1
|
Arroyo-Álvarez E, Chan-León A, Girón-Ramírez A, Fuentes G, Estrella-Maldonado H, Santamaría JM. Genome-Wide Analysis of WRKY and NAC Transcription Factors in Carica papaya L. and Their Possible Role in the Loss of Drought Tolerance by Recent Cultivars through the Domestication of Their Wild Ancestors. PLANTS (BASEL, SWITZERLAND) 2023; 12:2775. [PMID: 37570929 PMCID: PMC10421361 DOI: 10.3390/plants12152775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/18/2023] [Accepted: 02/07/2023] [Indexed: 08/13/2023]
Abstract
A genome-wide analysis for two families of key transcription factors (TF; WRKY and NAC) involved in drought response revealed 46 WRKY and 66 NAC members of the Carica papaya genome. A phylogenetic analysis grouped the CpWRKY proteins into three groups (I, II a, b, c, d, e and III), while the CpNAC proteins were clustered into 15 groups. The conserved domains, chromosomal localization and promoter cis-acting elements were also analyzed. In addition, from a previous transcriptome study of two contrasting genotypes in response to 14 days of water deficit stress (WDS), we found that 29 of the 46 CpWRKYs genes and 25 of the 66 CpNACs genes were differentially expressed in response to the WDS. In the present paper, the native wild genotype (WG) (collected in its center of origin) consistently showed a higher expression (transcripts per million; TPM and fold change; FC) than the commercial genotype (CG) in almost all the members of the CpWRKY and CpNAC gene families. To corroborate this, we selected CpWRKY50 and CpNAC83.1 for further evaluation by RT-qPCR. Consistently, the WG showed higher relative expression levels (REL) after 14 days of WDS than the CG, in both the leaves and roots. The results suggest that the CpWRKY and CpNAC TF families are important for drought tolerance in this species. The results may also suggest that, during the domestication process, the ability of the native (wild) C. papaya genotypes to respond to drought (including the overexpression of the CpWRKY and CpNAC genes) was somehow reduced in the current commercial genotypes.
Collapse
Affiliation(s)
- Erick Arroyo-Álvarez
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| | - Arianna Chan-León
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| | - Amaranta Girón-Ramírez
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| | - Gabriela Fuentes
- Independent Researcher, Calle 6ª, 279 a, Jardines de Vista Alegre, Mérida 97138, Yucatán, Mexico
| | - Humberto Estrella-Maldonado
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Tlapacoyan 93600, Veracruz, Mexico
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| |
Collapse
|
2
|
Szlachtowska Z, Rurek M. Plant dehydrins and dehydrin-like proteins: characterization and participation in abiotic stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1213188. [PMID: 37484455 PMCID: PMC10358736 DOI: 10.3389/fpls.2023.1213188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
Abiotic stress has a significant impact on plant growth and development. It causes changes in the subcellular organelles, which, due to their stress sensitivity, can be affected. Cellular components involved in the abiotic stress response include dehydrins, widely distributed proteins forming a class II of late embryogenesis abundant protein family with characteristic properties including the presence of evolutionarily conserved sequence motifs (including lysine-rich K-segment, N-terminal Y-segment, and often phosphorylated S motif) and high hydrophilicity and disordered structure in the unbound state. Selected dehydrins and few poorly characterized dehydrin-like proteins participate in cellular stress acclimation and are also shown to interact with organelles. Through their functioning in stabilizing biological membranes and binding reactive oxygen species, dehydrins and dehydrin-like proteins contribute to the protection of fragile organellar structures under adverse conditions. Our review characterizes the participation of plant dehydrins and dehydrin-like proteins (including some organellar proteins) in plant acclimation to diverse abiotic stress conditions and summarizes recent updates on their structure (the identification of dehydrin less conserved motifs), classification (new proposed subclasses), tissue- and developmentally specific accumulation, and key cellular activities (including organellar protection under stress acclimation). Recent findings on the subcellular localization (with emphasis on the mitochondria and plastids) and prospective applications of dehydrins and dehydrin-like proteins in functional studies to alleviate the harmful stress consequences by means of plant genetic engineering and a genome editing strategy are also discussed.
Collapse
|
3
|
Raza A, Mubarik MS, Sharif R, Habib M, Jabeen W, Zhang C, Chen H, Chen ZH, Siddique KHM, Zhuang W, Varshney RK. Developing drought-smart, ready-to-grow future crops. THE PLANT GENOME 2023; 16:e20279. [PMID: 36366733 DOI: 10.1002/tpg2.20279] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 05/10/2023]
Abstract
Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS-associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought-smart future crops. In short, we recommend incorporating several approaches, such as multi-omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought-smart cultivars to achieve the 'zero hunger' goal.
Collapse
Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | | | - Rahat Sharif
- Dep. of Horticulture, College of Horticulture and Plant Protection, Yangzhou Univ., Yangzhou, Jiangsu, 225009, China
| | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Rd., Islamabad, 45500, Pakistan
| | - Warda Jabeen
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National Univ. of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney Univ., Penrith, NSW, 2751, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The Univ. of Western Australia, Crawley, Perth, 6009, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch Univ., Murdoch, WA, 6150, Australia
| |
Collapse
|
4
|
Gillani SFA, Zhuang Z, Rasheed A, Haq IU, Abbasi A, Ahmed S, Wang Y, Khan MT, Sardar R, Peng Y. Brassinosteroids induced drought resistance of contrasting drought-responsive genotypes of maize at physiological and transcriptomic levels. FRONTIERS IN PLANT SCIENCE 2022; 13:961680. [PMID: 36388543 PMCID: PMC9641234 DOI: 10.3389/fpls.2022.961680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The present study investigated the brassinosteroid-induced drought resistance of contrasting drought-responsive maize genotypes at physiological and transcriptomic levels. The brassinosteroid (BR) contents along with different morphology characteristics, viz., plant height (PH), shoot dry weight (SDW), root dry weight (RDW), number of leaves (NL), the specific mass of the fourth leaf, and antioxidant activities, were investigated in two maize lines that differed in their degree of drought tolerance. In response to either control, drought, or brassinosteroid treatments, the KEGG enrichment analysis showed that plant hormonal signal transduction and starch and sucrose metabolism were augmented in both lines. In contrast, the phenylpropanoid biosynthesis was augmented in lines H21L0R1 and 478. Our results demonstrate drought-responsive molecular mechanisms and provide valuable information regarding candidate gene resources for drought improvement in maize crop. The differences observed for BR content among the maize lines were correlated with their degree of drought tolerance, as the highly tolerant genotype showed higher BR content under drought stress.
Collapse
Affiliation(s)
| | - Zelong Zhuang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| | - Adnan Rasheed
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Crop Breeding Department, Jilin Changfa Modern Agricultural Science and Technology Group, co., Ltd., Changchun, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University, Murree, Pakistan
| | - Shakil Ahmed
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Yinxia Wang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| | - Muhammad Tajammal Khan
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Rehana Sardar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Yunling Peng
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| |
Collapse
|
5
|
Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
Collapse
Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
| |
Collapse
|
6
|
He Y, Li Y, Yao Y, Zhang H, Wang Y, Gao J, Fan M. Overexpression of watermelon m 6A methyltransferase ClMTB enhances drought tolerance in tobacco by mitigating oxidative stress and photosynthesis inhibition and modulating stress-responsive gene expression. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:340-352. [PMID: 34688195 DOI: 10.1016/j.plaphy.2021.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/11/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
N6-methyladenosine (m6A) in RNA is a very important post-transcriptional modification mechanism in eukaryotes. It has been reported to have important regulatory roles in some stress responses in model plants, but there has been no research regarding m6A modifications in watermelon. In this study, we cloned and characterized m6A methyltransferase, ClMTB (mRNA adenosine methylase B, METTL14 human homolog protein) in watermelon. ClMTB expression could be weakly induced by drought stress as determined by the quantitative real-time PCR (qRT-PCR) and Promoter::GUS analyses. ClMTB over-expressed in tobacco plants increased drought tolerance via enhancing reactive oxygen species (ROS) scavenging system and alleviating photosynthesis inhibition under drought. Transcriptome profiles indicated the multiple hormone and stress-responsive genes were specifically induced in over-expressed ClMTB plants under drought conditions. These results suggest that ClMTB-mediated m6A modification serves as a positive regulatory factor of drought tolerance. This study is the first one to provide an understanding of the specific roles of ClMTB in watermelon adaptation to drought stress, and may also provide important insights into the signaling pathway mediated by m6A modification in response to stress conditions.
Collapse
Affiliation(s)
- Yanjun He
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China
| | - Yulin Li
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China; College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Yixiu Yao
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China; College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Huiqing Zhang
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China
| | - Yuhuan Wang
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China; College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Jie Gao
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Min Fan
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
| |
Collapse
|