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Xu Y, Cheng J, Hu H, Yan L, Jia J, Wu B. Genome-Wide Identification of NAC Family Genes in Oat and Functional Characterization of AsNAC109 in Abiotic Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1017. [PMID: 38611546 PMCID: PMC11013824 DOI: 10.3390/plants13071017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
The plant-specific NAC gene family is one of the largest transcription factor families, participating in plant growth regulation and stress response. Despite extensive characterization in various plants, our knowledge of the NAC family in oat is lacking. Herein, we identified 333 NAC genes from the latest release of the common oat genome. We provide a comprehensive overview of the oat NAC gene family, covering gene structure, chromosomal localization, phylogenetic characteristics, conserved motif compositions, and gene duplications. AsNAC gene expression in different tissues and the response to various abiotic stresses were characterized using RT-qPCR. The main driver of oat NAC gene family expansion was identified as segmental duplication using collinearity analysis. In addition, the functions of AsNAC109 in regulating abiotic stress tolerance in Arabidopsis were clarified. This is the first genome-wide investigation of the NAC gene family in cultivated oat, which provided a unique resource for subsequent research to elucidate the mechanisms responsible for oat stress tolerance and provides valuable clues for the improvement of stress resistance in cultivated oat.
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Affiliation(s)
- Yahui Xu
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Jialong Cheng
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Haibin Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
| | - Lin Yan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
| | - Juqing Jia
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Bin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
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Roche J, Guérin C, Dupuits C, Elmodafar C, Goupil P, Mouzeyar S. In silico analysis of the Seven IN Absentia (SINA) genes in bread wheat sheds light on their structure in plants. PLoS One 2023; 18:e0295021. [PMID: 38127955 PMCID: PMC10734943 DOI: 10.1371/journal.pone.0295021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Seven IN Absentia (SINA) is a small family of genes coding for ubiquitin-ligases that play major roles in regulating various plant growth and developmental processes, as well as in plant response to diverse biotic and abiotic stresses. Here, we studied the SINA genes family in bread wheat Triticum aestivum which is a culture of major importance for food security worldwide. One hundred and forty-one SINA family genes have been identified in bread wheat and showed that their number is very high compared to other plant species such as A. thaliana or rice. The expansion of this family seems to have been more important in monocots than in eudicots. In bread wheat, the chromosome 3 distal region is the site of a massive amplification of the SINA family, since we found that 83 of the 141 SINA genes are located on this chromosome in the Chinese Spring variety. This amplification probably occurred as a result of local duplications, followed by sequences divergence. The study was then extended to 4856 SINA proteins from 97 plant species. Phylogenetic and structural analyses identified a group of putative ancestral SINA proteins in plants containing a 58 aminoacid specific signature. Based on sequence homology and the research of that "Ancestral SINA motif" of 58 amino acids, a methodological process has been proposed and lead to the identification of functional SINA genes in a large family such as the Triticae that might be used for other species. Finally, tis paper gives a comprehensive overview of wheat gene family organization and functionalization taken the SINA genes as an example.
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Affiliation(s)
- Jane Roche
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont-Auvergne, INRAe, Clermont–Ferrand, France
| | - Claire Guérin
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont-Auvergne, INRAe, Clermont–Ferrand, France
| | - Céline Dupuits
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont-Auvergne, INRAe, Clermont–Ferrand, France
| | - Cherkaoui Elmodafar
- Faculté des Sciences et Techniques, Centre d’Agrobiotechnologie et Bioingénierie, Université Cadi Ayyad, Marrakech, Morocco
| | - Pascale Goupil
- UMR A547 Physiologie Intégrative de l’Arbre en environnement Fluctuant, Université Clermont-Auvergne, INRAe, Clermont–Ferrand, France
| | - Said Mouzeyar
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont-Auvergne, INRAe, Clermont–Ferrand, France
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Xu Y, Li P, Ma F, Huang D, Xing W, Wu B, Sun P, Xu B, Song S. Characterization of the NAC Transcription Factor in Passion Fruit ( Passiflora edulis) and Functional Identification of PeNAC-19 in Cold Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:1393. [PMID: 36987081 PMCID: PMC10051797 DOI: 10.3390/plants12061393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The NAC (NAM, ATAF and CUC) gene family plays an important role in plant development and abiotic stress response. However, up to now, the identification and research of the NAC (PeNAC) family members of passion fruit are still lacking. In this study, 25 PeNACs were identified from the passion fruit genome, and their functions under abiotic stress and at different fruit-ripening stages were analyzed. Furthermore, we analyzed the transcriptome sequencing results of PeNACs under four various abiotic stresses (drought, salt, cold and high temperature) and three different fruit-ripening stages, and verified the expression results of some genes by qRT-PCR. Additionally, tissue-specific analysis showed that most PeNACs were mainly expressed in flowers. In particular, PeNAC-19 was induced by four various abiotic stresses. At present, low temperatures have seriously endangered the development of passion fruit cultivation. Therefore, PeNAC-19 was transformed into tobacco, yeast and Arabidopsis to study their function of resisting low temperature. The results show that PeNAC-19 responded to cold stress significantly in tobacco and Arabidopsis, and could improve the low temperature tolerance of yeast. This study not only improved the understanding of the PeNAC gene family characteristics and evolution, but also provided new insights into the regulation of the PeNAC gene at different stages of fruit maturation and abiotic stresses.
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Affiliation(s)
- Yi Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Pengfei Li
- College of Tropical Crops, Yunnan Agricultural University, Kunming 650201, China
| | - Funing Ma
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Dongmei Huang
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Wenting Xing
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Bin Wu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Peiguang Sun
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Binqiang Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Shun Song
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
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Sehgal D, Dhakate P, Ambreen H, Shaik KHB, Rathan ND, Anusha NM, Deshmukh R, Vikram P. Wheat Omics: Advancements and Opportunities. PLANTS (BASEL, SWITZERLAND) 2023; 12:426. [PMID: 36771512 PMCID: PMC9919419 DOI: 10.3390/plants12030426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Mexico
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110076, India
| | - Heena Ambreen
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Khasim Hussain Baji Shaik
- Faculty of Agriculture Sciences, Georg-August-Universität, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nagenahalli Dharmegowda Rathan
- Indian Agricultural Research Institute (ICAR-IARI), New Delhi 110012, India
- Corteva Agriscience, Hyderabad 502336, Telangana, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
| | - Prashant Vikram
- Bioseed Research India Ltd., Hyderabad 5023324, Telangana, India
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Genome and Transcriptome-Wide Analysis of OsWRKY and OsNAC Gene Families in Oryza sativa and Their Response to White-Backed Planthopper Infestation. Int J Mol Sci 2022; 23:ijms232315396. [PMID: 36499722 PMCID: PMC9739594 DOI: 10.3390/ijms232315396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Plants are threatened by a wide variety of herbivorous insect assaults, and display a variety of inherent and induced defenses that shield them against herbivore attacks. Looking at the massive damage caused by the white-backed planthopper (WBPH), Sogatella furcifera, we undertook a study to identify and functionally annotate OsWRKY and OsNAC transcription factors (TFs) in rice, especially their involvement in WBPH stress. OsWRKY and OsNAC TFs are involved in various developmental processes and responses to biotic and abiotic stresses. However, no comprehensive reports are available on the specific phycological functions of most of the OsWRKY and OsNAC genes in rice during WBPH infestation. The current study aimed to comprehensively explore the OsWRKY and OsNAC genes by analyzing their phylogenetic relationships, subcellular localizations, exon-intron arrangements, conserved motif identities, chromosomal allocations, interaction networks and differential gene expressions during stress conditions. Comparative phylogenetic trees of 101 OsWRKY with 72 AtWRKY genes, and 121 OsNAC with 110 AtNAC genes were constructed to study relationships among these TFs across species. Phylogenetic relationships classified OsWRKY and OsNAC into eight and nine clades, respectively. Most TFs in the same clade had similar genomic features that represented similar functions, and had a high degree of co-expression. Some OsWRKYs (Os09g0417800 (OsWRKY62), Os11g0117600 (OsWRKY50), Os11g0117400 (OsWRKY104) and OsNACs (Os05g0442700, Os12g0630800, Os01g0862800 and Os12g0156100)) showed significantly higher expressions under WBPH infestation, based on transcriptome datasets. This study provides valuable information and clues about predicting the potential roles of OsWRKYs and OsNACs in rice, by combining their genome-wide characterization, expression profiling, protein-protein interactions and gene expressions under WBPH stress. These findings may require additional investigation to understand their metabolic and expression processes, and to develop rice cultivars that are resistant to WBPH.
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Guérin C, Dupuits C, Mouzeyar S, Roche J. Insights into Four NAC Transcription Factors Involved in Grain Development and in Response to Moderate Heat in the Triticeae Tribe. Int J Mol Sci 2022; 23:ijms231911672. [PMID: 36232974 PMCID: PMC9570169 DOI: 10.3390/ijms231911672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Abstract
NAC (NAM (no apical meristem)−ATAF (Arabidopsis transcription activation factor)−CUC (cup-shaped cotyledons)) are among the largest transcription factor families in plants, involved in a plethora of physiological mechanisms. This study focused on four NAC genes previously identified in bread wheat as specifically grain-expressed which could be considered as candidate genes for yield improvement under climate changes. Using in silico analyses, the Triticum aestivum “Grain-NAC” (TaGNAC) orthologs in 14 cereal species were identified. A conserved protein motif was identified only in Triticeae. The expression of TaGNAC and einkorn TmGNAC was studied in response to moderate heat stress during grain development and showed a similar expression pattern that is accelerated during cell division stages under heat stress. A conserved structure was found in the promoter of the Triticeae GNAC orthologs, which is absent in the other Poaceae species. A specific model of promoter structure in Triticeae was proposed, based on the presence of key cis-elements involved in the regulation of seed development, hormonal regulation and response to biotic and abiotic stresses. In conclusion, GNAC genes could play a central role in the regulation of grain development in the Triticeae tribe, particularly in the accumulation of storage proteins, as well as in response to heat stress and could be used as candidate genes for breeding.
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El-Shehawi AM, Elseehy MA, Elseehy MM. CpG Methylation of the Proximal Promoter Region Regulates the Expression of NAC6D Gene in Response to High Temperature in Wheat (Triticum aestivum). CYTOL GENET+ 2022. [DOI: 10.3103/s009545272205005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang M, Wang M, Zhao M, Wang M, Liu S, Tian Y, Moon B, Liang C, Li C, Shi W, Bai MY, Liu S, Zhang W, Hwang I, Xia G. TaSRO1 plays a dual role in suppressing TaSIP1 to fine tune mitochondrial retrograde signalling and enhance salinity stress tolerance. THE NEW PHYTOLOGIST 2022; 236:495-511. [PMID: 35751377 DOI: 10.1111/nph.18340] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Initially discovered in yeast, mitochondrial retrograde signalling has long been recognised as an essential in the perception of stress by eukaryotes. However, how to maintain the optimal amplitude and duration of its activation under natural stress conditions remains elusive in plants. Here, we show that TaSRO1, a major contributor to the agronomic performance of bread wheat plants exposed to salinity stress, interacted with a transmembrane domain-containing NAC transcription factor TaSIP1, which could translocate from the endoplasmic reticulum (ER) into the nucleus and activate some mitochondrial dysfunction stimulon (MDS) genes. Overexpression of TaSIP1 and TaSIP1-∆C (a form lacking the transmembrane domain) in wheat both compromised the plants' tolerance of salinity stress, highlighting the importance of precise regulation of this signal cascade during salinity stress. The interaction of TaSRO1/TaSIP1, in the cytoplasm, arrested more TaSIP1 on the membrane of ER, and in the nucleus, attenuated the trans-activation activity of TaSIP1, therefore reducing the TaSIP1-mediated activation of MDS genes. Moreover, the overexpression of TaSRO1 rescued the inferior phenotype induced by TaSIP1 overexpression. Our study provides an orchestrating mechanism executed by the TaSRO1-TaSIP1 module that balances the growth and stress response via fine tuning the level of mitochondria retrograde signalling.
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Affiliation(s)
- Mei Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Meng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Min Zhao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Shupeng Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Yanchen Tian
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Byeongho Moon
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Chaochao Liang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Chunlong Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Shuwei Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
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Gong F, Zhang T, Wang Z, Qi T, Lu Y, Liu Y, Zhao S, Liu R, Yi R, He J, Tu B, Zhang T, Zhang L, Hao M, Zheng Y, Liu D, Huang L, Wu B. Genome-Wide Survey and Functional Verification of the NAC Transcription Factor Family in Wild Emmer Wheat. Int J Mol Sci 2022; 23:ijms231911598. [PMID: 36232900 PMCID: PMC9569692 DOI: 10.3390/ijms231911598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 12/04/2022] Open
Abstract
The NAC transcription factor (TF) family is one of the largest TF families in plants, which has been widely reported in rice, maize and common wheat. However, the significance of the NAC TF family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of NAC genes was conducted in the wild emmer genome and 249 NAC family members (TdNACs) were identified. The results showed that all of these genes contained NAM/NAC-conserved domains and most of them were predicted to be located on the nucleus. Phylogenetic analysis showed that these 249 TdNACs can be classified into seven clades, which are likely to be involved in the regulation of grain protein content, starch synthesis and response to biotic and abiotic stresses. Expression pattern analysis revealed that TdNACs were highly expressed in different wheat tissues such as grain, root, leaves and shoots. We found that TdNAC8470 was phylogenetically close to NAC genes that regulate either grain protein or starch accumulation. Overexpression of TdNAC8470 in rice showed increased grain starch concentration but decreased grain Fe, Zn and Mn contents compared with wild-type plants. Protein interaction analysis indicated that TdNAC8470 might interact with granule-bound starch synthase 1 (TdGBSS1) to regulate grain starch accumulation. Our work provides a comprehensive understanding of the NAC TFs family in wild emmer wheat and establishes the way for future functional analysis and genetic improvement of increasing grain starch content in wheat.
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Affiliation(s)
- Fangyi Gong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tian Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhe Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiangang Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yusen Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuhong Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ruiqing Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Rui Yi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingshu He
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Tu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Ming Hao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.H.); (B.W.)
| | - Bihua Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.H.); (B.W.)
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Marín-Sanz M, Barro F. RNAi silencing of wheat gliadins alters the network of transcription factors that regulate the synthesis of seed storage proteins toward maintaining grain protein levels. FRONTIERS IN PLANT SCIENCE 2022; 13:935851. [PMID: 36003813 PMCID: PMC9395171 DOI: 10.3389/fpls.2022.935851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reduction of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated, respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are regulated independently of the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling.
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Magar MM, Liu H, Yan G. Genome-Wide Analysis of AP2/ERF Superfamily Genes in Contrasting Wheat Genotypes Reveals Heat Stress-Related Candidate Genes. FRONTIERS IN PLANT SCIENCE 2022; 13:853086. [PMID: 35498651 PMCID: PMC9044922 DOI: 10.3389/fpls.2022.853086] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 06/09/2023]
Abstract
The AP2/ERF superfamily is one of the largest groups of transcription factors (TFs) in plants, which plays important roles in regulating plant growth and development under heat stress. A complete genome-wide identification, characterization, and expression analysis of AP2/ERF superfamily genes focusing on heat stress response were conducted in bread wheat. This study identified 630 putative AP2/ERF superfamily TF genes in wheat, with 517 genes containing well-defined AP2-protein domains. They were classified into five sub-families, according to domain content, conserved motif, and gene structure. The unique genes identified in this study were 112 TaERF genes, 77 TaDREB genes, four TaAP2 genes, and one TaRAV gene. The chromosomal distribution analysis showed the unequal distribution of TaAP2/ERF genes in 21 wheat chromosomes, with 127 pairs of segmental duplications and one pair of tandem duplication, highly concentrated in TaERF and TaDREB sub-families. The qRT-PCR validation of differentially expressed genes (DEGs) in contrasting wheat genotypes under heat stress conditions revealed that significant DEGs in tolerant and susceptible genotypes could unequivocally differentiate tolerant and susceptible wheat genotypes. This study provides useful information on TaAP2/ERF superfamily genes and reveals candidate genes in response to heat stress, which forms a foundation for heat tolerance breeding in wheat.
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12
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Geng L, Su L, Fu L, Lin S, Zhang J, Liu Q, Jiang X. Genome-wide analysis of the rose (Rosa chinensis) NAC family and characterization of RcNAC091. PLANT MOLECULAR BIOLOGY 2022; 108:605-619. [PMID: 35169911 DOI: 10.1007/s11103-022-01250-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
A genome-wide analysis identified 116 NAC genes in rose, including stress-related ones with different expression patterns under drought and salt stress. Silencing of RcNAC091, a member of the ATAF subfamily, decreased dehydration tolerance in rose. The NAC (NAM, ATAF, and CUC) transcription factors (TFs) are plant-specific proteins that regulate various developmental processes and stress responses. However, knowledge of the NAC TFs in rose (Rosa chinensis), one of the most important horticultural crops, is limited. In this study, 116 NAC genes were identified from the rose genome and classified into 16 subfamilies based on protein phylogenetic analysis. Chromosomal mapping revealed that the RcNAC genes were unevenly distributed on the seven chromosomes of rose. Gene structure and motif analysis identified a total of ten conserved motifs, of which motifs 1-7 were highly conserved and present in most rose NACs, while motifs 8-10 were present only in a few subfamilies. Further study of the stress-related RcNACs based on the transcriptome data showed differences in the expression patterns among the organs, at various floral developmental stages, and under drought and salt stress in rose leaves and roots. The stress-related RcNACs possessed cis-regulatory elements (CREs) categorized into three groups corresponding to plant growth and development, phytohormone response, and abiotic and biotic stress response. Reverse transcription-quantitative real-time PCR (RT-qPCR) analysis of 11 representative RcNACs revealed their differential expression in rose leaves and roots under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) treatments. Furthermore, the silencing of RcNAC091 verified its role in positively regulating the dehydration stress response. Overall, the present study provides valuable insights into stress-related RcNACs and paves the way for stress tolerance in rose.
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Affiliation(s)
- Lifang Geng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Lin Su
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Lufeng Fu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Shang Lin
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Jianmei Zhang
- Yantai Service Center of Forest Resources Monitoring and Protection, Yantai, 264000, China
| | - Qinghua Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China.
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13
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Wang Z, Ni L, Liu D, Fu Z, Hua J, Lu Z, Liu L, Yin Y, Li H, Gu C. Genome-Wide Identification and Characterization of NAC Family in Hibiscus hamabo Sieb. et Zucc. under Various Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23063055. [PMID: 35328474 PMCID: PMC8949087 DOI: 10.3390/ijms23063055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/31/2022] Open
Abstract
NAC transcription factor is one of the largest plant gene families, participating in the regulation of plant biological and abiotic stresses. In this study, 182 NAC proteins (HhNACs) were identified based on genomic datasets of Hibiscus hamabo Sieb. et Zucc (H. hamabo). These proteins were divided into 19 subfamilies based on their phylogenetic relationship, motif pattern, and gene structure analysis. Expression analysis with RNA-seq revealed that most HhNACs were expressed in response to drought and salt stress. Research of quantitative real-time PCR analysis of nine selected HhNACs supported the transcriptome data’s dependability and suggested that HhNAC54 was significantly upregulated under multiple abiotic stresses. Overexpression of HhNAC54 in Arabidopsis thaliana (A. thaliana) significantly increased its tolerance to salt. This study provides a basis for a comprehensive analysis of NAC transcription factor and insight into the abiotic stress response mechanism in H. hamabo.
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Affiliation(s)
- Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
| | - Longjie Ni
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Dina Liu
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Zekai Fu
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Zhiguo Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Liangqin Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Huogen Li
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- Correspondence: ; Tel.: +86-25-84347051
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14
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Mao H, Li S, Chen B, Jian C, Mei F, Zhang Y, Li F, Chen N, Li T, Du L, Ding L, Wang Z, Cheng X, Wang X, Kang Z. Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat. MOLECULAR PLANT 2022; 15:276-292. [PMID: 34793983 DOI: 10.1016/j.molp.2021.11.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major environmental factor limiting wheat production worldwide, and developing drought-tolerant cultivars is a central challenge for wheat breeders globally. Therefore, it is important to identify genetic components determining drought tolerance in wheat. In this study, we identified a wheat NAC gene (TaNAC071-A) that is tightly associated with drought tolerance by a genome-wide association study. Knockdown of TaNAC071-A in wheat attenuated plant drought tolerance, whereas its overexpression significantly enhanced drought tolerance through improved water-use efficiency and increased expression of stress-responsive genes. This heightened water-saving mechanism mitigated the yield loss caused by water deficit. Further candidate gene association analysis showed that a 108-bp insertion in the promoter of TaNAC071-A alters its expression level and contributes to variation in drought tolerance among wheat accessions. This insertion contains two MYB cis-regulatory elements (CREs) that can be directly bound by the MYB transcription activator, TaMYBL1, thereby leading to increased TaNAC071-A expression and plant drought tolerance. Importantly, introgression of this 108-bp insertion allele, TaNAC071-AIn-693, into drought-sensitive cultivars could improve their drought tolerance, demonstrating that it is a valuable genetic resource for wheat breeding. Taken together, our findings highlight a major breakthrough in determining the genetic basis underlying phenotypic variation in wheat drought tolerance and showcase the potential of exploiting CRE-containing indels for improving important agronomical traits.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi 712100, China.
| | - Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi 712100, China; Yangling Seed Industry Innovation Center, Yangling, Shaanxi 712100, China.
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15
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Peng Y, Zhao Y, Yu Z, Zeng J, Xu D, Dong J, Ma W. Wheat Quality Formation and Its Regulatory Mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:834654. [PMID: 35432421 PMCID: PMC9006054 DOI: 10.3389/fpls.2022.834654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/09/2022] [Indexed: 05/07/2023]
Abstract
Elucidation of the composition, functional characteristics, and formation mechanism of wheat quality is critical for the sustainable development of wheat industry. It is well documented that wheat processing quality is largely determined by its seed storage proteins including glutenins and gliadins, which confer wheat dough with unique rheological properties, making it possible to produce a series of foods for human consumption. The proportion of different gluten components has become an important target for wheat quality improvement. In many cases, the processing quality of wheat is closely associated with the nutritional value and healthy effect of the end-products. The components of wheat seed storage proteins can greatly influence wheat quality and some can even cause intestinal inflammatory diseases or allergy in humans. Genetic and environmental factors have great impacts on seed storage protein synthesis and accumulation, and fertilization and irrigation strategies also greatly affect the seed storage protein content and composition, which together determine the final end-use quality of wheat. This review summarizes the recent progress in research on the composition, function, biosynthesis, and regulatory mechanism of wheat storage proteins and their impacts on wheat end-product quality.
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Affiliation(s)
- Yanchun Peng
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yun Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Zitong Yu
- Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jing Dong
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- *Correspondence: Wujun Ma,
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16
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Nie G, Yang Z, He J, Liu A, Chen J, Wang S, Wang X, Feng G, Li D, Peng Y, Huang L, Zhang X. Genome-Wide Investigation of the NAC Transcription Factor Family in Miscanthus sinensis and Expression Analysis Under Various Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:766550. [PMID: 34804100 PMCID: PMC8600139 DOI: 10.3389/fpls.2021.766550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The NAC transcription factor family is deemed to be a large plant-specific gene family that plays important roles in plant development and stress response. Miscanthus sinensis is commonly planted in vast marginal land as forage, ornamental grass, or bioenergy crop which demand a relatively high resistance to abiotic stresses. The recent release of a draft chromosome-scale assembly genome of M. sinensis provided a basic platform for the genome-wide investigation of NAC proteins. In this study, a total of 261 M. sinensis NAC genes were identified and a complete overview of the gene family was presented, including gene structure, conserved motif compositions, chromosomal distribution, and gene duplications. Results showed that gene length, molecular weights (MW), and theoretical isoelectric points (pI) of NAC family were varied, while gene structure and motifs were relatively conserved. Chromosomal mapping analysis found that the M. sinensis NAC genes were unevenly distributed on 19 M. sinensis chromosomes, and the interchromosomal evolutionary analysis showed that nine pairs of tandem duplicates genes and 121 segmental duplications were identified, suggesting that gene duplication, especially segmental duplication, is possibly associated with the amplification of M. sinensis NAC gene family. The expression patterns of 14 genes from M. sinensis SNAC subgroup were analyzed under high salinity, PEG, and heavy metals, and multiple NAC genes could be induced by the treatment. These results will provide a very useful reference for follow-up study of the functional characteristics of NAC genes in the mechanism of stress-responsive and potential roles in the development of M. sinensis.
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17
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Mehari TG, Xu Y, Magwanga RO, Umer MJ, Shiraku ML, Hou Y, Wang Y, Wang K, Cai X, Zhou Z, Liu F. Identification and functional characterization of Gh_D01G0514 (GhNAC072) transcription factor in response to drought stress tolerance in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:361-375. [PMID: 34153881 DOI: 10.1016/j.plaphy.2021.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/31/2021] [Indexed: 05/10/2023]
Abstract
Cotton encounters long-term drought stress problems resulting in major yield losses. Transcription factors (TFs) plays an important role in response to biotic and abiotic stresses. The coexpression patterns of gene networks associated with drought stress tolerance were investigated using transcriptome profiles. Applying a weighted gene coexpression network analysis, we discovered a salmon module with 144 genes strongly linked to drought stress tolerance. Based on coexpression and RT-qPCR analysis GH_D01G0514 was selected as the candidate gene, as it was also identified as a hub gene in both roots and leaves with a consistent expression in response to drought stress in both tissues. For validation of GH_D01G0514, Virus Induced Gene Silencing was performed and VIGS plants showed significantly higher excised leaf water loss and ion leakage, while lower relative water and chlorophyll contents as compared to WT (Wild type) and positive control plants. Furthermore, the WT and positive control seedlings showed higher CAT and SOD activities, and lower activities of hydrogen peroxide and MDA enzymes as compared to the VIGS plants. Gh_D01G0514 (GhNAC072) was localized in the nucleus and cytoplasm. Y2H assay demonstrates that Gh_D01G0514 has a potential of auto activation. It was observed that the Gh_D01G0514 was highly upregulated in both tissues based on RNA Seq and RT-qPCR analysis. Thus, we inferred that, this candidate gene might be responsible for drought stress tolerance in cotton. This finding adds significantly to the existing knowledge of drought stress tolerance in cotton and deep molecular analysis are required to understand the molecular mechanisms underlying drought stress tolerance in cotton.
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Affiliation(s)
- Teame Gereziher Mehari
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China; Ethiopian Institute of Agricultural Research, Mekhoni Agricultural Research Center, P.O Box 47, Mekhoni, Tigray, Ethiopia
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China; School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601, Bondo, Kenya
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Margaret Linyerera Shiraku
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China.
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18
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Forlani S, Mizzotti C, Masiero S. The NAC side of the fruit: tuning of fruit development and maturation. BMC PLANT BIOLOGY 2021; 21:238. [PMID: 34044765 PMCID: PMC8157701 DOI: 10.1186/s12870-021-03029-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/10/2021] [Indexed: 05/16/2023]
Abstract
Fruits and seeds resulting from fertilization of flowers, represent an incredible evolutionary advantage in angiosperms and have seen them become a critical element in our food supply.Many studies have been conducted to reveal how fruit matures while protecting growing seeds and ensuring their dispersal. As result, several transcription factors involved in fruit maturation and senescence have been isolated both in model and crop plants. These regulators modulate several cellular processes that occur during fruit ripening such as chlorophyll breakdown, tissue softening, carbohydrates and pigments accumulation.The NAC superfamily of transcription factors is known to be involved in almost all these aspects of fruit development and maturation. In this review, we summarise the current knowledge regarding NACs that modulate fruit ripening in model species (Arabidopsis thaliana and Solanum lycopersicum) and in crops of commercial interest (Oryza sativa, Malus domestica, Fragaria genus, Citrus sinensis and Musa acuminata).
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Affiliation(s)
- Sara Forlani
- Department of Biosciences, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Chiara Mizzotti
- Department of Biosciences, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Simona Masiero
- Department of Biosciences, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy.
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19
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Wang H, Li T, Li W, Wang W, Zhao H. Identification and analysis of Chrysanthemum nankingense NAC transcription factors and an expression analysis of OsNAC7 subfamily members. PeerJ 2021; 9:e11505. [PMID: 34123596 PMCID: PMC8164415 DOI: 10.7717/peerj.11505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/03/2021] [Indexed: 11/26/2022] Open
Abstract
NAC (NAM, ATAF1-2, and CUC2) transcription factors (TFs) play a vital role in plant growth and development, as well as in plant response to biotic and abiotic stressors (Duan et al., 2019; Guerin et al., 2019). Chrysanthemum is a plant with strong stress resistance and adaptability; therefore, a systematic study of NAC TFs in chrysanthemum is of great significance for plant breeding. In this study, 153 putative NAC TFs were identified based on the Chrysanthemum nankingense genome. According to the NAC family in Arabidopsis and rice, a rootless phylogenetic tree was constructed, in which the 153 CnNAC TFs were divided into two groups and 19 subfamilies. Moreover, the expression levels of 12 CnNAC TFs belonging to the OsNAC7 subfamily were analyzed in C. nankingense under osmotic and salt stresses, and different tissues were tested during different growth periods. The results showed that these 12 OsNAC7 subfamily members were involved in the regulation of root and stem growth, as well as in the regulation of drought and salt stresses. Finally, we investigated the function of the CHR00069684 gene, and the results showed that CHR00069684 could confer improved salt and low temperature resistance, enhance ABA sensitivity, and lead to early flowering in tobacco. It was proved that members of the OsNAC7 subfamily have dual functions including the regulation of resistance and the mediation of plant growth and development. This study provides comprehensive information on analyzing the function of CnNAC TFs, and also reveals the important role of OsNAC7 subfamily genes in response to abiotic stress and the regulation of plant growth. These results provide new ideas for plant breeding to control stress resistance and growth simultaneously.
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Affiliation(s)
- Hai Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tong Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wang Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huien Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
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20
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Gao Y, An K, Guo W, Chen Y, Zhang R, Zhang X, Chang S, Rossi V, Jin F, Cao X, Xin M, Peng H, Hu Z, Guo W, Du J, Ni Z, Sun Q, Yao Y. The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality. THE PLANT CELL 2021; 33:603-622. [PMID: 33955492 PMCID: PMC8136912 DOI: 10.1093/plcell/koaa040] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/16/2020] [Indexed: 05/03/2023]
Abstract
In wheat (Triticum aestivum L.), breeding efforts have focused intensively on improving grain yield and quality. For quality, the content and composition of seed storage proteins (SSPs) determine the elasticity of wheat dough and flour processing quality. Moreover, starch levels in seeds are associated with yield. However, little is known about the mechanisms that coordinate SSP and starch accumulation in wheat. In this study, we explored the role of the endosperm-specific NAC transcription factor TaNAC019 in coordinating SSP and starch accumulation. TaNAC019 binds to the promoters of TaGlu-1 loci, encoding high molecular weight glutenin (HMW-GS), and of starch metabolism genes. Triple knock-out mutants of all three TaNAC019 homoeologs exhibited reduced transcript levels for all SSP types and genes involved in starch metabolism, leading to lower gluten and starch contents, and in flour processing quality parameters. TaNAC019 directly activated the expression of HMW-GS genes by binding to a specific motif in their promoters and interacting with the TaGlu-1 regulator TaGAMyb. TaNAC019 also indirectly regulated the expression of TaSPA, an ortholog of maize Opaque2 that activates SSP accumulation. Therefore, TaNAC019 regulation of starch- and SSP-related genes has key roles in wheat grain quality. Finally, we identified an elite allele (TaNAC019-BI) associated with flour processing quality, providing a candidate gene for breeding wheat with improved quality.
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Affiliation(s)
- Yujiao Gao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kexin An
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weiwei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ruijie Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xue Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Siyuan Chang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Vincenzo Rossi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, I-24126 Bergamo, Italy
| | - Fangming Jin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xinyou Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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21
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Shen L, Luo G, Song Y, Xu J, Ji J, Zhang C, Gregová E, Yang W, Li X, Sun J, Zhan K, Cui D, Liu D, Zhang A. A novel NAC family transcription factor SPR suppresses seed storage protein synthesis in wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:992-1007. [PMID: 33305445 PMCID: PMC8131056 DOI: 10.1111/pbi.13524] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/11/2020] [Accepted: 12/01/2020] [Indexed: 05/23/2023]
Abstract
The synthesis of seed storage protein (SSP) is mainly regulated at the transcriptional level. However, few transcriptional regulators of SSP synthesis have been characterized in common wheat (Triticum aestivum) owing to the complex genome. As the A genome donor of common wheat, Triticum urartu could be an elite model in wheat research considering its simple genome. Here, a novel NAC family transcription factor TuSPR from T. urartu was found preferentially expressed in developing endosperm during grain-filling stages. In common wheat transgenically overexpressing TuSPR, the content of total SSPs was reduced by c. 15.97% attributed to the transcription declines of SSP genes. Both in vitro and in vivo assays showed that TuSPR bound to the cis-element 5'-CANNTG-3' distributed in SSP gene promoters and suppressed the transcription. The homolog in common wheat TaSPR shared a conserved function with TuSPR on SSP synthesis suppression. The knock-down of TaSPR in common wheat resulted in 7.07%-20.34% increases in the total SSPs. Both TuSPR and TaSPR could be superior targets in genetic engineering to manipulate SSP content in wheat, and this work undoubtedly expands our knowledge of SSP gene regulation.
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Affiliation(s)
- Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
- Agronomy DepartmentUniversity of FloridaGainesvilleFLUSA
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
- Agronomy CollegeNational Key Laboratory of Wheat and Maize Crop ScienceCollaborative Innovation Center of Grain Crops in HenanHenan Agricultural UniversityZhengzhouChina
| | | | | | - Chi Zhang
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Edita Gregová
- National Agricultural and Food CentreResearch Institute of Plant ProductionPiešťanySlovakia
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Kehui Zhan
- Agronomy CollegeNational Key Laboratory of Wheat and Maize Crop ScienceCollaborative Innovation Center of Grain Crops in HenanHenan Agricultural UniversityZhengzhouChina
| | - Dangqun Cui
- Agronomy CollegeNational Key Laboratory of Wheat and Maize Crop ScienceCollaborative Innovation Center of Grain Crops in HenanHenan Agricultural UniversityZhengzhouChina
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
- Advanced Biotechnology and Application Research CenterSchool of Chemistry and Biological EngineeringUniversity of Science and Technology BeijingBeijingChina
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijingChina
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22
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The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress. Int J Mol Sci 2021; 22:ijms22063111. [PMID: 33803701 PMCID: PMC8002965 DOI: 10.3390/ijms22063111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
FBX proteins are subunits of the SCF complex (Skp1-cullin-FBX) belonging to the E3 ligase family, which is involved in the ubiquitin-proteasome 26S (UPS) pathway responsible for the post-translational protein turnover. By targeting, in a selective manner, key regulatory proteins for ubiquitination and 26S proteasome degradation, FBX proteins play a major role in plant responses to diverse developmental and stress conditions. Although studies on the genomic organization of the FBX gene family in various species have been reported, knowledge related to bread wheat (Triticum aestivum) is scarce and needs to be broadened. Using the latest assembly of the wheat genome, we identified 3670 TaFBX genes distributed non-homogeneously within the three subgenomes (A, B and D) and between the 21 chromosomes, establishing it as one of the richest gene families among plant species. Based on the presence of the five different chromosomal regions previously identified, the present study focused on the genomic distribution of the TaFBX family and the identification of differentially expressed genes during the embryogenesis stages and in response to heat and drought stress. Most of the time, when comparing the expected number of genes (taking into account the formal gene distribution on the entire wheat genome), the TaFBX family harbors a different pattern at the various stratum of observation (subgenome, chromosome, chromosomal regions). We report here that the local gene expansion of the TaFBX family must be the consequence of multiple and complex events, including tandem and small-scale duplications. Regarding the differentially expressed TaFBX genes, while the majority of the genes are localized in the distal chromosomal regions (R1 and R3), differentially expressed genes are more present in the interstitial regions (R2a and R2b) than expected, which could be an indication of the preservation of major genes in those specific chromosomal regions.
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23
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Yang Z, Nie G, Feng G, Han J, Huang L, Zhang X. Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.). BMC Genomics 2021; 22:178. [PMID: 33711917 PMCID: PMC7953825 DOI: 10.1186/s12864-021-07485-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 02/25/2021] [Indexed: 01/07/2023] Open
Abstract
Background Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season perennial forage grasses that is widely cultivated in the world and is highly tolerant to stressful conditions. However, little is known about the mechanisms underlying this tolerance. The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is a large plant-specific gene family that actively participates in plant growth, development, and response to abiotic stress. At present, owing to the absence of genomic information, NAC genes have not been systematically studied in orchardgrass. The recent release of the complete genome sequence of orchardgrass provided a basic platform for the investigation of DgNAC proteins. Results Using the recently released orchardgrass genome database, a total of 108 NAC (DgNAC) genes were identified in the orchardgrass genome database and named based on their chromosomal location. Phylogenetic analysis showed that the DgNAC proteins were distributed in 14 subgroups based on homology with NAC proteins in Arabidopsis, including the orchardgrass-specific subgroup Dg_NAC. Gene structure analysis suggested that the number of exons varied from 1 to 15, and multitudinous DgNAC genes contained three exons. Chromosomal mapping analysis found that the DgNAC genes were unevenly distributed on seven orchardgrass chromosomes. For the gene expression analysis, the expression levels of DgNAC genes in different tissues and floral bud developmental stages were quite different. Quantitative real-time PCR analysis showed distinct expression patterns of 12 DgNAC genes in response to different abiotic stresses. The results from the RNA-seq data revealed that orchardgrass-specific NAC exhibited expression preference or specificity in diverse abiotic stress responses, and the results indicated that these genes may play an important role in the adaptation of orchardgrass under different environments. Conclusions In the current study, a comprehensive and systematic genome-wide analysis of the NAC gene family in orchardgrass was first performed. A total of 108 NAC genes were identified in orchardgrass, and the expression of NAC genes during plant growth and floral bud development and response to various abiotic stresses were investigated. These results will be helpful for further functional characteristic descriptions of DgNAC genes and the improvement of orchardgrass in breeding programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07485-6.
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Affiliation(s)
- Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
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24
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Mei F, Chen B, Li F, Zhang Y, Kang Z, Wang X, Mao H. Overexpression of the wheat NAC transcription factor TaSNAC4-3A gene confers drought tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:37-50. [PMID: 33454635 DOI: 10.1016/j.plaphy.2021.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/04/2021] [Indexed: 05/07/2023]
Abstract
NAC transcription factors (TFs) play critical roles in plant abiotic stress responses. However, information on the roles of NAC TFs is limited in wheat (Triticum aestivum L.). In this study, we isolated three wheat TaSNAC4 homeologous genes, TaSNAC4-3A, TaSNAC4-3B, and TaSNAC4-3D, and characterized the function of TaSNAC4-3A in plant drought tolerance. TaSNAC4 is highly expressed in seedling leaves, and expression is induced by various abiotic stresses. Transient expression and transactivation assays showed that TaSNAC4-3A is localized to the nucleus, and the C-terminal region has transcriptional activation activity. Overexpression of TaSNAC4-3A in Arabidopsis led to stimulated germination and root growth when exposed to salt and osmotic stresses, and drought stress tolerance was significantly increased in the TaSNAC4-3A transgenic lines. When compared to the control plants, the transgenic lines overexpressing TaSNAC4-3A exhibited reduced stomatal aperture size under drought stress, and therefore had lower water loss rates. In addition, the overexpression of TaSNAC4-3A led to abscisic acid (ABA) hypersensitivity at the root elongation and seed germination stages. Further transcriptomic analysis demonstrated that there was a significant up-regulation of stress responsive genes in the TaSNAC4-3A transgenic lines. Our findings have revealed the important role of TaSNAC4-3A in plant drought tolerance.
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Affiliation(s)
- Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China; College of Plant Science, Tarim University, Alar, Xinjiang, 843300, China
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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25
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Ma J, Yuan M, Sun B, Zhang D, Zhang J, Li C, Shao Y, Liu W, Jiang L. Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat ( Triticum aestivum L.). PLANTS 2021; 10:plants10020382. [PMID: 33671285 PMCID: PMC7922369 DOI: 10.3390/plants10020382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed that NAC transcription factors in plants undergo an appearance stage from water to land and a number expansion stage from gymnosperm to angiosperm. Investigating the evolutionary process of the NAC transcription factors from diploid species to hexaploid wheat revealed that tandem replications during the polyploidization process is an important event for increasing the number of NAC transcription factors in wheat. Then, the molecular characteristics, phylogenetic relationships, and expression patterns of 462 NAC transcription factors of hexaploid wheat (TaNACs) were analyzed. The protein structure results showed that TaNAC was relatively conservative at the N-terminal that contains five subdomains. All these TaNACs were divided into Group I and Group II by phylogenetic analysis, and the TaNACs in Group I should undergo strong artificial selection based on single nucleotide polymorphism (SNP) analysis. Through genome synteny and phylogenetic analysis, these TaNACs were classified into 88 groups and 9 clusters. The biased expression results of these TaNACs showed that there are 24 groups and 67 groups of neofunctionalization genes under biotic and abiotic stress, respectively, and 16 groups and 59 groups of subfunctionalization genes. This shows that neofunctionalization plays an important role in coping with different stresses. Our study provides new insights into the evolution of NAC transcription factors in hexaploid wheat.
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Affiliation(s)
- Jianhui Ma
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Meng Yuan
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Bo Sun
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Daijing Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Jie Zhang
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China;
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunxi Li
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Yun Shao
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Wei Liu
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China;
- Correspondence: (W.L.); (L.J.)
| | - Lina Jiang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
- Correspondence: (W.L.); (L.J.)
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26
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Yuan C, Li C, Lu X, Zhao X, Yan C, Wang J, Sun Q, Shan S. Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut. BMC PLANT BIOLOGY 2020; 20:454. [PMID: 33008287 PMCID: PMC7532626 DOI: 10.1186/s12870-020-02678-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. RESULTS We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. CONCLUSION Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.
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Affiliation(s)
- Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaodong Lu
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, 266100, China.
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, 266100, China.
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27
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Liu H, Mullan D, Zhang C, Zhao S, Li X, Zhang A, Lu Z, Wang Y, Yan G. Major genomic regions responsible for wheat yield and its components as revealed by meta-QTL and genotype-phenotype association analyses. PLANTA 2020; 252:65. [PMID: 32970252 DOI: 10.1007/s00425-020-03466-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022]
Abstract
MAIN CONCLUSION Meta-QTL (MQTL) analysis was done for yield-related traits in wheat. Candidate genes were identified within the refined MQTL and further validated by genotype-phenotype association analysis. Extensive studies have been undertaken on quantitative trait locus/loci (QTL) for wheat yield and its component traits. This study conducted a meta-analysis of 381 QTL related to wheat yield under various environments, including irrigated, drought- and/or heat-stressed conditions. Markers flanking meta-QTL (MQTL) were mapped on the wheat reference genome for their physical positions. Putative candidate genes were examined for MQTL with a physical interval of less than 20 Mbp. A total of 86 MQTL were identified as responsible for yield, of which 34 were for irrigated environments, 39 for drought-stressed environments, 36 for heat-stressed environments, and 23 for both drought- and heat-stressed environments. The high-confidence genes within the physical positions of the MQTL flanking markers were screened in the reference genome RefSeq V1.0, which identified 210 putative candidate genes. The phenotypic data for 14 contrasting genotypes with either high or low yield performance-according to the Australian National Variety Trials-were associated with their genotypic data obtained through ddRAD sequencing, which validated 18 genes or gene clusters associated with MQTL that had important roles for wheat yield. The detected and refined MQTL and candidate genes will be useful for marker-assisted selection of high yield in wheat breeding.
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Affiliation(s)
- Hui Liu
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Mullan
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chi Zhang
- Beijing Genomics Institute, Shenzhen, 518053, China
| | - Shancen Zhao
- Beijing Genomics Institute, Shenzhen, 518053, China
| | - Xin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chicness Academy of Sciences, Beijing, 100101, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chicness Academy of Sciences, Beijing, 100101, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, No. 22, Yuquan Qu Zhaojun Lu, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yong Wang
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Guijun Yan
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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28
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Large-Scale Cloning and Comparative Analysis of TaNAC Genes in Response to Stripe Rust and Powdery Mildew in Wheat ( Triticum aestivum L.). Genes (Basel) 2020; 11:genes11091073. [PMID: 32932603 PMCID: PMC7564338 DOI: 10.3390/genes11091073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
The NAM, ATAF1/2, and CUC2 (NAC) transcription factors (TFs) constitute the largest plant-specific TF superfamily, and play important roles in various physiological processes, including stress responses. Stripe rust and powdery mildew are the most damaging of the fungal diseases that afflict wheat (Triticum aestivum L.). However, studies on Triticum aestivum NAC (TaNAC)s’ role in resistance to the two diseases are still limited, especially in an overall comparative analysis of TaNACs responding or not to fungal stress. In the present study, 186 TaNAC transcripts were obtained from the resistant hexaploid wheat line N9134 under fungal stress, and 180 new transcripts were submitted to GenBank. Statistical results show that 35.1% (54/154) of TaNAC genes responded to stripe rust and powdery mildew in the seedling stage. “Abnormal” coding transcripts of differentially expressed (DE)-TaNAC genes in wheat responding to fungal stress were found in a significantly higher proportion (24/117 vs. 8/69, p = 0.0098) than in non-DE-NACs. This hinted that the alternative splicing of TaNAC genes was active in transcriptional or post-transcriptional regulation during plant-pathogen interactions. Full-length NAC proteins were classified into nine groups via phylogenetic analysis. Multiple-sequence alignment revealed diversity in the C-terminal structural organization, but the differentially expressed gene (DEG)-encoding proteins enriched in Subgroups VI and VII were conserved, with WV[L/V]CR amino acid residues in Motif 7 following the NAM domain. Our data that showed TaNAC TFs responded to fungal disease, which was affected by expression levels and by the regulation of multifarious transcript variants. These data for TaNAC responses to stripe rust and/or powdery mildew and their numerous structural variants provide a good resource for NAC function–mechanism analysis in the context of biotic-stress tolerance in wheat.
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Liu M, Sun W, Ma Z, Yu G, Li J, Wang Y, Wang X. Comprehensive multiomics analysis reveals key roles of NACs in plant growth and development and its environmental adaption mechanism by regulating metabolite pathways. Genomics 2020; 112:4897-4911. [PMID: 32916257 DOI: 10.1016/j.ygeno.2020.08.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 01/17/2023]
Abstract
Abnormal environmental conditions induce polyploidization and exacerbate vulnerability to agricultural production. Polyploidization is a pivotal event for plant adaption to stress and the expansion of transcription factors. NACs play key roles in plant stress resistance and growth and development, but the adaptive mechanism of NACs during plant polyploidization remain to be explored. Here, we identified and analyzed NACs from 15 species and found that the expansion of NACs was contributed by polyploidization. The regulatory networks were systematically analyzed based on polyomics. NACs might influence plant phenotypes and were correlated with amino acids acting as nitrogen source, indicating that NACs play a vital role in plant development. More importantly, in quinoa and Arabidopsis thaliana, NACs enabled plants to resist stress by regulating flavonoid pathways, and the universality was further confirmed by the Arabidopsis population. Our study provides a cornerstone for future research into improvement of important agronomic traits by transcription factors in a changing global environment.
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Affiliation(s)
- Moyang Liu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Wenjun Sun
- Sichuan Agricultural University, College of Life Science, Ya'an, China.
| | - Zhaotang Ma
- Sichuan Agricultural University, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Chengdu, China.
| | - Guolong Yu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Jiahao Li
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Yudong Wang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Xu Wang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
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Bonnot T, Martre P, Hatte V, Dardevet M, Leroy P, Bénard C, Falagán N, Martin-Magniette ML, Deborde C, Moing A, Gibon Y, Pailloux M, Bancel E, Ravel C. Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency. PLANT PHYSIOLOGY 2020; 183:501-516. [PMID: 32295821 PMCID: PMC7271774 DOI: 10.1104/pp.19.00842] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/27/2020] [Indexed: 05/06/2023]
Abstract
Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (Triticum monococcum). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.
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Affiliation(s)
- Titouan Bonnot
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Pierre Martre
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Victor Hatte
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Mireille Dardevet
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Philippe Leroy
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Camille Bénard
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Natalia Falagán
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Marie-Laure Martin-Magniette
- L'Institut des Sciences des Plantes (IPS2), CNRS, INRAE, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91400 Orsay, France
- Mathématiques et informatique appliqués (MIA)-Paris, AgroParisTech, INRAE, Université Paris-Saclay, 75231 Paris, France
| | - Catherine Deborde
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Annick Moing
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Yves Gibon
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Marie Pailloux
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes, Centre National de la Recherche Scientifique (CNRS), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Emmanuelle Bancel
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Catherine Ravel
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
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Shan Z, Jiang Y, Li H, Guo J, Dong M, Zhang J, Liu G. Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress. BMC Genomics 2020; 21:96. [PMID: 32000662 PMCID: PMC6993341 DOI: 10.1186/s12864-020-6479-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet. RESULTS In the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR. CONCLUSION In this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance.
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Affiliation(s)
- Zhongying Shan
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- College of Ecology and Garden Architecture, Dezhou University, Dezhou, 253023, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Jinjie Guo
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Ming Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Jianan Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China.
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HajSalah El Beji I, Mouzeyar S, Bouzidi MF, Roche J. Expansion and Functional Diversification of SKP1-Like Genes in Wheat ( Triticum aestivum L.). Int J Mol Sci 2019; 20:ijms20133295. [PMID: 31277523 PMCID: PMC6650978 DOI: 10.3390/ijms20133295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/06/2019] [Accepted: 07/02/2019] [Indexed: 01/17/2023] Open
Abstract
The ubiquitin proteasome 26S system (UPS), involving monomeric and multimeric E3 ligases is one of the most important signaling pathways in many organisms, including plants. The SCF (SKP1/Cullin/F-box) multimeric complex is particularly involved in response to development and stress signaling. The SKP1 protein (S-phase kinase-associated protein 1) is the core subunit of this complex. In this work, we firstly identified 92 and 87 non-redundant Triticum aestivumSKP1-like (TaSKP) genes that were retrieved from the latest release of the wheat genome database (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0) and the genome annotation of the TGAC v1 respectively. We then investigated the structure, phylogeny, duplication events and expression patterns of the SKP1-like gene family in various tissues and environmental conditions using a wheat expression platform containing public data. TaSKP1-like genes were expressed differentially in response to stress conditions, displaying large genomic variations or short insertions/deletions which suggests functional specialization within TaSKP1-like genes. Finally, interactions between selected wheat FBX (F-box) proteins and putative ancestral TaSKP1-like proteins were tested using the yeast two-hybrid (Y2H) system to examine the molecular interactions. These observations suggested that six Ta-SKP1 genes are likely to be ancestral genes, having similar functions as ASK1 and ASK2 in Arabidopsis, OSK1 and OSK20 in rice and PpSKP1 and PpSKP2 in Physcomitrella patens.
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Affiliation(s)
- Imen HajSalah El Beji
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France
| | - Said Mouzeyar
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France
| | - Mohammed-Fouad Bouzidi
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France
| | - Jane Roche
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France.
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Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa. Genes (Basel) 2019; 10:genes10070500. [PMID: 31262002 PMCID: PMC6678211 DOI: 10.3390/genes10070500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/28/2022] Open
Abstract
The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon-intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa's strong salinity tolerance.
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