1
|
Fang H, Huang S, Li R, Wang P, Jiang Q, Zhong C, Yang Y, Yu W. Combined BSA-Seq and RNA-Seq to Identify Potential Genes Regulating Fruit Size in Bottle Gourd ( Lagenaria siceraria L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2154. [PMID: 39124272 PMCID: PMC11314176 DOI: 10.3390/plants13152154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
Fruit size is a crucial agronomic trait in bottle gourd, impacting both yield and utility. Despite its significance, the regulatory mechanism governing fruit size in bottle gourd remains largely unknown. In this study, we used bottle gourd (small-fruited H28 and large-fruited H17) parent plants to measure the width and length of fruits at various developmental stages, revealing a single 'S' growth curve for fruit expansion. Paraffin section observations indicated that both cell number and size significantly influence bottle gourd fruit size. Through bulked segregant analysis and combined genotype-phenotype analysis, the candidate interval regulating fruit size was pinpointed to 17,747,353 bp-18,185,825 bp on chromosome 9, encompassing 0.44 Mb and including 44 genes. Parental fruits in the rapid expansion stage were subjected to RNA-seq, highlighting that differentially expressed genes were mainly enriched in pathways related to cell wall biosynthesis, sugar metabolism, and hormone signaling. Transcriptome and resequencing analysis, combined with gene function annotation, identified six genes within the localized region as potential regulators of fruit size. This study not only maps the candidate interval of genes influencing fruit size in bottle gourd through forward genetics, but also offers new insights into the potential molecular mechanisms underlying this trait through transcriptome analysis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Wenjin Yu
- College of Agriculture, Guangxi University, Nanning 530004, China; (H.F.); (S.H.); (R.L.); (P.W.); (Q.J.); (C.Z.); (Y.Y.)
| |
Collapse
|
2
|
Méndez-Yáñez A, Carrasco-Orellana C, Ramos P, Morales-Quintana L. Alpha-expansins: more than three decades of wall creep and loosening in fruits. PLANT MOLECULAR BIOLOGY 2024; 114:84. [PMID: 38995453 DOI: 10.1007/s11103-024-01481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024]
Abstract
Expansins are proteins without catalytic activity, but able to break hydrogen bonds between cell wall polysaccharides hemicellulose and cellulose. This proteins were reported for the first time in 1992, describing cell wall extension in cucumber hypocotyls caused particularly by alpha-expansins. Although these proteins have GH45 and CBM63 domains, characteristic of enzymes related with the cleavage of cell wall polysaccharides, demonstrating in vitro that they extend plant cell wall. Its participation has been associated to molecular processes such as development and growing, fruit ripening and softening, tolerance and resistance to biotic and abiotic stress and seed germination. Structural insights, facilitated by bioinformatics approaches, are highlighted, shedding light on the intricate interactions between alpha-expansins and cell wall polysaccharides. After more than thirty years of its discovery, we want to celebrate the knowledge of alpha-expansins and emphasize their importance to understand the phenomena of disassembly and loosening of the cell wall, specifically in the fruit ripening phenomena, with this state-of-the-art dedicated to them.
Collapse
Affiliation(s)
- Angela Méndez-Yáñez
- Multidisciplinary Agroindustry Research Laboratory, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Cinco Poniente No. 1670, Talca, Chile.
| | - Cristian Carrasco-Orellana
- División Agroindustrial de Empresas Carozzi S. A., Desarrollo E Innovación Aplicada Agrozzi, Centro Tecnológico de Investigación, Teno, Chile
| | - Patricio Ramos
- Plant Microorganism Interaction Laboratory, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Cinco Poniente No. 1670, Talca, Chile.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Ochoa-Alejo N, Gómez-Jiménez MC, Martínez O. Editorial: Transcriptomics of fruit growth, development and ripening. FRONTIERS IN PLANT SCIENCE 2024; 15:1399376. [PMID: 38645390 PMCID: PMC11026863 DOI: 10.3389/fpls.2024.1399376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Neftali Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | | | - Octavio Martínez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| |
Collapse
|
5
|
Liu Z, Li XY, Yang L, Cheng YS, Nie XS, Wu T. Comparative physiological, metabolomic and transcriptomic analyses reveal the mechanisms of differences in pear fruit quality between distinct training systems. BMC PLANT BIOLOGY 2024; 24:28. [PMID: 38172675 PMCID: PMC10765702 DOI: 10.1186/s12870-023-04716-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Canopy architecture is critical in determining the fruit-zone microclimate and, ultimately, in determining an orchard's success in terms of the quality and quantity of the fruit produced. However, few studies have addressed how the canopy environment leads to metabolomic and transcriptomic alterations in fruits. Designing strategies for improving the quality of pear nutritional components relies on uncovering the related regulatory mechanisms. RESULTS We performed an in-depth investigation of the impact of canopy architecture from physiological, metabolomic and transcriptomic perspectives by comparing pear fruits grown in a traditional freestanding system (SP) or a flat-type trellis system (DP). Physiological studies revealed relatively greater fruit sizes, soluble solid contents and titratable acidities in pear fruits from DP systems with open canopies. Nontargeted metabolite profiling was used to characterize fruits at the initial ripening stage. Significant differences in fruit metabolites, including carbohydrates, nucleic acids, alkaloids, glycerophospholipids, sterol lipids, and prenol lipids, were observed between the two groups. Transcriptomic analysis indicated that a series of organic substance catabolic processes (e.g., the glycerol-3-phosphate catabolic process, pectin catabolic process and glucan catabolic process) were overrepresented in fruits of the DP system. Moreover, integrative analysis of the metabolome and transcriptome at the pathway level showed that DP pear fruits may respond to the canopy microenvironment by upregulating phenylpropanoid biosynthesis pathway genes such as PpPOD. Transient assays revealed that the contents of malic acid and citric acid were lower in the pear flesh of PpPOD RNAi plants, which was associated with regulating the expression of organic acid metabolism-related genes. CONCLUSIONS Our results provide fundamental evidence that at the physiological and molecular levels, open-canopy architecture contributes to improving pear fruit quality and is correlated with increased levels of carbohydrates and lipid-like molecules. This study may lead to the development of rational culture practices for enhancing the nutritional traits of pear fruits.
Collapse
Affiliation(s)
- Zheng Liu
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Xie-Yu Li
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Li Yang
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Yin-Sheng Cheng
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Xian-Shuang Nie
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Tao Wu
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China.
| |
Collapse
|
6
|
Carrera M. Food Safety-Transcriptomics and Proteomics. Int J Mol Sci 2023; 24:17127. [PMID: 38138956 PMCID: PMC10743159 DOI: 10.3390/ijms242417127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Food safety is a critical aspect of public health and involves the handling, preparation, and storage of food to avoid contamination and foodborne illnesses [...].
Collapse
Affiliation(s)
- Mónica Carrera
- Food Technology Department, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Pontevedra, Spain
| |
Collapse
|
7
|
Chen T, Cao H, Wang M, Qi M, Sun Y, Song Y, Yang Q, Meng D, Lian N. Integrated transcriptome and physiological analysis revealed core transcription factors that promote flavonoid biosynthesis in apricot in response to pathogenic fungal infection. PLANTA 2023; 258:64. [PMID: 37555984 DOI: 10.1007/s00425-023-04197-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023]
Abstract
MAIN CONCLUSION Integrated transcriptome and physiological analysis of apricot leaves after Fusarium solani treatment. In addition, we identified core transcription factors and flavonoid-related synthase genes which may function in apricot disease resistance. Apricot (Prunus armeniaca) is an important economic fruit species, whose yield and quality of fruit are limited owing to its susceptibility to diseases. However, the molecular mechanisms underlying the response of P. armeniaca to diseases is still unknown. In this study, we used physiology and transcriptome analysis to characterize responses of P. armeniaca subjected to Fusarium solani. The results showed increasing malondialdehyde (MDA) content, enhanced peroxidase (POD) and catalase (CAT) activity during F. solani infestation. A large number of differentially expressed genes (DEGs), which included 4281 upregulated DEGs and 3305 downregulated DEGs, were detected in P. armeniaca leaves exposed to F. solani infestation. Changes in expression of transcription factors (TFs), including bHLH, AP2/ERF, and WRKY indicated their role in triggering pathogen-responsive genes in P. armeniaca. During the P. armeniaca response to F. solani infestation, the content of total flavonoid was changed, and we identified enzyme genes associated with flavonoid biosynthesis. Ectopic overexpression of PabHLH15 and PabHLH102 in Nicotiana benthamiana conferred elevated resistance to Fspa_1. Moreover, PabHLH15 and PabHLH102 positively interact with the promoter of flavonoid biosynthesis-related genes. A regulatory network of TFs regulating enzyme genes related to flavonoid synthesis affecting apricot disease resistance was constructed. These results reveal the potential underlying mechanisms of the F. solani response of P. armeniaca, which would help improve the disease resistance of P. armeniaca and may cultivate high-quality disease-resistant varieties in the future.
Collapse
Affiliation(s)
- Ting Chen
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Hongyan Cao
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Mengying Wang
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Meng Qi
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | | | - Yangbo Song
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016, China
| | - Qing Yang
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Dong Meng
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|