antioxidant systems. By contrast, W and F were more beneficial than P for inducing the accumulation of soluble sugar. OPLS-DA identified superoxide dismutase, malondialdehyde, and peroxidase as critical physiological indices for the three cultivation measures. Transcriptome analyses revealed 1,012 differentially expressed genes (DEGs) in the P treatment, 1,035 DEGs in the W treatment, and 1,175 DEGs in the F treatment; these DEGs were mainly enriched in Gene Ontology terms related to the stress response and signal transduction. Weighted gene coexpression network analyses indicated that specific gene modules were significantly correlated with MDA (one module) and soluble sugar (four modules). Functional annotation of the hub genes differentially expressed in MDA and soluble sugar-related modules revealed that Q. mongolica responded and adapted to different cultivation measures by altering signal transduction, hormone levels, reactive oxygen species, metabolism, and transcription factors. The hub genes HOP3, CIPK11, WRKY22, and BHLH35 in the coexpression networks may played a central role in responses to the cultivation practices. These results reveal the mechanism behind the response of Q. mongolica to different cultivation measures at the physiological and molecular levels and provide insight into the response of plants to cultivation measures.
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Affiliation(s)
- Min Jiang
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Xinman Li
- College of Forestry, Hebei Agricultural University, Baoding, China
| | | | - Guowei Zhang
- Hongyashan State-Owned Forest Farm, Baoding, China
| | | | - Junjie Ren
- Hongyashan State-Owned Forest Farm, Baoding, China
| | - Jinmao Wang
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Minsheng Yang
- College of Forestry, Hebei Agricultural University, Baoding, China
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13
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Yue C, Chen Q, Hu J, Li C, Luo L, Zeng L. Genome-Wide Identification and Characterization of GARP Transcription Factor Gene Family Members Reveal Their Diverse Functions in Tea Plant ( Camellia sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:947072. [PMID: 35845671 PMCID: PMC9280663 DOI: 10.3389/fpls.2022.947072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Golden2, ARR-B, Psr1 (GARP) proteins are plant-specific transcription factors that play vital and diverse roles in plants. However, systematic research on the GARP gene family in plants, including tea plant (Camellia sinensis), is scarce. In this study, a total of 69 GARP genes were identified and characterized from the tea plant genome based on the B-motif sequence signature. The CsGARP genes were clustered into five subfamilies: PHR1/PHL1, KAN, NIGT1/HRS1/HHO, GLK and ARR-B subfamilies. The phylogenetic relationships, gene structures, chromosomal locations, conserved motifs and regulatory cis-acting elements of the CsGARP family members were comprehensively analyzed. The expansion of CsGARP genes occurred via whole-genome duplication/segmental duplication, proximal duplication, and dispersed duplication under purifying selective pressure. The expression patterns of the CsGARP genes were systematically explored from various perspectives: in different tissues during different seasons; in different leaf color stages of tea plant; under aluminum treatment and nitrogen treatment; and in response to abiotic stresses such as cold, drought and salt and to biotic stress caused by Acaphylla theae. The results demonstrate that CsGARP family genes are ubiquitously expressed and play crucial roles in the regulation of growth and development of tea plant and the responses to environmental stimuli. Collectively, these results not only provide valuable information for further functional investigations of CsGARPs in tea plant but also contribute to broadening our knowledge of the functional diversity of GARP family genes in plants.
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Affiliation(s)
- Chuan Yue
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hu
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Congcong Li
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liyong Luo
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Liang Zeng
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
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14
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Effects of Microbial Inoculants on Fermentation Quality and Aerobic Stability of Paper Mulberry Silages Prepared with Molasses or Cellulase. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8040167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Paper mulberry (Broussonetia papyrifera L.) is an unconventional forage with high crude protein content and is widely used in China. In order to evaluate the pattern of fermentation quality and the aerobic stability when inoculated with lactic acid bacteria, laboratory-scale silage was prepared. The experimental groups included a control group (CK), a Lactobacillus plantarum ‘LC365283’ (selected from paper mulberry silage) treatment (L1), a commercial inoculant Lactobacillus plantarum treatment (GF), a commercial inoculant Lactobacillus buchneri treatment (FR), a 3% molasses treatment (MO), a 150 U/g cellulase treatment (CE), and their combinations (MO + L1, MO + GF, MO + FR, CE + L1, CE + GF, and CE + FR). The changes in bacterial community and composition of the fermentation products were evaluated after being ensiled for 30 days and unsealed for 1, 3, 5, and 7 days. Compared with the CK, MO and CE, the silages treated with L1, MO + L1, and CE + L1 showed higher lactic acid concentrations, lower pH values, and lower ammonia nitrogen concentrations (p < 0.05). During the first 3 days of aerobic exposure, the pH values and organic acid content changed slightly in all treatments. The present study suggests that addition of L1 was better than commercial inoculum, and the paper mulberry silages could be well preserved after being unsealed for 3 days.
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15
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Yang Q, Xiang W, Li Z, Nian Y, Fu X, Zhou G, Li L, Zhang J, Huang G, Han X, Xu L, Bai X, Liu L, Wu D. Genome-Wide Characterization and Expression Analysis of HD-ZIP Gene Family in Dendrobium officinale. Front Genet 2022; 13:797014. [PMID: 35368655 PMCID: PMC8971680 DOI: 10.3389/fgene.2022.797014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
The homeodomain-leucine zipper (HD-ZIP) gene family, as one of the plant-specific transcription factor families, plays an important role in regulating plant growth and development as well as in response to diverse stresses. Although it has been extensively characterized in many plants, the HD-ZIP family is not well-studied in Dendrobium officinale, a valuable ornamental and traditional Chinese medicinal herb. In this study, 37 HD-ZIP genes were identified in Dendrobium officinale (Dohdzs) through the in silico genome search method, and they were classified into four subfamilies based on phylogenetic analysis. Exon–intron structure and conserved protein domain analyses further supported the prediction with the same group sharing similar gene and protein structures. Furthermore, their expression patterns were investigated in nine various tissues and under cold stress based on RNA-seq datasets to obtain the tissue-specific and cold-responsive candidates. Finally, Dohdz5, Dohdz9, and Dohdz12 were selected to validate their expression through qRT-PCR analysis, and they displayed significantly differential expression under sudden chilling stress, suggesting they might be the key candidates underlying cold stress response. These findings will contribute to better understanding of the regulatory roles of the HD-ZIP family playing in cold stress and also will provide the vital targets for further functional studies of HD-ZIP genes in D. officinale.
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Affiliation(s)
- Qianyu Yang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Weibo Xiang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Zhihui Li
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Yuxin Nian
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiaoyun Fu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Guangzhu Zhou
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Linbao Li
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Jun Zhang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Guiyun Huang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Xiao Han
- Natural Resources Affairs Service Center of Dalian, Dalian, China
| | - Lu Xu
- College of Horticulture, Hunan Agricultural University, Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha, China
| | - Xiao Bai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lei Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Lei Liu, ; Di Wu,
| | - Di Wu
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
- *Correspondence: Lei Liu, ; Di Wu,
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16
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Vergara A, Haas JC, Aro T, Stachula P, Street NR, Hurry V. Norway spruce deploys tissue-specific responses during acclimation to cold. PLANT, CELL & ENVIRONMENT 2022; 45:427-445. [PMID: 34873720 DOI: 10.1111/pce.14241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.
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Affiliation(s)
- Alexander Vergara
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Julia C Haas
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Tuuli Aro
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Paulina Stachula
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Vaughan Hurry
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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Genome-Wide Analysis of BpYABs and Function Identification Involving in the Leaf and Silique Development in Transgenic Arabidopsis. Int J Mol Sci 2022; 23:ijms23031670. [PMID: 35163600 PMCID: PMC8836020 DOI: 10.3390/ijms23031670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
YABs play an important role in the leaf development of the paper mulberry (Broussonetia papyrifera) and of the heterophylly. Thus, we investigated the function of BpYABs. Gene cloning, phylogenetic analysis, motif identification, subcellular localization, transactivation activity assay, qRT-PCR, in situ hybridization, and ectopic expression were used in our study. Six BpYABs were isolated, and four of them had transcriptional activity. BpYAB1, BpYAB3, BpYAB4, and BpYAB5 were localized to the nucleus. BpYAB1 was only expressed in the flower, while BpYAB6 was not expressed in any detected tissues; the four remaining BpYABs were expressed in the bud, leaf and flower, and their expression level decreased with leaf development. Further in situ hybridization showed that BpYAB3 and BpYAB5 were expressed in the vascular tissues and lamina, but neither showed the adaxial–abaxial polarity distribution pattern in the mature leaf lamina. Ectopic expression of BpYAB2, BpYAB3, BpYAB4 and BpYAB5 induced increased expression of AtWOX1 and caused the leaf of Arabidopsis to become smaller and curl downwards. Ectopic expression also led to shorter siliques and smaller seeds, but not for BpYAB5. These results suggest that BpYABs have functional divergency and redundancy in regulating leaf and silique development.
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18
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Zhang BQ, Song XP, Zhang XQ, Huang YX, Liang YJ, Zhou S, Yang CF, Yang LT, Huang X, Li YR. Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress. Genes (Basel) 2022; 13:genes13020246. [PMID: 35205291 PMCID: PMC8871730 DOI: 10.3390/genes13020246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/15/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter’s low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.
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Affiliation(s)
- Bao-Qing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
| | - Xiao-Qiu Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
| | - Yu-Xin Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
| | - Yong-Jian Liang
- College of Agriculture, Guangxi University, Nanning 530005, China; (Y.-J.L.); (L.-T.Y.)
| | - Shan Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
| | - Cui-Fang Yang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning 530005, China; (Y.-J.L.); (L.-T.Y.)
| | - Xing Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
- Correspondence: (X.H.); (Y.-R.L.); Tel./Fax: +86-771-389-9033 (Y.-R.L.)
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (B.-Q.Z.); (X.-P.S.); (X.-Q.Z.); (Y.-X.H.); (S.Z.); (C.-F.Y.)
- College of Agriculture, Guangxi University, Nanning 530005, China; (Y.-J.L.); (L.-T.Y.)
- Correspondence: (X.H.); (Y.-R.L.); Tel./Fax: +86-771-389-9033 (Y.-R.L.)
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Addition of Lactic Acid Bacteria Can Promote the Quality and Feeding Value of Broussonetia papyrifera (Paper Mulberry) Silage. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8010025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this study, the influence of two lactic acid bacteria (LAB) strains [Lactobacillus rhamnosus BDy (LR-BDy) and Lactobacillus buchneri TSy (LB-TSy)] selected from Southwest China on the fermentation characteristics and in vitro gas production of Broussonetia papyrifera (paper mulberry) silage were experimentally explored. The experimental groups were a control group (C), an LB-TSy treatment (LB), an LR-BDy treatment (LR), and an LR-BDy + LB-TSy hybrid group (LR × LB). After the LAB were added, the pH value of paper mulberry silage significantly declined (p < 0.05), and the crude protein content was effectively preserved (p < 0.05). However, no significant changes were found in the levels of neutral detergent fiber, acid detergent fiber, and crude ash (p > 0.05). The lactic acid content in paper mulberry silage was evidently increased (p < 0.05). The in vitro gas production in the LR at 36, 48, and 72 h were markedly higher than that in the other treatments (p < 0.05). Owing to the addition of LAB, the microbial diversity in paper mulberry silage was reduced, while the relative bacterial abundance of Lactobacillus was enhanced. Hence, the addition of LAB selected from the warm and humid region in Southwest China can improve the quality of paper mulberry silage and elevate its feeding value in this region.
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20
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Xiang N, Hu JG, Yan S, Guo X. Plant Hormones and Volatiles Response to Temperature Stress in Sweet Corn ( Zea mays L.) Seedlings. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6779-6790. [PMID: 34115469 DOI: 10.1021/acs.jafc.1c02275] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This work aims to emphasize on disclosing the regulative mechanism of sweet corn seedlings response to extreme temperature stress; transcriptomics and metabolomics for volatiles and plant hormones were integrated in this study. Results showed that low-temperature stress significantly impressed 20 volatiles; abscisic acid and salicylic acid accumulated, while auxin and jasmonic acid decreased. The regulatory patterns of vp14 and ABF for abscisic acid accumulation and signal transduction were elucidated in low-temperature stress. High-temperature stress influenced 31 volatiles and caused the reductions on zeatin, salicylic acid, jasmonic acid, and auxin. The up-regulation of an ARR-B gene emphasized its function on zeatin signal transduction under high-temperature stress. Correlations among gene modules, phytohormones, and volatiles were analyzed for building the regulative network of sweet corn seedlings under temperature stress. The attained result might build foundations for improving early development of sweet corn by biological intervention or genomic-level modulation.
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Affiliation(s)
- Nan Xiang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jian-Guang Hu
- Key Laboratory of Crops Genetics Improvement of Guangdong Province, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xinbo Guo
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
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21
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Guo L, Wang X, Lin Y, Yang X, Ni K, Yang F. Microorganisms that are critical for the fermentation quality of paper mulberry silage. Food Energy Secur 2021. [DOI: 10.1002/fes3.304] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Linna Guo
- College of Grassland Science and Technology China Agricultural University Beijing China
| | - Xuekai Wang
- College of Grassland Science and Technology China Agricultural University Beijing China
| | - Yanli Lin
- Beijing Sure Academy of Biosciences Beijing China
| | - Xueping Yang
- College of Grassland Science and Technology China Agricultural University Beijing China
| | - Kuikui Ni
- College of Grassland Science and Technology China Agricultural University Beijing China
| | - Fuyu Yang
- College of Grassland Science and Technology China Agricultural University Beijing China
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22
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Shen C, Zhang Y, Li Q, Liu S, He F, An Y, Zhou Y, Liu C, Yin W, Xia X. PdGNC confers drought tolerance by mediating stomatal closure resulting from NO and H 2 O 2 production via the direct regulation of PdHXK1 expression in Populus. THE NEW PHYTOLOGIST 2021; 230:1868-1882. [PMID: 33629353 DOI: 10.1111/nph.17301] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/14/2021] [Indexed: 05/28/2023]
Abstract
Drought is one of the primary abiotic stresses, seriously implicating plant growth and productivity. Stomata play a crucial role in regulating drought tolerance. However, the molecular mechanism on stomatal movement-mediated drought tolerance remains unclear. Using genetic, molecular and biochemical techniques, we identified that the PdGNC directly activating the promoter of PdHXK1 by binding the GATC element, a hexokinase (HXK) synthesis key gene. Here, PdGNC, a member of the GATA transcription factor family, was greatly induced by abscisic acid and dehydration. Overexpressing PdGNC in poplar (Populus clone 717) resulted in reduced stomatal aperture with greater water-use efficiency and increased water deficit tolerance. By contrast, CRISPR/Cas9-mediated poplar mutant gnc exhibited increased stomatal aperture and water loss with reducing drought resistance. PdGNC activates PdHXK1 (a hexokinase synthesis key gene), resulting in a remarkable increase in hexokinase activity in poplars subjected to water deficit. Furthermore, hexokinase promoted nitric oxide (NO) and hydrogen peroxide (H2 O2 ) production in guard cells, which ultimately reduced stomatal aperture and increased drought resistance. Together, PdGNC confers drought stress tolerance by reducing stomatal aperture caused by NO and H2 O2 production via the direct regulation of PdHXK1 expression in poplars.
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Affiliation(s)
- Chao Shen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yue Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shujing Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Fang He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yi An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yangyan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weilun Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Jiang C, Lv G, Ge J, He B, Zhang Z, Hu Z, Zeng B. Genome-wide identification of the GATA transcription factor family and their expression patterns under temperature and salt stress in Aspergillus oryzae. AMB Express 2021; 11:56. [PMID: 33876331 PMCID: PMC8055810 DOI: 10.1186/s13568-021-01212-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
GATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X2-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.
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24
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Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio. PLoS One 2021; 16:e0246615. [PMID: 33784314 PMCID: PMC8009359 DOI: 10.1371/journal.pone.0246615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Global warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat in Nothofagus pumilio, an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20°C (control) or 34°C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat in Arabidopsis thaliana, Populus tomentosa and N. pumilio we provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.
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25
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Zhang B, Chen N, Peng X, Shen S. Identification of the PP2C gene family in paper mulberry (Broussonetia papyrifera) and its roles in the regulation mechanism of the response to cold stress. Biotechnol Lett 2021; 43:1089-1102. [PMID: 33751277 DOI: 10.1007/s10529-021-03110-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/27/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVES To study the possible roles of type-2C protein phosphatases (PP2Cs) which have been confirmed to play roles in the response to diverse abiotic stresses in paper mulberry, we launched a series of genomic and functional studies of BpPP2Cs. RESULTS Sixty-three PP2C proteins in paper mulberry (Broussonetia papyrifera) were classified into 13 clades. Four BpPP2Cs with kinase domains were verified to be highly conserved in organisms ranging from algae to dicots. Seven pairs of BpPP2C genes were found to be expanding, and 18 BpPP2C genes had orthologues in Arabidopsis. BpPP2Cs showed broad expression in different tissues; the expression levels of 18 BpPP2Cs were changed and the phosphorylation levels of seven BpPP2C proteins increased at low temperature. Cold-response elements were found in the promoter region of 31 BpPP2Cs. Finally, Bp01g0320 was found to act as a hub protein and Bp01g0512 and Bp09g1278 played key roles in the ABA-signaling pathway and MAPK cascades, respectively. CONCLUSION These results suggest that the PP2C gene family of paper mulberry is evolutionarily conserved and participates the regulation of the response to cold stress, which will play a vital role in further research on phosphatases in paper mulberry.
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Affiliation(s)
- Bohan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Naizhi Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
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26
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Martínez-Vázquez JP, Loera-Muro A, Gómez-Aguirre YA, Morales-Domínguez JF. Identification and characterization of the EXPA7, EXPA18 and EXT10 genes in Turbinicarpus lophophoroides (Werderm.) Buxb. & Backeb; and their expression analysis in the root under abiotic stress. Mol Biol Rep 2021; 48:1633-1644. [PMID: 33606149 DOI: 10.1007/s11033-021-06157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
Expansin and extensin are proteins involved in resistance to various abiotic stresses by processes of cell wall modification and in the formation and elongation of the hairy root. They are located in several organs of the plant included root epidermis. Turbinicarpus lophophoroides is a cactus model to studies these genes in adventitious and transformed roots. In this study, we identified and characterized the expansin7, expansin18 and extensin10 genes in T. lophophoroides. Bioinformatic analysis indicated that the expansin sequences contained the motifs: HTFYG, HFD, YRR, VPC and YW; and certain conserved cysteine (C) residues. Regarding extensin10, the sequence contains the conserved SPPPP (SP4), YYS and YV motifs. The expression analysis in adventitious and transformed roots under osmotic stress (300 mM mannitol), heat (37 °C) and cold (4 °C); shows a higher expression of TlExpA18 in both roots, a decrease in TlExpA7 in transformed roots and a null expression in TlExt10 in both roots. In addition, a morphological comparison of the maturation/differentiation zone, meristem and cap between adventitious and transformed roots by SEM was performed, finding differences in the quantity and length of the hairy roots and the shape of the root cap. Overall, the study concluded that TlExpA18 and TlExpA7 belong to expansin family and TlExt10 belong to extensin family. The expression characteristics of TlExpA18, TlExpA7 and TlExt10 will facilitate the investigation of its function in stress response and other physiological processes in T. lophophoroides.
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Affiliation(s)
- J P Martínez-Vázquez
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad #940, Fracc. C. U., C.P, 20131, Aguascalientes, Mexico
| | - A Loera-Muro
- CONACyT-Centro de Investigaciones Biológicas del Noroeste, SC. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, B.C.S. C.P. 23096, La Paz, Mexico
| | - Yenny A Gómez-Aguirre
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad #940, Fracc. C. U., C.P, 20131, Aguascalientes, Mexico
| | - J F Morales-Domínguez
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad #940, Fracc. C. U., C.P, 20131, Aguascalientes, Mexico.
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27
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Huang X, Liang Y, Zhang B, Song X, Li Y, Qin Z, Li D, Chen R, Zhou Z, Deng Y, Wei J, Wu J. Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress. Front Genet 2021; 11:581993. [PMID: 33569078 PMCID: PMC7868625 DOI: 10.3389/fgene.2020.581993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/11/2020] [Indexed: 11/26/2022] Open
Abstract
Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.
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Affiliation(s)
- Xing Huang
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | | | - Baoqing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Xiupeng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Yangrui Li
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Zhengqiang Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Dewei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Rongfa Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Zhongfeng Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Yuchi Deng
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Jiguang Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Jianming Wu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
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28
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Wang J, Xia J, Song Q, Liao X, Gao Y, Zheng F, Yang C. Genome-wide identification, genomic organization and expression profiles of SlARR-B gene family in tomato. J Appl Genet 2020; 61:391-404. [PMID: 32666420 DOI: 10.1007/s13353-020-00565-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 01/13/2023]
Abstract
The type-B authentic response regulators (ARR-Bs) function as positive regulators of cytokinin signal transduction and play important roles in abiotic stress resistance and plant development. However, little of ARR-B family is known in tomato. In this study, we performed a comprehensive analysis of ARR-B family factors in tomato. In total, 12 genes encoding ARR-B transcription factors (named as SlARR-B1-SlARR-B12) were identified from tomato. We analyzed the structures, chromosome locations, phylogeny, protein motifs, and expression profiles of these SlARR-B genes. Gene structure analysis showed that 5-12 exons and 4-11 introns existed in the SlARR-B genes. These SlARR-B genes were asymmetrically distributed on eight chromosomes in tomato. Phylogenetic tree of SlARR-B genes from tomato and other plant species revealed that SlARR-B genes were classified into 6 subfamilies. SlARR-B proteins had typical conserved domains, including Motif 1 and Motif 2. The investigation of the expression profiles of SlARR-B genes in all the examined tissues demonstrated that these genes were differentially expressed, including roots, stems, leaves, flowers, and fruits at developmental stages. Notably, the expression of SlARR-B11 and SlARR-B12 exhibited high expression levels in flowers. Each gene was induced by at least one of different phytohormones (SA, IAA, ABA, IBA, 6-BA, JA, GA, and ETH) and four abiotic stress treatments (heat, drought, salt, and cold). This study sets a good foundation for further characterization of the SlARR-B transcription factors in plant development and abiotic stress responses of tomato.
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Affiliation(s)
- Junqiang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Junhui Xia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qiushuo Song
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanna Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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29
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Estravis-Barcala M, Mattera MG, Soliani C, Bellora N, Opgenoorth L, Heer K, Arana MV. Molecular bases of responses to abiotic stress in trees. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3765-3779. [PMID: 31768543 PMCID: PMC7316969 DOI: 10.1093/jxb/erz532] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 05/05/2023]
Abstract
Trees are constantly exposed to climate fluctuations, which vary with both time and geographic location. Environmental changes that are outside of the physiological favorable range usually negatively affect plant performance and trigger responses to abiotic stress. Long-living trees in particular have evolved a wide spectrum of molecular mechanisms to coordinate growth and development under stressful conditions, thus minimizing fitness costs. The ongoing development of techniques directed at quantifying abiotic stress has significantly increased our knowledge of physiological responses in woody plants. However, it is only within recent years that advances in next-generation sequencing and biochemical approaches have enabled us to begin to understand the complexity of the molecular systems that underlie these responses. Here, we review recent progress in our understanding of the molecular bases of drought and temperature stresses in trees, with a focus on functional, transcriptomic, epigenetic, and population genomic studies. In addition, we highlight topics that will contribute to progress in our understanding of the plastic and adaptive responses of woody plants to drought and temperature in a context of global climate change.
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Affiliation(s)
- Maximiliano Estravis-Barcala
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - María Gabriela Mattera
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Carolina Soliani
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Nicolás Bellora
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - Lars Opgenoorth
- Department of Ecology, Philipps University Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, BirmensdorfSwitzerland
| | - Katrin Heer
- Department of Conservation Biology, Philipps University Marburg, Marburg Germany
| | - María Verónica Arana
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
- Correspondence:
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Ni J, Su S, Li H, Geng Y, Zhou H, Feng Y, Xu X. Distinct physiological and transcriptional responses of leaves of paper mulberry (Broussonetia kazinoki × B. papyrifera) under different nitrogen supply levels. TREE PHYSIOLOGY 2020; 40:667-682. [PMID: 32211806 DOI: 10.1093/treephys/tpaa021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Paper mulberry, a vigorous pioneer species used for ecological reclamation and a high-protein forage plant for economic development, has been widely planted in China. To further develop its potential value, it is necessary to explore the regulatory mechanism of nitrogen metabolism for rational nitrogen utilization. In this study, we investigated the morphology, physiology and transcriptome of a paper mulberry hybrid (Broussonetia kazinoki × B. papyrifera) in response to different nitrogen concentrations. Moderate nitrogen promoted plant growth and biomass accumulation. Photosynthetic characteristics, concentration of nitrogenous compounds and activities of enzymes were stimulated under nitrogen treatment. However, these enhancements were slightly or severely inhibited under excessive nitrogen supply. Nitrite reductase and glutamate synthase were more sensitive than nitrate reductase and glutamine synthetase and more likely to be inhibited under high nitrogen concentrations. Transcriptome analysis of the leaf transcriptome identified 161,961 unigenes. The differentially expressed genes associated with metabolism of nitrogen, alanine, aspartate, glutamate and glycerophospholipid showed high transcript abundances after nitrogen application, whereas those associated with glycerophospholipid, glycerolipid, amino sugar and nucleotide sugar metabolism were down-regulated. Combined with weighted gene coexpression network analysis, we uncovered 16 modules according to similarity in expression patterns. Asparagine synthetase and inorganic pyrophosphatase were considered two hub genes in two modules, which were associated with nitrogen metabolism and phosphorus metabolism, respectively. The expression characteristics of these genes may explain the regulation of morphological, physiological and other related metabolic strategies harmoniously. This multifaceted study provides valuable insights to further understand the mechanism of nitrogen metabolism and to guide utilization of paper mulberry.
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Affiliation(s)
- Jianwei Ni
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shang Su
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yonghang Geng
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanzhi Feng
- Paulownia Research and Development Center of National Forestry and Grassland Administration, Zhengzhou, Henan 450003, China
| | - Xinqiao Xu
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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31
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Identification and Expression Analysis of the NAC Gene Family in Coffea canephora. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9110670] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.
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Tang W, Thompson WA. OsmiR528 Enhances Cold Stress Tolerance by Repressing Expression of Stress Response-related Transcription Factor Genes in Plant Cells. Curr Genomics 2019; 20:100-114. [PMID: 31555061 PMCID: PMC6728904 DOI: 10.2174/1389202920666190129145439] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background: MicroRNAs participate in many molecular mechanisms and signaling trans-duction pathways that are associated with plant stress tolerance by repressing expression of their target genes. However, how microRNAs enhance tolerance to low temperature stress in plant cells remains elusive. Objective: In this investigation, we demonstrated that overexpression of the rice microRNA528 (Os-miR528) increases cell viability, growth rate, antioxidants content, ascorbate peroxidase (APOX) activi-ty, and superoxide dismutase (SOD) activity and decreases ion leakage rate and thiobarbituric acid reac-tive substances (TBARS) under low temperature stress in Arabidopsis (Arabidopsis thaliana), pine (Pi-nus elliottii), and rice (Oryza sativa). Methods: To investigate the potential mechanism of OsmiR528 in increasing cold stress tolerance, we examined expression of stress-associated MYB transcription factors OsGAMYB-like1, OsMYBS3, OsMYB4, OsMYB3R-2, OsMYB5, OsMYB59, OsMYB30, OsMYB1R, and OsMYB20 in rice cells by qRT-PCR. Results:
Our experiments demonstrated that OsmiR528 decreases expression of transcription factor OsMYB30 by targeting a F-box domain containing protein gene (Os06g06050), which is a positive regulator of OsMYB30. In OsmiR528 transgenic rice, reduced OsMYB30 expression results in in-creased expression of BMY genes OsBMY2, OsBMY6, and OsBMY10. The transcript levels of the OsBMY2, OsBMY6, and OsBMY10 were elevated by OsMYB30 knockdown, but decreased by Os-MYB30 overexpression in OsmiR528 transgenic cell lines, suggesting that OsmiR528 increases low temperature tolerance by modulating expression of stress response-related transcription factor. Conclusion: Our experiments provide novel information in increasing our understanding in molecular mechanisms of microRNAs-associated low temperature tolerance and are valuable in plant molecular breeding from monocotyledonous, dicotyledonous, and gymnosperm plants.
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Affiliation(s)
- Wei Tang
- 1College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, P.R. China; 2Program of Cellular and Molecular Biology, Duke University, Durham, NC27708, USA
| | - Wells A Thompson
- 1College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, P.R. China; 2Program of Cellular and Molecular Biology, Duke University, Durham, NC27708, USA
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Peng X, Liu H, Chen P, Tang F, Hu Y, Wang F, Pi Z, Zhao M, Chen N, Chen H, Zhang X, Yan X, Liu M, Fu X, Zhao G, Yao P, Wang L, Dai H, Li X, Xiong W, Xu W, Zheng H, Yu H, Shen S. A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage. MOLECULAR PLANT 2019; 12:661-677. [PMID: 30822525 DOI: 10.1016/j.molp.2019.01.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 05/21/2023]
Abstract
Paper mulberry (Broussonetia papyrifera) is a well-known woody tree historically used for Cai Lun papermaking, one of the four great inventions of ancient China. More recently, Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents. In this study, we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches, including Illumina and PacBio sequencing platform as well as Hi-C, optical, and genetic maps. The assembled Paper mulberry genome consists of 386.83 Mb, which is close to the estimated size, and 99.25% (383.93 Mb) of the assembly was assigned to 13 pseudochromosomes. Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine, forage, papermaking, and barkcloth making. We also identified the root-associated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation. Collectively, these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition. Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making, and as forage. These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.
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Affiliation(s)
- Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Hui Liu
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Peilin Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Feng Tang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Yanmin Hu
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Fenfen Wang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Zhi Pi
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Meiling Zhao
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Naizhi Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Hui Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaokang Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Xueqing Yan
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xiaojun Fu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Guofeng Zhao
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Pu Yao
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Wei Xiong
- Quick Green Bio-Tec Co., Ltd., Dalian 116600, China
| | - Wencai Xu
- Beijing Jonathan Science and Technology Development Co., Ltd., Beijing 101314, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101300, China.
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; ChuangGou Science & Technology Co. Ltd., Beijing 100049, China.
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Fan H, Li K, Yao F, Sun L, Liu Y. Comparative transcriptome analyses on terpenoids metabolism in field- and mountain-cultivated ginseng roots. BMC PLANT BIOLOGY 2019; 19:82. [PMID: 30782123 PMCID: PMC6381674 DOI: 10.1186/s12870-019-1682-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/11/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND There exist differences in morphological traits and phytochemical compositions between field- and mountain-cultivated Panax ginseng (FCG and MCG), which might be attributed to variations of terpenoids metabolism adapting to different growth conditions. The present work aims to uncover these variations. RESULTS Among 26,648 differentially expressed genes, 496 genes distributed in seven dominant terpenoids pathways were identified. Diterpenoids and triterpenoids biosynthesis genes were significantly higher-expressed in FCG root. Conversely, biosynthesis of carotenoids was significantly more active in MCG root. Additionally, terpenoids backbones, monoterpenoids, sesquiterpenoids, and terpenoid-quinones biosyntheses were neither obviously inclined. Our determination also revealed that there were more gibberellins and steroids accumulated in FCG root which might be responsible for its quick vegetative growth, and enriched abscisic acid and germacrenes as well as protopanaxatriol-type ginsenosides might be major causes of enhanced stress-resistance in MCG root. CONCLUSIONS The study firstly provided an overview of terpenoids metabolism in roots of FCG and MCG in elucidating the underlying mechanisms for their different morphological appearances and phytochemical compositions.
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Affiliation(s)
- Hang Fan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083 China
| | - Ke Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083 China
- Research Institute of Advanced Eco-Environmental Protection Technology, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083 China
| | - Fan Yao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083 China
| | - Liwei Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083 China
| | - Yujun Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083 China
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Finatto T, Viana VE, Woyann LG, Busanello C, da Maia LC, de Oliveira AC. Can WRKY transcription factors help plants to overcome environmental challenges? Genet Mol Biol 2018; 41:533-544. [PMID: 30235398 PMCID: PMC6136380 DOI: 10.1590/1678-4685-gmb-2017-0232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
WRKY transcription factors (TFs) are responsible for the regulation of genes responsive to many plant growth and developmental cues, as well as to biotic and abiotic stresses. The modulation of gene expression by WRKY proteins primarily occurs by DNA binding at specific cis-regulatory elements, the W-box elements, which are short sequences located in the promoter region of certain genes. In addition, their action can occur through interaction with other TFs and the cellular transcription machinery. The current genome sequences available reveal a relatively large number of WRKY genes, reaching hundreds of copies. Recently, functional genomics studies in model plants have enabled the identification of function and mechanism of action of several WRKY TFs in plants. This review addresses the more recent studies in plants regarding the function of WRKY TFs in both model and crop plants for coping with environmental challenges, including a wide variety of abiotic and biotic stresses.
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Affiliation(s)
- Taciane Finatto
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vívian Ebeling Viana
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Leomar Guilherme Woyann
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carlos Busanello
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano Carlos da Maia
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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Yang Y, Luang S, Harris J, Riboni M, Li Y, Bazanova N, Hrmova M, Haefele S, Kovalchuk N, Lopato S. Overexpression of the class I homeodomain transcription factor TaHDZipI-5 increases drought and frost tolerance in transgenic wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1227-1240. [PMID: 29193733 PMCID: PMC5978581 DOI: 10.1111/pbi.12865] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/29/2017] [Accepted: 11/12/2017] [Indexed: 05/20/2023]
Abstract
Characterization of the function of stress-related genes helps to understand the mechanisms of plant responses to environmental conditions. The findings of this work defined the role of the wheat TaHDZipI-5 gene, encoding a stress-responsive homeodomain-leucine zipper class I (HD-Zip I) transcription factor, during the development of plant tolerance to frost and drought. Strong induction of TaHDZipI-5 expression by low temperatures, and the elevated TaHDZipI-5 levels of expression in flowers and early developing grains in the absence of stress, suggests that TaHDZipI-5 is involved in the regulation of frost tolerance at flowering. The TaHDZipI-5 protein behaved as an activator in a yeast transactivation assay, and the TaHDZipI-5 activation domain was localized to its C-terminus. The TaHDZipI-5 protein homo- and hetero-dimerizes with related TaHDZipI-3, and differences between DNA interactions in both dimers were specified at 3D molecular levels. The constitutive overexpression of TaHDZipI-5 in bread wheat significantly enhanced frost and drought tolerance of transgenic wheat lines with the appearance of undesired phenotypic features, which included a reduced plant size and biomass, delayed flowering and a grain yield decrease. An attempt to improve the phenotype of transgenic wheat by the application of stress-inducible promoters with contrasting properties did not lead to the elimination of undesired phenotype, apparently due to strict spatial requirements for TaHDZipI-5 overexpression.
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Affiliation(s)
- Yunfei Yang
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
| | - Sukanya Luang
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
- Present address:
Institute of Molecular BiosciencesMahidol UniversityNakhon‐PathomThailand
| | - John Harris
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
- Present address:
South Australian Research and Development InstituteGPO Box 397AdelaideSA5064Australia
| | - Matteo Riboni
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
| | - Yuan Li
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
| | - Natalia Bazanova
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
- Present address:
Commonwealth Scientific and Industrial Research OrganisationGlen OsmondSA5064Australia
| | - Maria Hrmova
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
| | - Stephan Haefele
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
- Present address:
Rothamsted ResearchWest Common HarpendenHertfordshireAl5 2JQUK
| | - Nataliya Kovalchuk
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
| | - Sergiy Lopato
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSAAustralia
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Yang Z, Gong Q, Wang L, Jin Y, Xi J, Li Z, Qin W, Yang Z, Lu L, Chen Q, Li F. Genome-Wide Study of YABBY Genes in Upland Cotton and Their Expression Patterns under Different Stresses. Front Genet 2018; 9:33. [PMID: 29467795 PMCID: PMC5808293 DOI: 10.3389/fgene.2018.00033] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the YABBY gene family, a small plant-specific family of genes, have been proposed to function in specifying abaxial cell fate. Although to date little has been learned about cotton YABBY genes, completion of the cotton genome enables a comprehensive genome-wide analysis of YABBY genes in cotton. Here, a total of 12, 12, and 23 YABBY genes were identified in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, [AD]t), respectively. Sequence analysis showed that the N-terminal zinc-finger and C-terminal YABBY domains in YABBY proteins are highly conserved among cotton, Arabidopsis, and rice. Eighty-five genes from eight sequenced species naturally clustered into five groups, and the YAB2-like group could be divided into three sub-groups, indicating that YABBYs are highly conserved among the examined species. Orthologs from the At and Dt sub-genomes (where “t” indicates tetraploid) showed good collinearity, indicating that YABBY loci are highly conserved between these two sub-genomes. Whole-genome duplication was the primary cause of upland cotton YABBY gene expansion, segmental duplication played important roles in YABBY gene expansion within the At and Dt sub-genomes, and the YAB5-like group was mainly generated by segmental duplication. The long-terminal repeat retroelements Copia and Gypsy were identified as major transposable elements accompanying the appearance of duplicated YABBY genes, suggesting that transposable element expansion might be involved in gene duplication. Selection pressure analyses using PAML revealed that relaxed purifying selection might be the main impetus during evolution of YABBY genes in the examined species. Furthermore, exon/intron pattern and motif analyses indicated that genes within the same group were significantly conserved between Arabidopsis and cotton. In addition, the expression patterns in different tissues suggest that YABBY proteins may play roles in ovule development because YABBYs are highly expressed in ovules. The expression pattern of YABBY genes showed that approximately half of the YABBYs were down-regulated under different stress treatments. Collectively, our results represent a comprehensive genome-wide study of the YABBY gene family, which should be helpful in further detailed studies on the gene function and evolution of YABBY genes in cotton.
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Affiliation(s)
- Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qian Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lingling Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuying Jin
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianping Xi
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhi Li
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenqiang Qin
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zuoren Yang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lili Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, China
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Xu Z, Yang G, Dong M, Wu L, Zhang W, Zhao Y. The complete chloroplast genome of an economic and ecological plant, paper mulberry ( Broussonetia kazinoki × Broussonetia papyifera). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 3:28-29. [PMID: 33474054 PMCID: PMC7799636 DOI: 10.1080/23802359.2017.1419088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The paper mulberry, Broussonetia kazinoki × Broussonetia papyifera, is a species within the family Moraceae, also is an economic and ecological plant. Complete chloroplast genome of paper mulberry was reported in this study. The total genome size was 160,903 bp in length, which is separated by a large single copy (LSC) region and a small single copy (SSC) region (89,220 and 20,079 bp in length, respectively). There were a total of 134 predicted functional genes, including 80 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 46 transfer RNA (tRNA) genes. The overall G + C content of the paper mulberry chloroplast genome was 35.74%, while the corresponding values of the LSC, SSC, and IR regions are 33.33%, 28.50%, and 42.72%, respectively. The phylogenetic analysis between Moraceae trees showed chloroplast genome of paper mulberry was closely related to Morus multicaulis.
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Affiliation(s)
- Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China.,School of Chemical and Material Engineering, Hunan City University, Yiyang, China
| | - Guiyan Yang
- College of Forestry, Northwest A&F University, Yangling, China
| | - Meng Dong
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Liang Wu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Wan Zhang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
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İnal B, Büyük İ, İlhan E, Aras S. Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions. 3 Biotech 2017; 7:302. [PMID: 28955602 DOI: 10.1007/s13205-017-0933-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 08/29/2017] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to identify and characterize the C2C2-YABBY family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative PvulYABBY genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids. The isoelectric points (pIs) of YABBY proteins were between 5.18 and 9.34 and ranged from acidic to alkaline, and the molecular weight of PvulYABBYs were between 18978.4 and 28916.8 Da. Three segmentally duplicated gene couples among the identified eight PvulYABBY genes were detected. These segmentally duplicated gene couples were PvulYABBY-1/PvulYABBY-3, PvulYABBY-5/PvulYABBY-7 and PvulYABBY-6/PvulYABBY-8. The predicted number of exons among the PvulYABBY genes varied from 6 to 8 exons. Additionally, all genes found included introns within ORFs. PvulYABBY-2, -4, -5 and -7 genes were targeted by miRNAs of five plant species and a total of five miRNA families (miR5660, miR1157, miR5769, miR5286 and miR8120) were detected. According to RNA-seq analysis, all genes were up- or down-regulated except for PvulYABBY-1 and PvulYABBY-6 after salt stress treatment in leaf and root tissues of common bean. According to the qPCR analysis, six out of eight genes were expressed in the leaves but only four out of eight genes were expressed in the roots and these genes exhibited tissue- and cultivar-specific expression patterns.
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Identification and Functional Divergence Analysis of WOX Gene Family in Paper Mulberry. Int J Mol Sci 2017; 18:ijms18081782. [PMID: 28813005 PMCID: PMC5578171 DOI: 10.3390/ijms18081782] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/02/2017] [Accepted: 08/12/2017] [Indexed: 01/08/2023] Open
Abstract
The WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor involved in plant development and stress response. However, few studies have been reported on the WOX gene in woody plants. In this study, 10 BpWOX genes were isolated from paper mulberry by RACE-PCR and categorized into three clades through phylogenetic analysis, ancient, intermediate and WUS clade. Among them, five members had the transcriptional activity detected by yeast one-hybrid and seven were uniquely localized to the nucleus through green fluorescent protein (GFP) observation. The expression patterns of BpWOX genes in different tissues and under diverse treatments were quantified by the qRT-PCR method. Results showed that BpWUS was expressed in the apical bud, stem and root, BpWOX5 and BpWOX7 functioned only in the root tip, and three BpWOXs regulated leaf development redundantly. BpWOX9 and BpWOX10 were induced by indole-3-acetic acid (IAA) or jasmonic acid (JA), while BpWOX2 was repressed by five phytohormones. Interestingly, most BpWOX genes were responsive to the abiotic stress stimuli of drought, salt, cold, and cadmium (CdCl2). Together, our study revealed that BpWOXs were functionally divergent during paper mulberry development and environmental adaptation, which might be related to their evolutionary relationships. Our work will benefit the systematic understanding of the precise function of WOX in plant development and environmental stress responses.
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Yang Z, Gong Q, Qin W, Yang Z, Cheng Y, Lu L, Ge X, Zhang C, Wu Z, Li F. Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses. BMC PLANT BIOLOGY 2017; 17:113. [PMID: 28683794 PMCID: PMC5501002 DOI: 10.1186/s12870-017-1065-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/25/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton. RESULTS In this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, (AD)t), respectively. Sequence logos showed that homeobox domains were significantly conserved among the WOX genes in cotton, Arabidopsis, and rice. A total of 168 genes from three typical monocots and six dicots were naturally divided into three clades, which were further classified into nine sub-clades. A good collinearity was observed in the synteny analysis of the orthologs from At and Dt (t represents tetraploid) sub-genomes. Whole genome duplication (WGD) and segmental duplication within At and Dt sub-genomes played significant roles in the expansion of WOX genes, and segmental duplication mainly generated the WUS clade. Copia and Gypsy were the two major types of transposable elements distributed upstream or downstream of WOX genes. Furthermore, through comparison, we found that the exon/intron pattern was highly conserved between Arabidopsis and cotton, and the homeobox domain loci were also conserved between them. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of WOX genes under different stress treatments showed that the different genes were induced by different stresses. CONCLUSION In present work, WOX genes, classified into three clades, were identified in the upland cotton genome. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. Moreover, the expression patterns suggested that the duplicated genes might have experienced a functional divergence. Together, these results shed light on the evolution of the WOX gene family, and would be helpful in future research.
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Affiliation(s)
- Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qian Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Cheng
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Ge
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhixia Wu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China.
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Pi Z, Zhao ML, Peng XJ, Shen SH. Phosphoproteomic Analysis of Paper Mulberry Reveals Phosphorylation Functions in Chilling Tolerance. J Proteome Res 2017; 16:1944-1961. [PMID: 28357858 DOI: 10.1021/acs.jproteome.6b01016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paper mulberry is a valuable woody species with a good chilling tolerance. In this study, phosphoproteomic analysis, physiological measurement, and mRNA quantification were employed to explore the molecular mechanism of chilling (4 °C) tolerance in paper mulberry. After chilling for 6 h, 427 significantly changed phosphoproteins were detected in paper mulberry seedlings without obvious physiological injury. When obvious physiological injury occurred after chilling for 48 h, a total of 611 phosphoproteins were found to be significantly changed at the phosphorylation level. Several protein kinases, especially CKII, were possibly responsible for these changes according to conserved sequence analysis. The results of Gene Ontology analysis showed that phosphoproteins were mainly responsible for signal transduction, protein modification, and translation during chilling. Additionally, transport and cellular component organization were enriched after chilling for 6 and 48 h, respectively. On the basis of the protein-protein interaction network analysis, a protein kinase and phosphatases hub protein (P1959) were found to be involved in cross-talk between Ca2+, BR, ABA, and ethylene-mediated signaling pathways. We also highlighted the phosphorylation of BpSIZ1 and BpICE1 possibly impacted on the CBF/DREB-responsive pathway. From these results, we developed a schematic for the chilling tolerance mechanism at phosphorylation level.
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Affiliation(s)
- Zhi Pi
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences , Beijing 100093, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Mei-Ling Zhao
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences , Beijing 100093, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xian-Jun Peng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences , Beijing 100093, China
| | - Shi-Hua Shen
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences , Beijing 100093, China
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Lafuente MT, Establés-Ortíz B, González-Candelas L. Insights into the Molecular Events That Regulate Heat-Induced Chilling Tolerance in Citrus Fruits. FRONTIERS IN PLANT SCIENCE 2017; 8:1113. [PMID: 28694818 PMCID: PMC5483458 DOI: 10.3389/fpls.2017.01113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/08/2017] [Indexed: 05/20/2023]
Abstract
Low non-freezing temperature may cause chilling injury (CI), which is responsible for external quality deterioration in many chilling-sensitive horticultural crops. Exposure of chilling-sensitive citrus cultivars to non-lethal high-temperature conditioning may increase their chilling tolerance. Very little information is available about the molecular events involved in such tolerance. In this work, the molecular events associated with the low temperature tolerance induced by heating Fortune mandarin, which is very sensitive to chilling, for 3 days at 37°C prior to cold storage is presented. A transcriptomic analysis reveals that heat-conditioning has an important impact favoring the repression of genes in cold-stored fruit, and that long-term heat-induced chilling tolerance is an active process that requires activation of transcription factors involved in transcription initiation and of the WRKY family. The analysis also shows that chilling favors degradation processes, which affect lipids and proteins, and that the protective effect of the heat-conditioning treatment is more likely to be related to the repression of the genes involved in lipid degradation than to the modification of fatty acids unsaturation, which affects membrane permeability. Another major factor associated with the beneficial effect of the heat treatment on reducing CI is the regulation of stress-related proteins. Many of the genes that encoded such proteins are involved in secondary metabolism and in oxidative stress-related processes.
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Noman A, Kanwal H, Khalid N, Sanaullah T, Tufail A, Masood A, Sabir SUR, Aqeel M, He S. Perspective Research Progress in Cold Responses of Capsella bursa-pastoris. FRONTIERS IN PLANT SCIENCE 2017; 8:1388. [PMID: 28855910 PMCID: PMC5557727 DOI: 10.3389/fpls.2017.01388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/25/2017] [Indexed: 05/14/2023]
Abstract
Plants respond to cold stress by modulating biochemical pathways and array of molecular events. Plant morphology is also affected by the onset of cold conditions culminating at repression in growth as well as yield reduction. As a preventive measure, cascades of complex signal transduction pathways are employed that permit plants to endure freezing or chilling periods. The signaling pathways and related events are regulated by the plant hormonal activity. Recent investigations have provided a prospective understanding about plant response to cold stress by means of developmental pathways e.g., moderate growth involved in cold tolerance. Cold acclimation assays and bioinformatics analyses have revealed the role of potential transcription factors and expression of genes like CBF, COR in response to low temperature stress. Capsella bursa-pastoris is a considerable model plant system for evolutionary and developmental studies. On different occasions it has been proved that C. bursa-pastoris is more capable of tolerating cold than A. thaliana. But, the mechanism for enhanced low or freezing temperature tolerance is still not clear and demands intensive research. Additionally, identification and validation of cold responsive genes in this candidate plant species is imperative for plant stress physiology and molecular breeding studies to improve cold tolerance in crops. We have analyzed the role of different genes and hormones in regulating plant cold resistance with special reference to C. bursa-pastoris. Review of collected data displays potential ability of Capsella as model plant for improvement in cold stress regulation. Information is summarized on cold stress signaling by hormonal control which highlights the substantial achievements and designate gaps that still happen in our understanding.
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Affiliation(s)
- Ali Noman
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Botany, Government College UniversityFaisalabad, Pakistan
| | - Hina Kanwal
- Department of Botany, Government College Women UniversityFaisalabad, Pakistan
| | - Noreen Khalid
- Department of Botany, Government College Women UniversitySialkot, Pakistan
| | - Tayyaba Sanaullah
- Institute of Pure and Applied Biology, Bahauddin Zakariya UniversityMultan, Pakistan
| | - Aasma Tufail
- Division of Science & Technology, Department of Botany, University of EducationLahore, Pakistan
| | - Atifa Masood
- Department of Botany, University of LahoreSargodha, Pakistan
| | - Sabeeh-ur-Rasool Sabir
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science, Lanzhou UniversityLanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science, Lanzhou UniversityLanzhou, China
- *Correspondence: Muhammad Aqeel
| | - Shuilin He
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- Shuilin He
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Kovalchuk N, Chew W, Sornaraj P, Borisjuk N, Yang N, Singh R, Bazanova N, Shavrukov Y, Guendel A, Munz E, Borisjuk L, Langridge P, Hrmova M, Lopato S. The homeodomain transcription factor TaHDZipI-2 from wheat regulates frost tolerance, flowering time and spike development in transgenic barley. THE NEW PHYTOLOGIST 2016; 211:671-87. [PMID: 26990681 DOI: 10.1111/nph.13919] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
Homeodomain leucine zipper class I (HD-Zip I) transcription factors (TFs) play key roles in the regulation of plant growth and development under stresses. Functions of the TaHDZipI-2 gene isolated from the endosperm of developing wheat grain were revealed. Molecular characterization of TaHDZipI-2 protein included studies of its dimerisation, protein-DNA interactions and gene activation properties using pull-down assays, in-yeast methods and transient expression assays in wheat cells. The analysis of TaHDZipI-2 gene functions was performed using transgenic barley plants. It included comparison of developmental phenotypes, yield components, grain quality, frost tolerance and the levels of expression of potential target genes in transgenic and control plants. Transgenic TaHDZipI-2 lines showed characteristic phenotypic features that included reduced growth rates, reduced biomass, early flowering, light-coloured leaves and narrowly elongated spikes. Transgenic lines produced 25-40% more seeds per spike than control plants, but with 50-60% smaller grain size. In vivo lipid imaging exposed changes in the distribution of lipids between the embryo and endosperm in transgenic seeds. Transgenic lines were significantly more tolerant to frost than control plants. Our data suggest the role of TaHDZipI-2 in controlling several key processes underlying frost tolerance, transition to flowering and spike development.
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Affiliation(s)
- Nataliya Kovalchuk
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - William Chew
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Pradeep Sornaraj
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Nikolai Borisjuk
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Nannan Yang
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Rohan Singh
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Natalia Bazanova
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Yuri Shavrukov
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Andre Guendel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
| | - Eberhard Munz
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
| | - Peter Langridge
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Sergiy Lopato
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
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Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes. PLoS One 2015; 10:e0134419. [PMID: 26266806 PMCID: PMC4534374 DOI: 10.1371/journal.pone.0134419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/08/2015] [Indexed: 12/04/2022] Open
Abstract
Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli.
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