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Liu J, Peng L, Cao C, Bai C, Wang Y, Li Z, Zhu H, Wen Q, He S. Identification of WRKY Family Members and Characterization of the Low-Temperature-Stress-Responsive WRKY Genes in Luffa ( Luffa cylindrica L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:676. [PMID: 38475522 DOI: 10.3390/plants13050676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The plant-specific WRKY transcription factor family members have diverse regulatory effects on the genes associated with many plant processes. Although the WRKY proteins in Arabidopsis thaliana and other species have been thoroughly investigated, there has been relatively little research on the WRKY family in Luffa cylindrica, which is one of the most widely grown vegetables in China. In this study, we performed a genome-wide analysis to identify L. cylindrica WRKY genes, which were subsequently classified and examined in terms of their gene structures, chromosomal locations, promoter cis-acting elements, and responses to abiotic stress. A total of 62 LcWRKY genes (471-2238 bp) were identified and divided into three phylogenetic groups (I, II, and III), with group II further divided into five subgroups (IIa, IIb, IIc, IId, and IIe) in accordance with the classification in other plants. The LcWRKY genes were unevenly distributed across 13 chromosomes. The gene structure analysis indicated that the LcWRKY genes contained 0-11 introns (average of 4.4). Moreover, 20 motifs were detected in the LcWRKY proteins with conserved motifs among the different phylogenetic groups. Two subgroup IIc members (LcWRKY16 and LcWRKY31) contained the WRKY sequence variant WRKYGKK. Additionally, nine cis-acting elements related to diverse responses to environmental stimuli were identified in the LcWRKY promoters. The subcellular localization analysis indicated that three LcWRKY proteins (LcWRKY43, LcWRKY7, and LcWRKY23) are localized in the nucleus. The tissue-specific LcWRKY expression profiles reflected the diversity in LcWRKY expression. The RNA-seq data revealed the effects of low-temperature stress on LcWRKY expression. The cold-induced changes in expression were verified via a qRT-PCR analysis of 24 differentially expressed WRKY genes. Both LcWRKY7 and LcWRKY12 were highly responsive to the low-temperature treatment (approximately 110-fold increase in expression). Furthermore, the LcWRKY8, LcWRKY12, and LcWRKY59 expression levels increased by more than 25-fold under cold conditions. Our findings will help clarify the evolution of the luffa WRKY family while also providing valuable insights for future studies on WRKY functions.
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Affiliation(s)
- Jianting Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Lijuan Peng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengjuan Cao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changhui Bai
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Yuqian Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zuliang Li
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Haisheng Zhu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Shuilin He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Shadrach FD, Kandasamy G, Neelakandan S, Lingaiah TB. Optimal transfer learning based nutrient deficiency classification model in ridge gourd (Luffa acutangula). Sci Rep 2023; 13:14108. [PMID: 37644146 PMCID: PMC10465599 DOI: 10.1038/s41598-023-41120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
The efficient detection of nutrient deficiency and proper fertilizer for that deficiency becomes the critical challenges various farmers face. The family Cucurbitaceae includes members cultivated globally as a source of indigenous medicines, food, and fiber. Luffa acutangula (L.) Roxb, generally called Ridge gourd, belongs to the Cucurbitaceae family and is an annual herb originating in several areas of India, particularly in the coastal regions. Nutrient deficiency detection in ridge gourd is essential to improve crop productivity. In agricultural practises, the early identification and categorization of nutrient deficiencies in crops is essential for sustaining optimal growth and production. Addressing these nutrient deficiencies, we applied the Ring Toss Game Optimization with a Deep Transfer Learning-based Nutrient Deficiency Classification (RTGODTL-NDC) to Ridge Gourd (Luffa acutangula). This research proposes a new ring toss game optimization with a deep transfer learning-based nutrient deficiency classification (RTGODTL-NDC) method. The RTGODTL-NDC technique uses pre-processing, segmentation, feature extraction, hyperparameter tuning, and classification. The Gabor filter (GF) is mainly used for image pre-processing, and the Adam optimizer with SqueezeNet model is utilized for feature extraction. Finally, the RTGO algorithm with the deep hybrid learning (HDL) model is applied to classify nutrient deficiencies. The suggested framework has the potential to improve crop management practises by allowing for proactive and targeted interventions, which will result in improved agricultural health, production, and resource utilisation. The outcomes represented by the RTGODTL-NDC method have resulted in improved performance. For example, based on accuracy and specificity, the RTGODTL-NDC methodology rendered maximum [Formula: see text] of 97.16% and specificity of 98.29%. The outcomes show how effective the transfer learning-based model is in identifying nutrient deficits in ridge gourd plants, as seen by its high level of accuracy.
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Affiliation(s)
- Finney Daniel Shadrach
- Department of Electronics and Communication Engineering, KPR Institute of Engineering and Technology, Coimbatore, India
| | - Gunavathi Kandasamy
- Department of Electronics and Communication Engineering, PSG College of Technology, Coimbatore, India
| | - S Neelakandan
- Department of Computer Science and Engineering, R.M.K Engineering College, Tiruvallur, India
| | - T Bheema Lingaiah
- School of Biomedical Engineering, Jimma Institute of Technology, Jimma, Ethiopia.
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Basanagouda G, Ramesh S, Siddu CB, Chandana BR, Kalpana MP, Rotti K, Sathish H. A non-synonymous SNP in homolog of BADH2 gene is associated with fresh pod fragrance in dolichos bean ( Lablab purpureus var. lignosus (Prain) Kumari). GENETIC RESOURCES AND CROP EVOLUTION 2023; 70:373-380. [PMID: 36628131 PMCID: PMC9817452 DOI: 10.1007/s10722-022-01535-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Fresh pods are harvestable and marketable economic product in dolichos bean. Fresh pod fragrance is one of the 'farmers' and 'consumers' preferred traits in dolichos bean varieties. The pods with high fragrance fetch a premium price in the market. In breeding programmes, pod fragrance is routinely assessed by organoleptic (sensory) means, which is highly relative and subjective. Identification of linked DNA markers not only offer an objective means but also enable selection of fragment genotypes at seedling stage itself. Betaine aldehyde dehydrogenase (BADH) is known to be the key gene responsible for fragrance in other legumes such as vegetable soybean and mung bean. Taking cues from highly conserved domains in proteins coded by BADH genes, we isolated dolichos bean homolog (LpBADH2) of soybean GmBADH2 gene using reported degenerate primers designed to conserved domains. Analysis of the translated amino acid sequence of LpBADH2 showed high degree of similarity (97.30%) with those of soybean homolog (GmBADH2). Conserved amino acid sequence of aldehyde dehydrogenase-super family were also identified in LpBADH2. Multiple sequence alignment of nucleotide sequences of LpBADH2 with those of related legumes using "ClustalW" revealed the presence of a single non-synonymous single nucleotide polymorphic (SNPs) and three synonymous SNP sites in LpBADH2. The substitution of the amino acid tyrosine in (fragrant genotypes) with phenyl alanine (non-fragrant genotypes) in protein coded by LpBADH2 appeared to be the cause for switch over from fragrance to non-fragrance in dolichos bean. These results are discussed in relation to strategies to breed dolichos bean cultivars with desired level of pod fragrance.
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Affiliation(s)
- Gonal Basanagouda
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
| | - Sampangi Ramesh
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
| | - Chindi Basavaraj Siddu
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
| | - Basalapura Rangegowda Chandana
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
| | - Mugali Pundalik Kalpana
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
| | - Kirankumar Rotti
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
| | - Hosakoti Sathish
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, Karnataka India
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Chaubey T, Sagar V, Singh RK, Chanotiya CS, Pandey S, Singh PM, Karmakar P, Singh J, Singh B, Singh DP, Pandey KK, Behera TK. Volatile Compounds Governed by Single Recessive Gene Impart Aroma in Sponge Gourd ( Luffa cylindrica L. Roem). PLANTS (BASEL, SWITZERLAND) 2022; 11:2881. [PMID: 36365333 PMCID: PMC9656515 DOI: 10.3390/plants11212881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
As a vegetable crop, sponge gourd is widely consumed worldwide due to its health promoting and nutraceutical value. This study describes genetics of an aromatic genotype VRSG-7-17 and deciphers the genetic control and volatile compound composition of sponge gourd. To study the inheritance of this trait, a cross was made between aromatic light-green-fruited VRSG-7-17 and non-aromatic dark-green-fruited VRSG-194 genotypes. The F1s were found to be non-aromatic and have a green fruit colour. Chi-square (χ2) analysis of backcross and F2 population segregating for aroma suggested that the inheritance of aroma in VRSG-7-17 is governed by a single recessive gene in a simple Mendelian fashion. The SPME-GC/MS analysis of the volatile compounds suggested that the compounds responsible for Basmati rice-like aroma were mainly hexanal, 1-octen-3-ol, 3-octanone and limonene. The aroma persists in the cooked VRSG-7-17 fruits, that did not lose fragrance traits at high temperatures. The inheritance of fruit colour was found to be controlled by a single gene with incomplete dominance. The segregation analysis showed that the aroma and fruit colour were not linked, and they segregated independently. The findings will lead to understanding the inheritance of the aromatic compounds in the sponge gourd and may be utilised in the breeding programmes for developing improved aromatic varieties.
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Affiliation(s)
- Tribhuvan Chaubey
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Vidya Sagar
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Ramesh Kumar Singh
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | | | - Sudhakar Pandey
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Prabhakar M. Singh
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Pradip Karmakar
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Jagdish Singh
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Bijendra Singh
- Acharya Narendra Deva University of Agriculture & Technology, Kumarganj, Ayodhya 224229, India
| | | | | | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
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