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Yu Z, Chen X, Li Y, Shah SHA, Xiao D, Wang J, Hou X, Liu T, Li Y. ETHYLENE RESPONSE FACTOR 070 inhibits flowering in Pak-choi by indirectly impairing BcLEAFY expression. PLANT PHYSIOLOGY 2024; 195:986-1004. [PMID: 38269601 DOI: 10.1093/plphys/kiae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
APETALA2/ethylene responsive factors respond to ethylene and participate in many biological and physiological processes, such as plant morphogenesis, stress resistance, and hormone signal transduction. Ethylene responsive factor 070 (BcERF070) is important in flowering. However, the underlying molecular mechanisms of BcERF070 in floral transition in response to ethylene signaling have not been fully characterized. Herein, we explored the function of BcERF070 in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Ethylene treatment induced BcERF070 expression and delayed flowering in Pak-choi. Silencing of BcERF070 induced flowering in Pak-choi. BcERF070 interacted with major latex protein-like 328 (BcMLP328), which forms a complex with helix-loop-helix protein 30 (BcbHLH30) to enhance the transcriptional activity of BcbHLH30 on LEAFY (BcLFY), ultimately promoting flowering. However, BcERF070 impaired the BcMLP328-BcbHLH30 complex activation of LEAFY (BcLFY), ultimately inhibiting flowering in Pak-choi. BcERF070 directly promoted the expression of the flowering inhibitor gene B-box 29 (BcBBX29) and delayed flowering by reducing FLOWERING LOCUS T (BcFT) expression. These results suggest that BcERF070 mediates ethylene-reduced flowering by impairing the BcMLP328-BcbHLH30 complex activation of BcLFY and by directly promoting the gene expression of the flowering inhibition factor BcBBX29 to repress BcFT expression. The findings contribute to understanding the molecular mechanisms underlying floral transition in response to ethylene in plants.
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Affiliation(s)
- Zhanghong Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoshan Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sayyed Hamad Ahmad Shah
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Zhai X, Wang X, Yang X, Huang Q, Wu D, Wang Y, Kang H, Sha L, Fan X, Zhou Y, Zhang H. Genome-wide identification of bHLH transcription factors and expression analysis under drought stress in Pseudoroegneria libanotica at germination. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:467-481. [PMID: 38633269 PMCID: PMC11018577 DOI: 10.1007/s12298-024-01433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/24/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is the second largest in plants. bHLH transcription factor is not only universally involved in plant growth and metabolism, including photomorphogenesis, light signal transduction, and secondary metabolism, but also plays an important role in plant response to stress. However, the function of bHLH TFs in Pseudoroegneria species has not been studied yet. Pseudoroegneria (Nevski) Á. Löve is a perennial genus of the Triticeae. Pseudoroegneria species are mostly distributed in arid/semi-arid areas and they show good drought tolerance. In this study, we identified 152 PlbHLH TFs in Pseudoroegneria libanotica, which could be classified into 15 groups. Collinearity analysis indicates that 122 PlbHLH genes share homology with wbHLH genes in wheat, and it has lower homology with AtbHLH genes in Arabidopsis. Based on transcriptome profiling under an experiment with three PEG concentrations (0%, 10%, and 20%), 10 up-regulated genes and 11 down-regulated PlbHLH genes were screened. Among them, PlbHLH6, PlbHLH55 and PlbHLH64 as candidate genes may be the key genes related to drought tolerance response at germination, and they have been demonstrated to respond to drought, salt, oxidative, heat, and heavy metal stress in yeast. This study lays the foundation for an in-depth study of the biological roles of PlbHLHs in Pse. libanotica, and discovered new drought-tolerance candidate genes to enhance the genetic background of Triticeae crops. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01433-w.
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Affiliation(s)
- Xingguan Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xia Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Qingxiang Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
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3
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Liu X, Lin Y, Wu C, Yang Y, Su D, Xian Z, Zhu Y, Yu C, Hu G, Deng W, Li Z, Bouzayen M, Chen R, Hao Y. The SlARF4-SlHB8 regulatory module mediates leaf rolling in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111790. [PMID: 37454820 DOI: 10.1016/j.plantsci.2023.111790] [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: 04/10/2023] [Revised: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Leaf is the main photosynthetic organ in plants and the primary energy source all along the plant life. Given the beneficial role of leaf rolling in improving photosynthetic efficiency and yield in specific environmental conditions, a better understanding of the factors and molecular mechanisms underlying this process is highly suited. Previously, the SlARF4 knocking out mutant exhibited upward curly leaf showed higher resistance to water deficit which driving us to uncover the function of SlARF4 in regulating the curly leaf formation. In this study, we unraveled the unexplored role of the SlARF4-SlHB8 module of transcription factors in the development of leaf rolling. Both SlARF4 loss-of-function and SlHB8 overexpressing tomato plants exhibited upward-rolled leaves, reflecting the active role of the two genes in controlling leaf rolling. Dual-luciferase reporter assays and phenotypic analysis of hybrid progenies suggested that SlHB8 acts downstream of SlARF4 in curly leaf formation. SlARF4 and SlHB8 influence the development of leaf palisade tissues via modulating the expression of genes associated with curly leaf formation. SEM analysis revealed no significant differences in leaf epidermal cells between the two leaf-rolling mutants and the wild type, indicating that curly leaves of arf4 and SlHB8-OE do not result from the asymmetric leaf epidermal cell growth. Our data provide novel insight into the molecular mechanism of abaxial-adaxial determination involving SlARF4 and SlHB8 and reveals that leaf rolling operates via different regulation mechanisms in tomato and Arabidopsis model plant.
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Affiliation(s)
- Xiaojuan Liu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yuxiang Lin
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Caiyu Wu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yang Yang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Zhiqiang Xian
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yiyi Zhu
- BioGround Biotechnology Institution, International Park of Entrepreneur' Port, Shapingba, Chongqing, China
| | - Canye Yu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Guojian Hu
- UMR990 INRA/INP-ENSAT, Université de Toulouse, Castanet-Tolosan, France
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Mondher Bouzayen
- UMR990 INRA/INP-ENSAT, Université de Toulouse, Castanet-Tolosan, France
| | - Riyuan Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Yanwei Hao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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Hou J, Xu Y, Zhang S, Yang X, Wang S, Hong J, Dong C, Zhang P, Yuan L, Zhu S, Chen G, Tang X, Huang X, Zhang J, Wang C. Auxin participates in regulating the leaf curl development of Wucai (Brassica campestris L.). PHYSIOLOGIA PLANTARUM 2023; 175:e13908. [PMID: 37022777 DOI: 10.1111/ppl.13908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) belongs to the Brassica genus of the Cruciferae family, and its leaf curl is a typical feature that distinguishes Wucai from other nonheading cabbage subspecies. Our previous research found that plant hormones were involved in the development of the leaf curl in Wucai. However, the molecular mechanisms and the hormones regulating the formation of leaf curl in Wucai have not yet been reported. This study aimed to understand the molecular functions related to hormone metabolism during the formation of leaf curl in Wucai. A total of 386 differentially expressed genes (DEGs) were identified by transcriptome sequencing of two different morphological parts of the same leaf of Wucai germplasm W7-2, and 50 DEGs were found to be related to plant hormones, which were mainly involved in the auxin signal transduction pathway. Then, we measured the content of endogenous hormones in two different forms of the same leaf of Wucai germplasm W7-2. A total of 17 hormones with differential content were identified, including auxin, cytokinins, jasmonic acids, salicylic acids, and abscisic acid. And we found that treatment with auxin transport inhibitor N-1-naphthylphthalamic acid can affect the leaf curl phenotype of Wucai and pak choi (Brassica rapa L. subsp. Chinensis). These results indicated that plant hormones, especially auxin, are involved in developing the leaf curl of Wucai. Our findings provide a potentially valuable reference for future research on the development of leaf curls.
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Affiliation(s)
- Jinfeng Hou
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Ying Xu
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Shengnan Zhang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Xiaona Yang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Shuangshuang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Jie Hong
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Cuina Dong
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Ping Zhang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Shidong Zhu
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Xiaoyan Tang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Xingxue Huang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Jinlong Zhang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, China
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Wang Y, Xi Z, Wang X, Zhang Y, Liu Y, Yuan S, Zhao S, Sheng J, Meng D. Identification of bHLH family genes in Agaricus bisporus and transcriptional regulation of arginine catabolism-related genes by AbbHLH1 after harvest. Int J Biol Macromol 2023; 226:496-509. [PMID: 36521696 DOI: 10.1016/j.ijbiomac.2022.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/23/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors (TFs) are widely distributed in eukaryotes and play an important role in biological growth and development. The identification and functional analyses of bHLH genes/proteins in edible mushrooms (Agaricus bisporus) have yet to be reported. In the present study, we identified 10 putative bHLH members carrying the conserved bHLH domains. Phylogenetic analyses revealed that the 10 AbbHLHs were the closest to sequences of species belonging to 7 different fungal subgroups, which was supported by loop length, intron patterns, and key amino acid residues. The substantial increase after harvest and continuously elevated expression of AbbHLH1 during the development until the disruption of mushroom velum, and the preferential expression in cap and gill tissues suggest the important function of AbbHLH1 in postharvest development of A. bisporus. The relationship of arginine catabolism-related genes with the early stage of postharvest continuing development also was revealed by expression determination. Subcellular localization showed that AbbHLH1 could be localized in nucleus. Importantly, the electrophoretic mobility shift and dual-luciferase reporter assays showed that AbbHLH1 activated the promoters of AbOAT, AbSPDS, and AbSAMDC and suppressed the expression of AbARG, AbUREA, and AbODC, probably for the modulation of arginine catabolism and thus control of postharvest mushroom development. Taken together, the available data provide valuable functional insight into the role of AbbHLH proteins in postharvest mushrooms.
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Affiliation(s)
- Yating Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Zhiai Xi
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Xiuhong Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Yuyu Zhang
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, People's Republic of China
| | - Yongguo Liu
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, People's Republic of China
| | - Shuai Yuan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Shirui Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Jiping Sheng
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing 100872, People's Republic of China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China; Tianjin Gasin-DH Preservation Technology Co., Ltd, Tianjin 300300, People's Republic of China.
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Zhu Z, Wang J, Li C, Li L, Mao X, Hu G, Wang J, Chang J, Jing R. A transcription factor TaMYB5 modulates leaf rolling in wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:897623. [PMID: 36082295 PMCID: PMC9445664 DOI: 10.3389/fpls.2022.897623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Leaf rolling is an important agronomic trait in wheat (Triticum aestivum L.). Moderate leaf rolling keeps leaves upright and maintains the relatively normal photosynthesis of plants under drought stress. However, the molecular mechanism of wheat leaf rolling remains unclear. Here, we identified a candidate gene TaMYB5-3A that regulates leaf rolling by using a genome-wide association study (GWAS) in a panel of 323 wheat accessions. Phenotype analysis indicated that the leaves of tamyb5 mutants were flatter than that of the wild type under drought condition. A nucleotide variation in the TaMYB5-3A coding region resulted in a substitution of Thr to Lys, which corresponds to two alleles SNP-3A-1 and SNP-3A-2. The leaf rolling index (LRI) of the SNP-3A-1 genotype was significantly lower than that of the SNP-3A-2 genotype. In addition, TaMYB5-3A alleles were associated with canopy temperature (CT) in multiple environments. The CT of the SNP-3A-1 genotype was lower than that of the SNP-3A-2 genotype. Gene expression analysis showed that TaMYB5-3A was mainly expressed in leaves and down-regulated by PEG and ABA treatment. TaMYB5 induces TaNRL1 gene expression through the direct binding to the AC cis-acting element of the promoter of the target gene, which was validated by EMSA (electrophoretic mobility shift assay). Our results revealed a crucial molecular mechanism in wheat leaf rolling and provided the theoretical basis and a gene resource for crop breeding.
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Affiliation(s)
- Zhi Zhu
- Shanxi Institute of Organic Dryland Farming, Organic Dry Farming of Shanxi Province Key Laboratory, Shanxi Agricultural University, Jinzhong, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ge Hu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Jianzhong Chang
- Shanxi Institute of Organic Dryland Farming, Organic Dry Farming of Shanxi Province Key Laboratory, Shanxi Agricultural University, Jinzhong, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Xia X, Gong R, Zhang C. Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals. BMC PLANT BIOLOGY 2022; 22:401. [PMID: 35974307 PMCID: PMC9380304 DOI: 10.1186/s12870-022-03762-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/15/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Color is the major ornamental feature of the Rhododendron genus, and it is related to the contents of flavonoid in petals. However, the regulatory mechanism of flavonoid biosynthesis in Rhododendron pulchrum remains unknown. The transcriptome and metabolome analysis of Rhododendron pulchrum with white, pink and purple color in this study aimed to reveal the mechanism of flavonoid biosynthesis and to provide insight for improving the petal color. RESULTS Flavonoids and flavonols are the major components of flavonoid metabolites in R.pulchrum, such as laricitrin, apigenin, tricin, luteolin, isoorientin, isoscutellarein, diosmetin and their glycosides derivatives. With transcriptome and metabolome analysis, we found CHS, FLS, F3'H, F3'5'H, DFR, ANS, GT, FNS, IFR and FAOMT genes showed significantly differential expression in cultivar 'Zihe'. FNS and IFR were discovered to be associated with coloration in R.pulchrum for the first time. The FNS gene existed in the form of FNSI. The IFR gene and its related metabolites of medicarpin derivatives were highly expressed in purple petal. In cultivar 'Fenhe', up-regulation of F3'H and F3'5'H and down-regulation of 4CL, DFR, ANS, and GT were associated with pink coloration. With the transcription factor analysis, a subfamily of DREBs was found to be specifically enriched in pink petals. This suggested that the DREB family play an important role in pink coloration. In cultivars 'Baihe', flavonoid biosynthesis was inhibited by low expression of CHS, while pigment accumulation was inhibited by low expression of F3'5'H, DFR, and GT, which led to a white coloration. CONCLUSIONS By analyzing the transcriptome and metabolome of R.pulchrum, principal differential expression genes and metabolites of flavonoid biosynthesis pathway were identified. Many novel metabolites, genes, and transcription factors associated with coloration have been discovered. To reveal the mechanism of the coloration of different petals, a model of the flavonoid biosynthesis pathway of R.pulchrum was constructed. These results provide in depth information regarding the coloration of the petals and the flavonoid metabolism of R.pulcherum. The study of transcriptome and metabolome profiling gains insight for further genetic improvement in Rhododendron.
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Affiliation(s)
- Xi Xia
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China
| | - Rui Gong
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China
| | - Chunying Zhang
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China.
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Coupel‐Ledru A, Pallas B, Delalande M, Segura V, Guitton B, Muranty H, Durel C, Regnard J, Costes E. Tree architecture, light interception and water-use related traits are controlled by different genomic regions in an apple tree core collection. THE NEW PHYTOLOGIST 2022; 234:209-226. [PMID: 35023155 PMCID: PMC9305758 DOI: 10.1111/nph.17960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/19/2021] [Indexed: 05/17/2023]
Abstract
Tree architecture shows large genotypic variability, but how this affects water-deficit responses is poorly understood. To assess the possibility of reaching ideotypes with adequate combinations of architectural and functional traits in the face of climate change, we combined high-throughput field phenotyping and genome-wide association studies (GWAS) on an apple tree (Malus domestica) core-collection. We used terrestrial light detection and ranging (T-LiDAR) scanning and airborne multispectral and thermal imagery to monitor tree architecture, canopy shape, light interception, vegetation indices and transpiration on 241 apple cultivars submitted to progressive field soil drying. GWAS was performed with single nucleotide polymorphism (SNP)-by-SNP and multi-SNP methods. Large phenotypic and genetic variability was observed for all traits examined within the collection, especially canopy surface temperature in both well-watered and water deficit conditions, suggesting control of water loss was largely genotype-dependent. Robust genomic associations revealed independent genetic control for the architectural and functional traits. Screening associated genomic regions revealed candidate genes involved in relevant pathways for each trait. We show that multiple allelic combinations exist for all studied traits within this collection. This opens promising avenues to jointly optimize tree architecture, light interception and water use in breeding strategies. Genotypes carrying favourable alleles depending on environmental scenarios and production objectives could thus be targeted.
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Affiliation(s)
- Aude Coupel‐Ledru
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Benoît Pallas
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Magalie Delalande
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Vincent Segura
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Baptiste Guitton
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Hélène Muranty
- IRHSSFR QuaSaVUniversité d’Angers, Institut Agro, INRAE49000AngersFrance
| | - Charles‐Eric Durel
- IRHSSFR QuaSaVUniversité d’Angers, Institut Agro, INRAE49000AngersFrance
| | - Jean‐Luc Regnard
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Evelyne Costes
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
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9
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He Z, Wang Z, Nie X, Qu M, Zhao H, Ji X, Wang Y. UNFERTILIZED EMBRYO SAC 12 phosphorylation plays a crucial role in conferring salt tolerance. PLANT PHYSIOLOGY 2022; 188:1385-1401. [PMID: 34904673 PMCID: PMC8825338 DOI: 10.1093/plphys/kiab549] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/28/2021] [Indexed: 06/14/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) UNFERTILIZED EMBRYO SAC 12 (AtUNE12) belongs to the basic helix-loop-helix DNA-binding superfamily of proteins. However, its function is not well known. Here, we found that AtUNE12 plays an important role in mediating salt tolerance. AtUNE12 is a transcriptional activator located in the nucleus whose expression is induced by NaCl, mannitol, and abscisic acid. In addition to binding to the G-box "CACGTG", AtUNE12 also binds to the low temperature responsive element 15 (LTRE15) "CCGAC". Furthermore, the serine residue at position 108 of AtUNE12 is phosphorylated during the salt stress response, enabling AtUNE12 to trigger gene expression by binding to G-box and/or LTRE15 motifs. Phosphorylated AtUNE12 regulates the expression of the genes involved in ion transport leading to reduced Na+ accumulation and K+ loss. At the same time, phosphorylation of AtUNE12 also induces the expression of AtMYB61 to decrease stomatal aperture, leading to a reduced transpiration rate. Overall, AtUNE12 serves as a transcriptional activator that is induced and phosphorylated upon salt stress, and the induction and phosphorylation of AtUNE12 in turn activate the salt-overly-sensitive pathway and decrease the stomatal aperture, enabling improved salt tolerance.
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Affiliation(s)
- Zihang He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xianguang Nie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ming Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Huimin Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiaoyu Ji
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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10
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Pathak AK, Singh SP, Sharma R, Nath V, Tuli R. Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size. 3 Biotech 2022; 12:47. [PMID: 35127302 PMCID: PMC8783947 DOI: 10.1007/s13205-021-03098-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/18/2021] [Indexed: 02/03/2023] Open
Abstract
Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers' preference and facilitates fruit processing. Seed specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to identify the genes associated with seed development. The transcriptomic sequence data from seeds at mid-development stages (16-28 days after anthesis) were de-novo assembled into 1,39,608 Trinity transcripts. Out of these, 6325 transcripts expressed differentially between the two contrasting genotypes. Several putative genes for salicylic acid, jasmonic acid and brassinosteriod pathways were down-regulated in seeds of the small-seeded litchi. The putative regulators of seed maturation and seed storage were down-regulated in the small-seeded genotype. Embryogenesis, cell expansion, seed size and stress related Trinity transcripts exhibited differential expression. Further studies on gene characterization will reveal the early regulators of seed size in litchi. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03098-8.
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Affiliation(s)
- Ashish K. Pathak
- grid.452674.60000 0004 1757 6145National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India ,grid.261674.00000 0001 2174 5640Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Sudhir P. Singh
- grid.452674.60000 0004 1757 6145National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India ,grid.454774.1Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
| | - Ritika Sharma
- grid.473732.6Sardar Swaran Singh National Institute of Bioenergy, Jalandhar, India
| | - Vishal Nath
- grid.506047.0ICAR-National Research Centre of Litchi, Muzaffarpur, India
| | - Rakesh Tuli
- grid.452674.60000 0004 1757 6145National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India ,grid.261674.00000 0001 2174 5640Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
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11
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Tu Z, Xia H, Yang L, Zhai X, Shen Y, Li H. The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2022; 13:816875. [PMID: 35154228 PMCID: PMC8829146 DOI: 10.3389/fpls.2022.816875] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 05/27/2023]
Abstract
The leaf and the flower are vital plant organs owing to their roles in photosynthesis and reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and transcription factors (TFs) are very important to the development of these organs. Liriodendron chinense is a common ornamental tree species in southern China with an unusual leaf shape and tulip-like flowers. The genetic mechanisms underlying leaf and flower development in L. chinense and the miRNA-lncRNA-TF regulatory networks are poorly studied. Through the integration and analysis of different types of sequencing data, we identified the miRNA-lncRNA-TF regulatory networks that were related to leaf and flower development. These networks contained 105 miRNAs, 258 lncRNAs, 393 TFs, and 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 and lch-lnc7374-miR156j-SPL9 were potential regulators of stamen and pistil development in L. chinense, respectively. miRNA-lncRNA-mRNA regulatory networks were shown to impact anther development, male and female fertility, and petal color by regulating the biosynthesis of phenylpropanoid metabolites. Phenylpropanoid metabolite biosynthesis genes and TFs that were targeted by miRNAs and lncRNAs were differentially expressed in the leaf and flower. Moreover, RT-qPCR analysis confirmed 22 differentially expressed miRNAs, among which most of them showed obvious leaf or flower specificity; miR157a-SPL and miR160a-ARF module were verified by using RLM-RACE, and these two modules were related to leaf and flower development. These findings provide insight into the roles of miRNA-lncRNA-mRNA regulatory networks in organ development and function in L. chinense, and will facilitate further investigation into the regulatory mechanisms of leaf and flower development in L. chinense.
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Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hui Xia
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lichun Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinyu Zhai
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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12
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Fan Y, Lai D, Yang H, Xue G, He A, Chen L, Feng L, Ruan J, Xiang D, Yan J, Cheng J. Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.). BMC Genomics 2021; 22:778. [PMID: 34717536 PMCID: PMC8557513 DOI: 10.1186/s12864-021-08095-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08095-y.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.,School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.
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13
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Shchennikova AV, Beletsky AV, Filyushin MA, Slugina MA, Gruzdev EV, Mardanov AV, Kochieva EZ, Ravin NV. Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs. FRONTIERS IN PLANT SCIENCE 2021; 12:643137. [PMID: 34122470 PMCID: PMC8194089 DOI: 10.3389/fpls.2021.643137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.
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14
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Overexpression of a Pak Choi Gene, BcAS2, Causes Leaf Curvature in Arabidopsis thaliana. Genes (Basel) 2021; 12:genes12010102. [PMID: 33467565 PMCID: PMC7830005 DOI: 10.3390/genes12010102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 11/29/2022] Open
Abstract
The LBD (Lateral Organ Boundaries Domain) family are a new group of plant-specific genes, which encode a class of transcription factors containing conserved Lateral Organization Boundary (LOB) domains, and play an important role in regulating the adaxial–abaxial polarity of plant leaves. In Arabidopsis thaliana, ASYMMETRIC LEAVES 2 (AS2) has a typical LOB domain and is involved in determining the adaxial cell fate. In this study, we isolated the BcAS2 gene from the pak choi cultivar “NHCC001”, and analyzed its expression pattern. The results showed that the BcAS2 encoded a protein made up of 202 amino acid residues which were located in the nucleus and cytomembrane. The Yeast two-hybrid system (Y2H) assay indicated that BcAS2 interacts with BcAS1-1 and BcAS1-2 (the homologous genes of AS1 gene in pak choi). In the transgenic Arabidopsis thaliana that overexpressed BcAS2 gene, it presented an abnormal phenotype with a curly shape. Taken together, our findings not only validate the function of BcAS2 in leaf development in Arabidopsis thaliana, but also contribute in unravelling the molecular regulatory mechanism of BcAS2, which fulfills a special role by forming complexes with BcAS1-1/2 in the establishment of the adaxial–abaxial polarity of the lateral organs in pak choi.
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15
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Cloning and Functional Analysis of BcMYB101 Gene Involved in Leaf Development in Pak Choi ( Brassica rapa ssp. Chinensis). Int J Mol Sci 2020; 21:ijms21082750. [PMID: 32326634 PMCID: PMC7254494 DOI: 10.3390/ijms21082750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 11/17/2022] Open
Abstract
As one of the largest transcription factor families, MYB transcription factors are widely present, and they are involved in a diverse range of physiological activities in plants, such as leaf development. GAMYB genes belong to the R2R3-MYB subfamily, which includes the MYB33/65/101 gene, and these genes are studied well in seed germination and flowering, but their roles in leaf development are poorly understood. In the current study, we isolated a GAMYB transcription factor from pak choi, BcMYB101, and analyzed its characteristics and function. The sequence structure analysis indicated that BcMYB101 has a highly conserved R2R3 DNA-binding domain in the N-terminal region and three GAMYB-specific motifs (Box1, Box2, and Box3). The expression pattern of diverse tissues revealed that BcMYB101 has a higher transcript level in the petiole, leaf, root, and floral organs. Furthermore, the expression level was significantly elevated after GA (gibberellin) treatment, suggesting that the BcMYB101 response was positively regulated by GA. Subcellular localization exhibited that BcMYB101 was only present in the nuclear region, consistent with the characterization of the transcription factor. The overexpression of BcMYB101 elucidated that BcMYB101 increased leaf number and resulted in downward-curling cauline leaves. Moreover, the virus-induced BcMYB101 silencing displayed that BcMYB101 is involved in the regulation of curly leaves. Furthermore, we discovered that BcMYB101 has two trans-activation activities and one interaction protein, BcTCH4, using a trans-activation activity assay and a yeast two-hybrid assay, respectively. In this study, we firstly isolated the BcMYB101 gene and explored its function in leaf development, thereby providing a solid foundation for further research on the regulatory mechanism of leaf shape in Brassica or other species.
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16
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Xu X, Wu P, Song H, Zhang J, Zheng S, Xing G, Hou L, Li M. Identification of candidate genes associated with photosynthesis in eggplant under elevated CO 2. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1809519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Xiaoyong Xu
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Peiqi Wu
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Hongxia Song
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Jing Zhang
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Shaowen Zheng
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Leiping Hou
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
| | - Meilan Li
- College of Horticulture, Shanxi Agricultural University; Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi, PR China
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Mao TY, Liu YY, Zhu HH, Zhang J, Yang JX, Fu Q, Wang N, Wang Z. Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera. PeerJ 2019; 7:e7153. [PMID: 31231599 PMCID: PMC6573809 DOI: 10.7717/peerj.7153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022] Open
Abstract
Lotus (Nelumbo nucifera Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115 NnbHLHs were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115 NnbHLHs were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted. NnbHLHs were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15 NnbHLHs were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of NnbHLHs in four tissues indicated that many NnbHLHs showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of NnbHLHs, and identifies candidate genes for stress resistance in lotus.
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Affiliation(s)
- Tian-Yu Mao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yao-Yao Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Huan-Huan Zhu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ju-Xiang Yang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiang Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Nian Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ze Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
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18
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Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis. Genes (Basel) 2019; 10:genes10020119. [PMID: 30736327 PMCID: PMC6410125 DOI: 10.3390/genes10020119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 01/28/2023] Open
Abstract
Upland cotton (Gossypium hirsutum) is grown for its elite fiber. Understanding differential gene expression patterns during fiber development will help to identify genes associated with fiber quality. In this study, we used two recombinant inbred lines (RILs) differing in fiber quality derived from an intra-hirsutum population to explore expression profiling differences and identify genes associated with high-quality fiber or specific fiber-development stages using RNA sequencing. Overall, 72/27, 1137/1584, 437/393, 1019/184, and 2555/1479 differentially expressed genes were up-/down-regulated in an elite fiber line (L1) relative to a poor-quality fiber line (L2) at 10, 15, 20, 25, and 30 days post-anthesis, respectively. Three-hundred sixty-three differentially expressed genes (DEGs) between two lines were colocalized in fiber strength (FS) quantitative trait loci (QTL). Short Time-series Expression Miner (STEM) analysis discriminated seven expression profiles; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were performed to identify difference in function between genes unique to L1 and L2. Co-expression network analysis detected five modules highly associated with specific fiber-development stages, especially for high-quality fiber tissues. The hub genes in each module were identified by weighted gene co-expression network analysis. Hub genes encoding actin 1, Rho GTPase-activating protein with PAK-box, TPX2 protein, bHLH transcription factor, and leucine-rich repeat receptor-like protein kinase were identified. Correlation networks revealed considerable interaction among the hub genes, transcription factors, and other genes.
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Rong F, Chen F, Huang L, Zhang J, Zhang C, Hou D, Cheng Z, Weng Y, Chen P, Li Y. A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cul) in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:113-123. [PMID: 30334067 DOI: 10.1007/s00122-018-3198-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/28/2018] [Indexed: 05/23/2023]
Abstract
We identified two curly-leaf (cul) mutants in cucumber. Map-based cloning revealed that both mutants are due to allelic mutations in the CsPHB gene, a homolog of the Arabidopsis PHABULOSA which encodes a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor. Leaf rolling is an important agronomic trait in crop breeding. Moderate leaf rolling minimizes shadowing between leaves, leading to improved photosynthetic efficiency. Although a number of genes controlling rolled leaf have been identified from rice and other plant species, none have been mapped or cloned in cucurbit crops. In this study, we identified and characterized two curly leaf (cul) mutants, cul-1 and cul-2 in cucumber. With map-based cloning, we show that cul-1 and cul-2 are allelic mutations and CsPHB (Csa6G525430) was the candidate gene for both mutants. The CsPHB gene encoded a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor. A single non-synonymous mutation in the fourth and fifth exons of the CsPHB was responsible for the cul-1 and cul-2 mutant phenotypes, respectively. The single-nucleotide substitutions in cul-1 and cul-2 were both located in cs-miRNA165/166 complementary sites of CsPHB. The expression level of CsPHB gene in multiple organs of cul-1 and cul-2 mutants was higher than that in the wild type, while the expression of cs-miRNA165/166 in the two genotypes showed the opposite trend. We speculate that disruption of the binding between the mutant allele of CsPHB and cs-miRNA165/166 leads to the curly-leaf phenotype. This is the first report to clone and characterize the CsPHB gene in the family Cucurbitaceae. Taken together, these results support CsPHB as an important player in the modulation of leaf shape development in cucumber.
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Affiliation(s)
- Fuxi Rong
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China
| | - Feifan Chen
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China
| | - Li Huang
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China
| | - Jiayu Zhang
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China
| | - Chaowen Zhang
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China
| | - Dong Hou
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, 730070, Lanzhou, Gansu, China
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Vegetable Crops Research Unit, USDA-ARS, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, 712100, Yangling, Shanxi, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, 712100, Yangling, Shanxi, China.
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Abstract
The reproductive adaptations of land plants have played a key role in their terrestrial colonization and radiation. This encompasses mechanisms used for the production, dispersal and union of gametes to support sexual reproduction. The production of small motile male gametes and larger immotile female gametes (oogamy) in specialized multicellular gametangia evolved in the charophyte algae, the closest extant relatives of land plants. Reliance on water and motile male gametes for sexual reproduction was retained by bryophytes and basal vascular plants, but was overcome in seed plants by the dispersal of pollen and the guided delivery of non-motile sperm to the female gametes. Here we discuss the evolutionary history of male gametogenesis in streptophytes (green plants) and the underlying developmental biology, including recent advances in bryophyte and angiosperm models. We conclude with a perspective on research trends that promise to deliver a deeper understanding of the evolutionary and developmental mechanisms of male gametogenesis in plants.
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Affiliation(s)
- Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
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Wang R, Zhao P, Kong N, Lu R, Pei Y, Huang C, Ma H, Chen Q. Genome-Wide Identification and Characterization of the Potato bHLH Transcription Factor Family. Genes (Basel) 2018; 9:genes9010054. [PMID: 29361801 PMCID: PMC5793205 DOI: 10.3390/genes9010054] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/09/2018] [Accepted: 01/18/2018] [Indexed: 11/24/2022] Open
Abstract
Plant basic/helix–loop–helix (bHLH) transcription factors participate in a number of biological processes, such as growth, development and abiotic stress responses. The bHLH family has been identified in many plants, and several bHLH transcription factors have been functionally characterized in Arabidopsis. However, no systematic identification of bHLH family members has been reported in potato (Solanum tuberosum). Here, 124 StbHLH genes were identified and named according to their chromosomal locations. The intron numbers varied from zero to seven. Most StbHLH proteins had the highly conserved intron phase 0, which accounted for 86.2% of the introns. According to the Neighbor-joining phylogenetic tree, 259 bHLH proteins acquired from Arabidopsis and potato were divided into 15 groups. All of the StbHLH genes were randomly distributed on 12 chromosomes, and 20 tandem duplicated genes and four pairs of duplicated gene segments were detected in the StbHLH family. The gene ontology (GO) analysis revealed that StbHLH mainly function in protein and DNA binding. Through the RNA-seq and quantitative real time PCR (qRT-PCR) analyses, StbHLH were found to be expressed in various tissues and to respond to abiotic stresses, including salt, drought and heat. StbHLH1, 41 and 60 were highly expressed in flower tissues, and were predicted to be involved in flower development by GO annotation. StbHLH45 was highly expressed in salt, drought and heat stress, which suggested its important role in abiotic stress response. The results provide comprehensive information for further analyses of the molecular functions of the StbHLH gene family.
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Affiliation(s)
- Ruoqiu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Nana Kong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ruize Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yue Pei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chenxi Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Haoli Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Qin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Mao K, Dong Q, Li C, Liu C, Ma F. Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:480. [PMID: 28443104 PMCID: PMC5387082 DOI: 10.3389/fpls.2017.00480] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/20/2017] [Indexed: 05/19/2023]
Abstract
The bHLH (basic helix-loop-helix) transcription factor family is the second largest in plants. It occurs in all three eukaryotic kingdoms, and plays important roles in regulating growth and development. However, family members have not previously been studied in apple. Here, we identified 188 MdbHLH proteins in apple "Golden Delicious" (Malus × domestica Borkh.), which could be classified into 18 groups. We also investigated the gene structures and 12 conserved motifs in these MdbHLHs. Coupled with expression analysis and protein interaction network prediction, we identified several genes that might be responsible for abiotic stress responses. This study provides insight and rich resources for subsequent investigations of such proteins in apple.
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