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Panda M, Pradhan S, Mukherjee PK. Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis. FRONTIERS IN PLANT SCIENCE 2024; 15:1386041. [PMID: 38863541 PMCID: PMC11165041 DOI: 10.3389/fpls.2024.1386041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
Introduction The Cucurbitaceae family comprises many agronomically important members, that bear nutritious fruits and vegetables of great economic importance. Coccinia grandis, commonly known as Ivy gourd, belongs to this family and is widely consumed as a vegetable. Members of this family are known to display an impressive range of variation in fruit morphology. Although there have been studies on flower development in Ivy gourd, fruit development remains unexplored in this crop. Methods In this study, comparative transcriptomics of two Ivy gourd cultivars namely "Arka Neelachal Kunkhi" (larger fruit size) and "Arka Neelachal Sabuja" (smaller fruit size) differing in their average fruit size was performed. A de novo transcriptome assembly for Ivy gourd was developed by collecting fruits at different stages of development (5, 10, 15, and 20 days after anthesis i.e. DAA) from these two varieties. The transcriptome was analyzed to identify differentially expressed genes, transcription factors, and molecular markers. Results The transcriptome of Ivy gourd consisted of 155205 unigenes having an average contig size of 1472bp. Unigenes were annotated on publicly available databases to categorize them into different biological functions. Out of these, 7635 unigenes were classified into 38 transcription factor (TF) families, of which Trihelix TFs were most abundant. A total of 11,165 unigenes were found to be differentially expressed in both the varieties and the in silico expression results were validated through real-time PCR. Also, 98768 simple sequence repeats (SSRs) were identified in the transcriptome of Ivy gourd. Discussion This study has identified a number of genes, including transcription factors, that could play a crucial role in the determination of fruit shape and size in Ivy gourd. The presence of polymorphic SSRs indicated a possibility for marker-assisted selection for crop breeding in Ivy gourd. The information obtained can help select candidate genes that may be implicated in regulating fruit development and size in other fruit crops.
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Affiliation(s)
- Mitrabinda Panda
- Biotechnology Research Innovation Council-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Seema Pradhan
- Biotechnology Research Innovation Council-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Pulok K. Mukherjee
- Biotechnology Research Innovation Council-Institute of Bioresources and Sustainable Development (BRIC-IBSD), Imphal, India
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Song HY, Zhao K, Pei YG, Chen HX, Wang XA, Jiang GL, Xie HJ, Chen D, Gong RG. Multi-omics analysis provides new insights into the changes of important nutrients and fructose metabolism in loquat bud sport mutant. FRONTIERS IN PLANT SCIENCE 2024; 15:1374925. [PMID: 38606078 PMCID: PMC11008694 DOI: 10.3389/fpls.2024.1374925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
Bud sport is a common and stable somatic variation in perennial fruit trees, and often leads to significant modification of fruit traits and affects the breeding value. To investigate the impact of bud sport on the main metabolites in the fruit of white-fleshed loquat, we conducted a multi-omics analysis of loquat fruits at different developmental stages of a white-fleshed bud sport mutant of Dongting loquat (TBW) and its wild type (TBY). The findings from the detection of main fruit quality indices and metabolites suggested that bud sport resulted in a reduction in the accumulation of carotenoids, fructose, titratable acid and terpenoids at the mature stage of TBW, while leading to the accumulation of flavonoids, phenolic acids, amino acids and lipids. The comparably low content of titratable acid further enhances the balanced and pleasent taste profile of TBW. Expression patterns of differentially expressed genes involved in fructose metabolism exhibited a significant increase in the expression level of S6PDH (EVM0006243, EVM0044405) prior to fruit maturation. The comparison of protein sequences and promoter region of S6PDH between TBY and TBW revealed no structural variations that would impact gene function or expression, indicating that transcription factors may be responsible for the rapid up-regulation of S6PDH before maturation. Furthermore, correlation analysis helped to construct a comprehensive regulatory network of fructose metabolism in loquat, including 23 transcription factors, six structural genes, and nine saccharides. Based on the regulatory network and existing studies, it could be inferred that transcription factors such as ERF, NAC, MYB, GRAS, and bZIP may promote fructose accumulation in loquat flesh by positively regulating S6PDH. These findings improve our understanding of the nutritional value and breeding potential of white-fleshed loquat bud sport mutant, as well as serve as a foundation for exploring the genes and transcription factors that regulate fructose metabolism in loquat.
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Affiliation(s)
- Hai-yan Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
- College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Ke Zhao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Yan-Gang Pei
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Hong-xu Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiao-an Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guo-Liang Jiang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Hong-Jiang Xie
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Dong Chen
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Rong-gao Gong
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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Li J, Guo S, Min Htwe Y, Sun X, Zhou L, Wang F, Zeng C, Chen S, Iqbal A, Yang Y. Genome-wide identification, classification and expression analysis of MYB gene family in coconut ( Cocos nucifera L.). FRONTIERS IN PLANT SCIENCE 2024; 14:1263595. [PMID: 38288415 PMCID: PMC10822967 DOI: 10.3389/fpls.2023.1263595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the MYB gene family present in coconut. According to the sequence of MYB genes in Arabidopsis thaliana, homologous MYB gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within MYB proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-MYB genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 MYB genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut MYB genes into 4-subfamilies: 124 R2R3-MYB, 4 3R-MYB types, 4 4R-MYB type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the CnMYB genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the CnMYB genes. Our research encompassed a thorough investigation of the R2R3-MYB genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely CnMYB8, CnMYB15, CnMYB27, CnMYB28, CnMYB61, CnMYB63, CnMYB68, CnMYB94, CnMYB101, CnMYB150, CnMYB153, and CnMYB164. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as CnMYB68, CnMYB101, and CnMYB28 exhibited high expression in majority of tissues and coconut species, while CnMYB94 and CnMYB164 showed lower expression. These findings shed light on the crucial functional divergence of CnMYB genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.
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Affiliation(s)
- Jing Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Shukuan Guo
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Yin Min Htwe
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Xiwei Sun
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Fangyuan Wang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Chunru Zeng
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Shuangyan Chen
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
- School of Tropical Crops, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Amjad Iqbal
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
- Department of Food Science & Technology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
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