1
|
Zhou Y, Shen Q, Cai L, Zhao H, Zhang K, Ma Y, Bo Y, Lyu X, Yang J, Hu Z, Zhang M. Promoter variations of ClERF1 gene determines flesh firmness in watermelon. BMC PLANT BIOLOGY 2024; 24:290. [PMID: 38627629 PMCID: PMC11020897 DOI: 10.1186/s12870-024-05000-z] [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: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Flesh firmness is a critical factor that influences fruit storability, shelf-life and consumer's preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon. RESULTS In this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis. CONCLUSIONS Our results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.
Collapse
Affiliation(s)
- Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lingmin Cai
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China.
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.
| |
Collapse
|
2
|
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
|
3
|
Qi C, Xv L, Xia W, Zhu Y, Wang Y, Zhang Z, Dai H, Miao M. Genome-Wide Identification and Expression Patterns of Cucumber Invertases and Their Inhibitor Genes. Int J Mol Sci 2023; 24:13421. [PMID: 37686228 PMCID: PMC10487868 DOI: 10.3390/ijms241713421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Invertases and their inhibitors play important roles in sucrose metabolism, growth and development, signal transduction, and biotic and abiotic stress tolerance in many plant species. However, in cucumber, both the gene members and functions of invertase and its inhibitor families remain largely unclear. In this study, in comparison with the orthologues of Citrullus lanatus (watermelon), Cucumis melo (melon), and Arabidopsis thaliana (Arabidopsis), 12 invertase genes and 12 invertase inhibitor genes were identified from the genome of Cucumis sativus (cucumber). Among them, the 12 invertase genes were classified as 4 cell wall invertases, 6 cytoplasmic invertases, and 2 vacuolar invertases. Most invertase genes were conserved in cucumber, melon, and watermelon, with several duplicate genes in melon and watermelon. Transcriptome analysis distinguished these genes into various expression patterns, which included genes CsaV3_2G025540 and CsaV3_2G007220, which were significantly expressed in different tissues, organs, and development stages, and genes CsaV3_7G034730 and CsaV3_5G005910, which might be involved in biotic and abiotic stress. Six genes were further validated in cucumber based on quantitative real-time PCR (qRT-PCR), and three of them showed consistent expression patterns as revealed in the transcriptome. These results provide important information for further studies on the physiological functions of cucumber invertases (CSINVs) and their inhibitors (CSINHs).
Collapse
Affiliation(s)
- Chenze Qi
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Liyun Xv
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Wenhao Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Yunyi Zhu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Yudan Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Haibo Dai
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics, The Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
4
|
Liu T, Amanullah S, Xu H, Gao P, Du Z, Hu X, Han M, Che Y, Zhang L, Qi G, Wang D. RNA-Seq Identified Putative Genes Conferring Photosynthesis and Root Development of Melon under Salt Stress. Genes (Basel) 2023; 14:1728. [PMID: 37761868 PMCID: PMC10530605 DOI: 10.3390/genes14091728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Melon is an important fruit crop of the Cucurbitaceae family that is being cultivated over a large area in China. Unfortunately, salt stress has crucial effects on crop plants and damages photosynthesis, membranal lipid components, and hormonal metabolism, which leads to metabolic imbalance and retarded growth. Herein, we performed RNA-seq analysis and a physiological parameter evaluation to assess the salt-induced stress impact on photosynthesis and root development activity in melon. The endogenous quantification analysis showed that the significant oxidative damage in the membranal system resulted in an increased ratio of non-bilayer/bilayer lipid (MGDG/DGDG), suggesting severe irregular stability in the photosynthetic membrane. Meanwhile, root development was slowed down by a superoxidized membrane system, and downregulated genes showed significant contributions to cell wall biosynthesis and IAA metabolism. The comparative transcriptomic analysis also exhibited that major DEGs were more common in the intrinsic membrane component, photosynthesis, and metabolism. These are all processes that are usually involved in negative responses. Further, the WGCN analysis revealed the involvement of two main network modules: the thylakoid membrane and proteins related to photosystem II. The qRT-PCR analysis exhibited that two key genes (MELO3C006053.2 and MELO3C023596.2) had significant variations in expression profiling at different time intervals of salt stress treatments (0, 6, 12, 24, and 48 h), which were also consistent with the RNA-seq results, denoting the significant accuracy of molecular dataset analysis. In summary, we performed an extensive molecular and metabolic investigation to check the salt-stress-induced physiological changes in melon and proposed that the PSII reaction centre may likely be the primary stress target.
Collapse
Affiliation(s)
- Tai Liu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Sikandar Amanullah
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (S.A.); (P.G.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Huichun Xu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (S.A.); (P.G.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zhiqiang Du
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Xixi Hu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Mo Han
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Ye Che
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Ling Zhang
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Guochao Qi
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Di Wang
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| |
Collapse
|
5
|
Ali MM, Gull S, Hu X, Hou Y, Chen F. Exogenously applied zinc improves sugar-acid profile of loquat (Eriobotrya japonica Lindl.) by regulating enzymatic activities and expression of their metabolism-related genes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107829. [PMID: 37329690 DOI: 10.1016/j.plaphy.2023.107829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Soluble sugars and organic acids are the most abundant components in ripe fruits, and they play critical roles in the development of fruit flavor and taste. In this study, loquat trees were sprayed with 0.1, 0.2 and 0.3% zinc sulphate. The contents of soluble sugars and organic acids were determined using HPLC-RID and UPLC-MS, respectively. The activities of key enzymes involved in sugar-acid metabolism were measured and expression profiling of related genes was done using RT-qPCR. The results revealed that 0.1% zinc sulphate was a promising treatment among other Zn applications with respect to the increased levels of soluble sugars and decreased acid contents in loquats. Correlation analysis showed that the enzymes i.e., SPS, SS, FK, and HK were may be involved in the regulation of fructose and glucose metabolism in the fruit pulp of loquat. While, the activity of NADP-ME showed negative and NAD-MDH showed a positive correlation with malic acid content. Meanwhile, EjSPS1-4, EjSS2-4, EjHK1-3, and EjFK1-6 may play an important role in soluble sugar metabolism in the pulp of loquat fruits. Similarly, EjPEPC2, EjPEPC3, EjNAD-MDH1, EjNAD-MDH3-5, EjNAD-MDH6 and EjNAD-MDH13 may have a vital contribution to malic acid biosynthesis in loquat fruits. This study provides new insights for future elucidation of key mechanisms regulating soluble sugars and malic acid biosynthesis in loquats.
Collapse
Affiliation(s)
- Muhammad Moaaz Ali
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shaista Gull
- Department of Horticulture, Bahauddin Zakariya University, Multan, 66000, Punjab, Pakistan
| | - Xiaobo Hu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youming Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
6
|
Kaseb MO, Umer MJ, Lu X, He N, Anees M, El-Remaly E, Yousef AF, Salama EAA, Kalaji HM, Liu W. Comparative physiological and biochemical mechanisms in diploid, triploid, and tetraploid watermelon (Citrullus lanatus L.) grafted by branches. Sci Rep 2023; 13:4993. [PMID: 36973331 PMCID: PMC10043263 DOI: 10.1038/s41598-023-32225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Seed production for polyploid watermelons is costly, complex, and labor-intensive. Tetraploid and triploid plants produce fewer seeds/fruit, and triploid embryos have a harder seed coat and are generally weaker than diploid seeds. In this study, we propagated tetraploid and triploid watermelons by grafting cuttings onto gourd rootstock (C. maxima × C. mochata). We used three different scions: the apical meristem (AM), one-node (1N), and two-node (2N) branches of diploid, triploid, and tetraploid watermelon plants. We then evaluated the effects of grafting on plant survival, some biochemical traits, oxidants, antioxidants, and hormone levels at different time points. We found significant differences between the polyploid watermelons when the 1N was used as a scion. Tetraploid watermelons had the highest survival rates and the highest levels of hormones, carbohydrates, and antioxidant activity compared to diploid watermelons, which may explain the high compatibility of tetraploid watermelons and the deterioration of the graft zone in diploid watermelons. Our results show that hormone production and enzyme activity with high carbohydrate content, particularly in the 2-3 days after transplantation, contribute to a high survival rate. Sugar application resulted in increased carbohydrate accumulation in the grafted combination. This study also presents an alternative and cost-effective approach to producing more tetraploid and triploid watermelon plants for breeding and seed production by using branches as sprouts.
Collapse
Affiliation(s)
- Mohamed Omar Kaseb
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou, 450009, China.
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza, 12611, Egypt.
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou, 450009, China
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou, 450009, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou, 450009, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou, 450009, China
| | - Eman El-Remaly
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza, 12611, Egypt
| | - Ahmed Fathy Yousef
- Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut, 71524, Egypt
| | - Ehab A A Salama
- Agricultural Botany Department, Faculty of Agriculture Saba Basha, Alexandria University, Alexandria, 21531, Egypt
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, TNAU, Coimbatore, 641003, India
| | - Hazem M Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, Warsaw, Poland
- Institute of Technology and Life Sciences, National Research Institute, Falenty, Al. Hrabska 3, 05-090, Raszyn, Poland
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou, 450009, China.
| |
Collapse
|
7
|
Amanullah S, Li S, Osae BA, Yang T, Abbas F, Gao M, Wang X, Liu H, Gao P, Luan F. Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon ( Citrullus lanatus L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1034952. [PMID: 36714694 PMCID: PMC9877429 DOI: 10.3389/fpls.2022.1034952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32-25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.
Collapse
Affiliation(s)
- Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Benjamin Agyei Osae
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Farhat Abbas
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Meiling Gao
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| |
Collapse
|
8
|
Ali MM, Anwar R, Rehman RNU, Ejaz S, Ali S, Yousef AF, Ercisli S, Hu X, Hou Y, Chen F. Sugar and acid profile of loquat ( Eriobotrya japonica Lindl.), enzymes assay and expression profiling of their metabolism-related genes as influenced by exogenously applied boron. FRONTIERS IN PLANT SCIENCE 2022; 13:1039360. [PMID: 36340346 PMCID: PMC9632665 DOI: 10.3389/fpls.2022.1039360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Soluble sugars and organic acids are the most abundant components in ripe fruits, and they play critical roles in the development of fruit flavor and taste. Some loquat cultivars have high acid content which seriously affect the quality of fruit and reduce the value of commodity. Consequently, studying the physiological mechanism of sugar-acid metabolism in loquat can clarify the mechanism of their formation, accumulation and degradation in the fruit. Minerals application has been reported as a promising way to improve sugar-acid balance of the fruits. In this study, loquat trees were foliar sprayed with 0.1, 0.2 and 0.3% borax, and changes in soluble sugars and organic acids were recorded. The contents of soluble sugars and organic acids were determined using HPLC-RID and UPLC-MS, respectively. The activities of enzymes responsible for the metabolism of sugars and acids were quantified and expressions of related genes were determined using quantitative real-time PCR. The results revealed that 0.2% borax was a promising treatment among other B applications for the increased levels of soluble sugars and decreased acid contents in loquats. Correlation analysis showed that the enzymes i.e., SPS, SS, FK, and HK were may be involved in the regulation of fructose and glucose metabolism in the fruit pulp of loquat. While the activity of NADP-ME showed negative and NAD-MDH showed a positive correlation with malic acid content. Meanwhile, EjSPS1, EjSPS3, EjSS3, EjHK1, EjHK3, EjFK1, EjFK2, EjFK5, and EjFK6 may play an important role in soluble sugars metabolism in fruit pulp of loquat. Similarly, EjPEPC2, EjPEPC3, EjNAD-ME1, EjNAD-MDH1, EjNAD-MDH5-8, EjNAD-MDH10, and EjNAD-MDH13 may have a vital contribution to malic acid biosynthesis in loquat fruits. This study provides new insights for future elucidation of key mechanisms regulating soluble sugars and malic acid biosynthesis in loquats.
Collapse
Affiliation(s)
- Muhammad Moaaz Ali
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Raheel Anwar
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Rana Naveed Ur Rehman
- Department of Horticulture, Faculty of Food and Crop Science, Pir Mehr Ali Shah (PMAS)-Arid Agriculture University, Rawalpindi, Pakistan
| | - Shaghef Ejaz
- Department of Horticulture, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sajid Ali
- Department of Horticulture, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Ahmed F. Yousef
- Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut, Egypt
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, Turkey
| | - Xiaobo Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youming Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Faxing Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
9
|
Liao L, Li Y, Bi X, Xiong B, Wang X, Deng H, Zhang M, Sun G, Jin Z, Huang Z, Wang Z. Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality. FRONTIERS IN PLANT SCIENCE 2022; 13:995913. [PMID: 36311145 PMCID: PMC9608513 DOI: 10.3389/fpls.2022.995913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/30/2022] [Indexed: 05/27/2023]
Abstract
Harumi tangor fruit with Ponkan as an interstock contains significantly higher levels of total soluble solids compared to Harumi tangor fruit cv.with no interstock. Transcriptome analysis of two graft combinations (Harumi/Hongjv (HP) and cv. cv.Harumi/Ponkan/Hongjv (HPP)) was conducted to identify the genes related to use of the Ponkan interstock. Soluble sugars and organic acids were also measured in the two graft combinations. The results showed that the contents of sucrose, glucose, and fructose were higher in the fruits of HPP than in those of HP; additionally, the titratable acid levels were lower in grafts with interstocks than in grafts without interstocks. Transcriptome analysis of HPP and HP citrus revealed that the interstock regulated auxin and ethylene signals, sugar and energy metabolism, and cell wall metabolism. Trend and Venn analyses suggested that genes related to carbohydrate-, energy-, and hormone-metabolic activities were more abundant in HPP plants than in HP plants during different periods. Moreover, weighted gene co-expression network analysis demonstrated that carbohydrates, hormones, cell wall, and transcription factors may be critical for interstock-mediated citrus fruit development and ripening. The contents of ethylene, auxin, cytokinin, transcription factors, starch, sucrose, glucose, fructose, and total sugar in HPP plants differed considerably than those in HP fruits. Interstocks may help to regulate the early ripening and quality of citrus fruit through the above-mentioned pathways. These findings provide information on the effects of interstock on plant growth and development.
Collapse
Affiliation(s)
- Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yunjie Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyi Bi
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Mingfei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhenghua Jin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zehao Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
10
|
Timms K, Holder B, Day A, Mclaughlin J, Forbes KA, Westwood M. Watermelon-Derived Extracellular Vesicles Influence Human Ex Vivo Placental Cell Behavior by Altering Intestinal Secretions. Mol Nutr Food Res 2022; 66:e2200013. [PMID: 35938208 PMCID: PMC9787345 DOI: 10.1002/mnfr.202200013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/20/2022] [Indexed: 12/30/2022]
Abstract
SCOPE During pregnancy, mother-to-fetus transfer of nutrients is mediated by the placenta; sub-optimal placental development and/or function results in fetal growth restriction (FGR), and the attendant risk of stillbirth, neurodevelopmental delay, and non-communicable diseases in adulthood. A maternal diet high in fruit and vegetables lowers the risk of FGR but the association cannot be explained fully by known macro- and micronutrients. METHODS AND RESULTS This study investigates if dietary-derived extracellular vesicles (EVs) can regulate placental function. The study characterizes the microRNA and protein cargo of EVs isolated from watermelon, show they are actively internalized by human intestinal epithelial cells in vitro, use mass spectrometry to demonstrate that they alter the intestinal secretome and bioinformatic analyses to predict the likely affected pathways in cells/tissues distal to gut. Application of the watermelon EV-modified intestinal secretome to human placental trophoblast cells and ex vivo tissue explants affects the trophoblast proteome and key aspects of trophoblast behavior, including migration and syncytialization. CONCLUSION Dietary-derived plant EVs can modify intestinal communication with distal tissues, including the placenta. Harnessing the beneficial properties of dietary-derived plant EVs and/or exploiting their potential as natural delivery agents may provide new ways to improve placental function and reduce rates of FGR.
Collapse
Affiliation(s)
- Kate Timms
- Maternal and Fetal Health Research CentreSchool of Medical SciencesUniversity of ManchesterManchesterM13 9WLUK,Manchester University NHS Foundation TrustManchester Academic Health Sciences CentreManchesterM13 9WLUK
| | - Beth Holder
- Department of MetabolismDigestion and ReproductionInstitute of Reproductive and Developmental BiologyImperial College LondonLondonUK
| | - Anil Day
- Division of Molecular and Cellular FunctionSchool of Biological SciencesUniversity of ManchesterManchesterM13 9PTUK
| | - John Mclaughlin
- Division of DiabetesEndocrinology and GastroenterologyUniversity of ManchesterManchesterM13 9PTUK,Department of GastroenterologySalford Royal NHS Foundation TrustSalfordM6 8HDUK
| | - Karen A. Forbes
- Discovery and Translational Science DepartmentLeeds Institute of Cardiovascular and Metabolic MedicineFaculty of Medicine and HealthUniversity of LeedsLeedsLS2 9JTUK
| | - Melissa Westwood
- Maternal and Fetal Health Research CentreSchool of Medical SciencesUniversity of ManchesterManchesterM13 9WLUK,Manchester University NHS Foundation TrustManchester Academic Health Sciences CentreManchesterM13 9WLUK
| |
Collapse
|
11
|
Chemotaxonomic Identification of Key Taste and Nutritional Components in 'Shushanggan Apricot' Fruits by Widely Targeted Metabolomics. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123870. [PMID: 35744991 PMCID: PMC9227342 DOI: 10.3390/molecules27123870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022]
Abstract
The chemotypic and the content variation in taste substances and nutrients in ‘Shushanggan apricot’ fruits were detected by UPLC-MS/MS. A total of 592 compounds were identified, of which sucrose contributed mainly to the sweet taste and malic acid and citric acid were important organic acids affecting sweet–sour taste. γ-linolenic acid, α-linolenic acid and linoleic acid were the dominant free fatty acids, and neochlorogenic acid and chlorogenic acid were the predominant phenolic acids. Fruit taste was positively correlated with sucrose and negatively correlated with malic acid and citric acid. The differential metabolites were significantly enriched in the biosynthesis of amino acids and 2-oxocarboxylic acid metabolism pathways, regulating the sugar and organic acid biosynthesis. Taste and nutrient differences could be revealed by variations in composition and abundance of carbohydrates, organic acids and amino acids. The purpose of this study was to provide a comprehensive chemical characterization of taste and nutrient compounds in ‘Shushanggan apricot’ fruits.
Collapse
|
12
|
Lv Y, Amanullah S, Liu S, Zhang C, Liu H, Zhu Z, Zhang X, Gao P, Luan F. Comparative Transcriptome Analysis Identified Key Pathways and Genes Regulating Differentiated Stigma Color in Melon ( Cucumis melo L.). Int J Mol Sci 2022; 23:ijms23126721. [PMID: 35743161 PMCID: PMC9224399 DOI: 10.3390/ijms23126721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
Stigma color is an important morphological trait in many flowering plants. Visual observations in different field experiments have shown that a green stigma in melons is more attractive to natural pollinators than a yellow one. In the current study, we evaluated the characterization of two contrasted melon lines (MR-1 with a green stigma and M4-7 with a yellow stigma). Endogenous quantification showed that the chlorophyll and carotenoid content in the MR-1 stigmas was higher compared to the M4-7 stigmas. The primary differences in the chloroplast ultrastructure at different developmental stages depicted that the stigmas of both melon lines were mainly enriched with granum, plastoglobulus, and starch grains. Further, comparative transcriptomic analysis was performed to identify the candidate pathways and genes regulating melon stigma color during key developmental stages (S1–S3). The obtained results indicated similar biological processes involved in the three stages, but major differences were observed in light reactions and chloroplast pathways. The weighted gene co-expression network analysis (WGCNA) of differentially expressed genes (DEGs) uncovered a “black” network module (655 out of 5302 genes), mainly corresponding to light reactions, light harvesting, the chlorophyll metabolic process, and the chlorophyll biosynthetic process, and exhibited a significant contribution to stigma color. Overall, the expression of five key genes of the chlorophyll synthesis pathway—CAO (MELO03C010624), CHLH (MELO03C007233), CRD (MELO03C026802), HEMA (MELO03C011113), POR (MELO03C016714)—were checked at different stages of stigma development in both melon lines using quantitative real time polymerase chain reaction (qRT-PCR). The results exhibited that the expression of these genes gradually increased during the stigma development of the MR-1 line but decreased in the M4-7 line at S2. In addition, the expression trends in different stages were the same as RNA-seq, indicating data accuracy. To sum up, our research reveals an in-depth molecular mechanism of stigma coloration and suggests that chlorophyll and related biological activity play an important role in differentiating melon stigma color.
Collapse
Affiliation(s)
- Yuanzuo Lv
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Sikandar Amanullah
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Chen Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xian Zhang
- Horticulture College of Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (P.G.); (F.L.)
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (P.G.); (F.L.)
| |
Collapse
|
13
|
Choi HR, Baek MW, Jeong CS, Tilahun S. Comparative Transcriptome Analysis of Softening and Ripening-Related Genes in Kiwifruit Cultivars Treated with Ethylene. Curr Issues Mol Biol 2022; 44:2593-2613. [PMID: 35735618 PMCID: PMC9221576 DOI: 10.3390/cimb44060177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and the transcriptome gene set was constructed by de novo assembly. A total of 1287 and 1724 unigenes were differentially expressed during the comparison of ethylene treatment with control in green ‘Hayward’ and gold ‘Haegeum’, respectively. From the differentially expressed unigenes, 594 and 906 were upregulated, and 693 and 818 were downregulated in the green and gold kiwifruit cultivars, respectively, when treated with ethylene. We also identified a list of genes that were expressed commonly and exclusively in the green and gold kiwifruit cultivars treated with ethylene. Several genes were expressed differentially during the ripening of kiwifruits, and their cumulative effect brought about the softening- and ripening-related changes. This work also identified and categorized genes related to softening and other changes during ripening. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) identified in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR) to validate the reliability of the expression profiles obtained from RNA-Seq. The data obtained from the present study will add to the information available on the molecular mechanisms of the effects of ethylene during the ripening of kiwifruits. This study will also provide resources for further studies of the genes related to ripening, helping kiwifruit breeders and postharvest technologists to improve ripening quality.
Collapse
Affiliation(s)
- Han Ryul Choi
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
| | - Min Woo Baek
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
| | - Cheon Soon Jeong
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
- Correspondence: (C.S.J.); (S.T.); Tel.: +82-033-250-6409 (C.S.J.)
| | - Shimeles Tilahun
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon 24341, Korea
- Department of Horticulture and Plant Sciences, Jimma University, Jimma 378, Ethiopia
- Correspondence: (C.S.J.); (S.T.); Tel.: +82-033-250-6409 (C.S.J.)
| |
Collapse
|
14
|
Germano TA, de Oliveira MFR, Aziz S, Oliveira AER, da Cruz Saraiva KD, Dos Santos CP, Moura CFH, Costa JH. Transcriptome profiling of cashew apples (Anacardium occidentale) genotypes reveals specific genes linked to firmness and color during pseudofruit development. PLANT MOLECULAR BIOLOGY 2022; 109:83-100. [PMID: 35332428 DOI: 10.1007/s11103-022-01257-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
We found 34 and 71 key genes potentially involved in flavonoid biosynthesis and cell wall disassembly, respectively, which could be associated with specific peel coloration and softening of each genotype. Cashew apple (Anacardium occidentale) has a great economic importance worldwide due to its high nutritional value, peculiar flavor and aroma. During ripening, the peduncle develops different peel color and becomes quickly fragile due to its oversoftening, impacting its consumers' acceptance. In view of this, the understanding about its transcriptional dynamics throughout ripening is imperative. In this study, we performed a transcriptome sequencing of two cashew apple genotypes (CCP 76 and BRS 265), presenting different firmness and color peel, in the immature and ripe stages. Comparative transcriptome analysis between immature and ripe cashew apple revealed 4374 and 3266 differentially expressed genes (DEGs) to CCP 76 and BRS 265 genotypes, respectively. These genes included 71 and 34 GDEs involved in the cell wall disassembly and flavonoid biosynthesis, respectively, which could be associated with firmness loss and anthocyanin accumulation during cashew apple development. Then, softer peduncle of CCP 76 could be justified by down-regulated EXP and up-regulation of genes involved in pectin degradation (PG, PL and PAE) and in cell wall biosynthesis. Moreover, genes related to flavonoid biosynthesis (PAL, C4H and CHS) could be associated with early high accumulation of anthocyanin in red-peel peduncle of BRS 265. Finally, expression patterns of the selected genes were tested by real-time quantitative PCR (qRT-PCR), and the qRT-PCR results were consistent with transcriptome data. The information generated in this work will provide insights into transcriptome responses to cashew apple ripening and hence, it will be helpful for cashew breeding programs aimed at developing genotypes with improved quality traits.
Collapse
Affiliation(s)
- Thais Andrade Germano
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Matheus Finger Ramos de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Shahid Aziz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Antonio Edson Rocha Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, CEP 05508-900, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Ciência e Tecnologia da Paraíba, Instituto Federal de Educação, Campus Princesa Isabel, Princesa Isabel, PB, CEP 58755-000, Brazil
| | - Clesivan Pereira Dos Santos
- Departamento de Química, Universidade Estadual de Ponta Grossa, Campus Uvaranas, Ponta Grossa, PR, CEP 84030-900, Brazil
| | | | - José Hélio Costa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil.
| |
Collapse
|
15
|
Liang R, Su Y, Qin X, Gao Z, Fu Z, Qiu H, Lin X, Zhu J. Comparative transcriptomic analysis of two Cucumis melo var. saccharinus germplasms differing in fruit physical and chemical characteristics. BMC PLANT BIOLOGY 2022; 22:193. [PMID: 35410167 PMCID: PMC9004126 DOI: 10.1186/s12870-022-03550-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/21/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Hami melon (Cucumis melo var. saccharinus) is a popular fruit in China because of its excellent taste, which is largely determined by its physicochemical characteristics, including flesh texture, sugar content, aroma, and nutrient composition. However, the mechanisms by which these characteristics are regulated have not yet been determined. In this study, we monitored changes in the fruits of two germplasms that differed in physicochemical characteristics throughout the fruit development period. RESULTS Ripe fruit of the bred variety 'Guimi' had significantly higher soluble sugar contents than the fruit of the common variety 'Yaolong.' Additionally, differences in fruit shape and color between these two germplasms were observed during development. Comparative transcriptome analysis, conducted to identify regulators and pathways underlying the observed differences at corresponding stages of development, revealed a higher number of differentially expressed genes (DEGs) in Guimi than in Yaolong. Moreover, most DEGs detected during early fruit development in Guimi were associated with cell wall biogenesis. Temporal analysis of the identified DEGs revealed similar trends in the enrichment of downregulated genes in both germplasms, although there were differences in the enrichment trends of upregulated genes. Further analyses revealed trends in differential changes in multiple genes involved in cell wall biogenesis and sugar metabolism during fruit ripening. CONCLUSIONS We identified several genes associated with the ripening of Hami melons, which will provide novel insights into the molecular mechanisms underlying the development of fruit characteristics in these melons.
Collapse
Affiliation(s)
- Renfan Liang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Yicheng Su
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xiaojuan Qin
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhongkui Gao
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhixin Fu
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Huijun Qiu
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xu Lin
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jinlian Zhu
- Guangxi Normal University for Nationalities, Chongzuo, 532200, China
| |
Collapse
|
16
|
Mashilo J, Shimelis H, Ngwepe RM, Thungo Z. Genetic Analysis of Fruit Quality Traits in Sweet Watermelon ( Citrullus lanatus var. lanatus): A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:834696. [PMID: 35392511 PMCID: PMC8981301 DOI: 10.3389/fpls.2022.834696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Fruit quality traits of sweet watermelon (Citrullus lanatus var. lanatus) are crucial for new product development and commercialization. Sweet watermelon fruit quality traits are affected by the compositions of phytochemical compounds, phytohormones, and fruit flesh firmness which are affected by genes, the growing environment and their interaction. These compositions determine fruit ripening, eating quality, and postharvest shelf-life. Knowledge of the genetic profile and analyses of quality traits in watermelon is vital to develop improved cultivars with enhanced nutritional compositions, consumer-preferred traits, and extended storage life. This review aims to present the opportunities and progress made on the genetic analysis of fruit quality traits in watermelon as a guide for quality breeding based on economic and end-user attributes. The first section of the review highlights the genetic mechanisms involved in the biosynthesis of phytochemical compounds (i.e., sugars, carotenoids, amino acids, organic acids, and volatile compounds), phytohormones (i.e., ethylene and abscisic acid) and fruit flesh structural components (i.e., cellulose, hemicellulose, and pectin) elicited during watermelon fruit development and ripening. The second section pinpoints the progress on the development of molecular markers and quantitative trait loci (QTL) analysis for phytochemical compounds, phytohormones and fruit quality attributes. The review presents gene-editing technology and innovations associated with fruit quality traits for selection and accelerated cultivar development. Finally, the paper discussed gene actions conditioning fruit ripening in citron watermelon (C. lanatus var. citroides [L. H. Bailey] Mansf. ex Greb.) as reference genetic resources to guide current and future breeding. Information presented in this review is useful for watermelon variety design, product profiling and development to serve the diverse value chains of the crop.
Collapse
Affiliation(s)
- Jacob Mashilo
- Limpopo Department of Agriculture and Rural Development, Agriculture Regulatory and Technology Development Directorate, Crop Science Division, Towoomba Research Station, Bela-Bela, South Africa
- African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Richard Mantlo Ngwepe
- Limpopo Department of Agriculture and Rural Development, Agriculture Regulatory and Technology Development Directorate, Crop Science Division, Towoomba Research Station, Bela-Bela, South Africa
- African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Zamalotshwa Thungo
- African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Vegetable, Industrial and Medicinal Plants, Agricultural Research Council, Pretoria, South Africa
| |
Collapse
|
17
|
Chu S, Wang S, Zhang R, Yin M, Yang X, Shi Q. Integrative analysis of transcriptomic and metabolomic profiles reveals new insights into the molecular foundation of fruit quality formation in Citrullus lanatus (Thunb.) Matsum. & Nakai. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
In this study, an integrated transcriptome and metabolome analysis was used to explore the molecular foundation of fruit quality in two parent lines of Citrullus lanatus with distinct flesh characteristics, including ‘14-1’ (sweet, red, and soft) and ‘W600’ (bitter, light yellow, and firm), as well as the corresponding F1 population (bitter, light yellow, and firm). Numerous differentially expressed genes (DEGs) were identified in the fruit samples: 3,766 DEGs for ‘14-1’ vs. ‘W600’, 2,767 for ‘14-1’ vs. F1, and 1,178 for F1 vs. ‘W600’ at the transition stage; and 4,221 for ‘14-1’ vs. ‘W600’, 2,447 for ‘14-1’ vs. F1, and 446 for F1 vs. ‘W600’ at the maturity stage. Weighted gene co-expression network analysis (WGCNA) revealed that a gene module including 1,111 DEGs was closely associated with flesh taste and color, and another gene module including 1,575 DEGs contributed significantly to flesh texture. The metabolomic results showed that there were 447 differential metabolites (DMs) for ‘14-1’ vs. ‘W600’ fruits, 394 for ‘14-1’ vs. F1, and 298 for F1 vs. ‘W600’ at the maturity stage. Combining WGNCA and metabolomic results, several DEGs and DMs were further identified as hub players in fruit quality formation: six DEGs with four DMs for flesh sweetness; six DEGs with 13 DMs for bitterness; nine DEGs with 10 DMs for flesh color; and nine DEGs with four DMs for flesh texture. Altogether, these observations not only expand our knowledge of the molecular basis of fruit quality in watermelon, but also provide potential targets for future watermelon improvement.
Collapse
|
18
|
Zhang Z, Shi Q, Wang B, Ma A, Wang Y, Xue Q, Shen B, Hamaila H, Tang T, Qi X, Fernie AR, Luo J, Li X. Jujube metabolome selection determined the edible properties acquired during domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1116-1133. [PMID: 34862996 DOI: 10.1111/tpj.15617] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/11/2021] [Accepted: 11/27/2021] [Indexed: 05/26/2023]
Abstract
Plants supply both food and medicinal compounds, which are ascribed to diverse metabolites produced by plants. However, studies on domestication-driven changes in the metabolome and genetic basis of bioactive molecules in perennial fruit trees are generally lacking. Here, we conducted multidimensional analyses revealing a singular domestication event involving the genomic and metabolomic selection of jujube trees (Ziziphus jujuba Mill.). The genomic selection for domesticated genes was highly enriched in metabolic pathways, including carbohydrates and specialized metabolism. Domesticated metabolome profiling indicated that 187 metabolites exhibited significant divergence as a result of directional selection. Malic acid was directly selected during domestication, and the simultaneous selection of specialized metabolites, including triterpenes, consequently lead to edible properties. Cyclopeptide alkaloids (CPAs) were specifically targeted for the divergence between dry and fresh cultivars. We identified 1080 significantly associated loci for 986 metabolites. Among them, 15 triterpenes were directly selected at six major loci, allowing the identification of a homologous cluster containing seven 2,3-oxidosqualene cyclases (OSCs). An OSC gene was found to contribute to the reduction in the content of triterpenes during domestication. The complete pathway for synthesizing ursolic acid was dissected by integration of the metabolome and transcriptome. Additionally, an N-methyltransferase involved in the biosynthesis of CPA and responsible for inter-cultivar content variation was identified. The present study promotes our understanding of the selection process of the global metabolome subsequent to fruit tree domestication and facilitates the genetic manipulation of specialized metabolites to enhance their edible traits.
Collapse
Affiliation(s)
- Zhong Zhang
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Qianqian Shi
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Aimin Ma
- Key Laboratory of Plant Molecular, Physiology Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongkang Wang
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taigu, 030815, China
| | - Qingtun Xue
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Bingqi Shen
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Halina Hamaila
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular, Physiology Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Xingang Li
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| |
Collapse
|
19
|
Zhu F, Wang Z, Fang Y, Tong J, Xiang J, Yang K, Wang R. Study on the Role of Phytohormones in Resistance to Watermelon Fusarium Wilt. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020156. [PMID: 35050045 PMCID: PMC8781552 DOI: 10.3390/plants11020156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 05/12/2023]
Abstract
Fusarium wilt disease is one of the major diseases causing a decline in watermelon yield and quality. Researches have informed that phytohormones play essential roles in regulating plants growth, development, and stress defendants. However, the molecular mechanism of salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in resistance to watermelon Fusarium wilt remains unknown. In this experiment, we established the SA, JA, and ABA determination system in watermelon roots, and analyzed their roles in against watermelon Fusarium wilt compared to the resistant and susceptible varieties using transcriptome sequencing and RT-qPCR. Our results revealed that the up-regulated expression of Cla97C09G174770, Cla97C05G089520, Cla97C05G081210, Cla97C04G071000, and Cla97C10G198890 genes in resistant variety were key factors against (Fusarium oxysporum f. sp. Niveum) FON infection at 7 dpi. Additionally, there might be crosstalk between SA, JA, and ABA, caused by those differentially expressed (non-pathogen-related) NPRs, (Jasmonate-resistant) JAR, and (Pyrabactin resistance 1-like) PYLs genes, to trigger the plant immune system against FON infection. Overall, our results provide a theoretical basis for watermelon resistance breeding, in which phytohormones participate.
Collapse
Affiliation(s)
- Feiying Zhu
- Hunan Provincial Key Laboratory of Phytohormones, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (F.Z.); (J.T.); (J.X.)
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
- Institute of Biotechnology, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (Z.W.); (K.Y.)
| | - Zhiwei Wang
- Institute of Biotechnology, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (Z.W.); (K.Y.)
| | - Yong Fang
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
- Institute of Biotechnology, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (Z.W.); (K.Y.)
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (F.Z.); (J.T.); (J.X.)
| | - Jing Xiang
- Hunan Provincial Key Laboratory of Phytohormones, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (F.Z.); (J.T.); (J.X.)
| | - Kankan Yang
- Institute of Biotechnology, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (Z.W.); (K.Y.)
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (F.Z.); (J.T.); (J.X.)
- Correspondence:
| |
Collapse
|
20
|
Yang T, Liu J, Li X, Amanullah S, Lu X, Zhang M, Zhang Y, Luan F, Liu H, Wang X. Transcriptomic Analysis of Fusarium oxysporum Stress-Induced Pathosystem and Screening of Fom-2 Interaction Factors in Contrasted Melon Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:961586. [PMID: 35937314 PMCID: PMC9354789 DOI: 10.3389/fpls.2022.961586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 05/03/2023]
Abstract
Fusarium wilt is one of the most destructive and less controllable diseases in melon, which is usually caused by fusarium oxysporum. In this study, transcriptome sequencing and Yeast Two-Hybrid (Y2H) methods were used for quantification of differentially expressed genes (DEGs) involved in fusarium oxysporum (f. sp. melonis race 1) stress-induced mechanisms in contrasted melon varieties (M4-45 "susceptible" and MR-1 "resistant"). The interaction factors of Fom-2 resistance genes were also explored in response to the plant-pathogen infection mechanism. Transcriptomic analysis exhibited total 1,904 new genes; however, candidate DEGs analysis revealed a total of 144 specific genes (50 upregulated and 94 downregulated) for M4-45 variety and 104 specific genes (71 upregulated and 33 downregulated) for MR-1 variety, respectively. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway depicted some candidate DEGs, including Phenylalanine metabolism, phenylpropane biosynthesis, plants-pathogen interaction, and signal transduction of plant hormones, which were mainly involved in disease resistance metabolic pathways. The weighted gene co-expression network analysis (WGCNA) analysis revealed a strong correlation module and exhibited the disease resistance-related genes encoding course proteins, transcription factors, protein kinase, benzene propane biosynthesis path, plants-pathogen interaction pathway, and glutathione S-transferase. Meanwhile, the resistance-related specific genes expression was relatively abundant in MR-1 compared to the M4-45, and cell wall-associated receptor kinases (MELO3C008452 and MELO3C008453), heat shock protein (Cucumis_melo_newGene_172), defensin-like protein (Cucumis_melo_newGene_5490), and disease resistance response protein (MELO3C016325), activator response protein (MELO3C021623), leucine-rich repeat receptor protein kinase (MELO3C024412), lactyl glutathione ligase (Cucumis_melo_newGene_36), and unknown protein (MELO3C007588) were persisted by exhibiting the upregulated expressions. At the transcription level, the interaction factors between the candidate genes in response to the fusarium oxysporum induced stress, and Y2H screening signified the main contribution of MYB transcription factors (MELO3C009678 and MELO3C014597), BZIP (MELO3C011839 and MELO3C019349), unknown proteins, and key enzymes in the ubiquitination process (4XM334FK014). The candidate genes were further verified in exogenously treated melon plants with f. oxysporum (Fom-2, Race 1), Abscisic acid (ABA), Methyl Jasmonite (MeJA), and Salicylic acid (SA), using the fluorescence quantitative polymerase chain reaction (qRT-PCR) analysis. The overall expression results indicated that the SA signal pathway is involved in effective regulation of the Fom-2 gene activity.
Collapse
Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Jiajun Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xiaomei Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xueyan Lu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Mingchong Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yanhang Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- *Correspondence: Hongyu Liu,
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- Xuezheng Wang,
| |
Collapse
|
21
|
Wang Y, Jia N, Wang P, Liu J, Sun J, Ye W, Fan B. Flavonoid biosynthesis in four Dendrobium species based on transcriptome sequencing and metabolite analysis. Mol Biol Rep 2021; 49:2047-2057. [PMID: 34851480 DOI: 10.1007/s11033-021-07023-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/25/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Dendrobium is a genus of plants used as traditional Chinese herbal medicines, with high economic and medicinal value. METHODS AND RESULTS To reveal the mechanism of flavonoid biosynthesis in Dendrobium, the metabolites and transcriptomes of four Dendrobium species (D. chrysotoxum, D. nobile, D. fimbriatum, and D. denneanum) were analyzed comprehensively. Ultra-high-performance liquid chromatography-tandem mass spectrometry analysis revealed ten flavonoid compounds in Dendrobium. In total, 100,096 unigenes were obtained from the transcript database of the four Dendrobium species. Among the identified differentially expressed genes, 51 were associated with flavonoid biosynthesis, and 670 differentially expressed transcription factors were predicted, including 194 MYB, 87 bHLH, and 100 WRKY family transcription factors, respectively. Transcriptome analysis showed that the expression levels of structural genes such as chalcone synthase (CHS), cinnamate-4-hydroxylase (C4H), and flavonoid 3'-hydroxylase (F3'H) were lower in D. chrysotoxum, D. nobile, and D. fimbriatum than those in D. denneanum, which may be the main reason for the low flavonoid contents in D. chrysotoxum, D. nobile, and D. fimbriatum. CONCLUSIONS The expression level of structural genes corresponded to the accumulation level of flavonols in the different Dendrobium species. The results deepen the understanding of the molecular mechanism of flavonoid biosynthesis in Dendrobium and provide novel insights into the synthesis and accumulation of flavonoids in Dendrobium.
Collapse
Affiliation(s)
- Yajuan Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Laboratory of Quality & Safety Risk Assessment on Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Ning Jia
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Laboratory of Quality & Safety Risk Assessment on Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Peiyu Wang
- Institute of Medicinal Plant Sciences, Sanming Academy of Agricultural Sciences, Shaxian, 365050, Fujian, China
| | - Jiameng Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Laboratory of Quality & Safety Risk Assessment on Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Jing Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Laboratory of Quality & Safety Risk Assessment on Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Wei Ye
- Institute of Medicinal Plant Sciences, Sanming Academy of Agricultural Sciences, Shaxian, 365050, Fujian, China
| | - Bei Fan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Laboratory of Quality & Safety Risk Assessment on Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China.
| |
Collapse
|
22
|
Joshi V, Nimmakayala P, Song Q, Abburi V, Natarajan P, Levi A, Crosby K, Reddy UK. Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon. PeerJ 2021; 9:e12343. [PMID: 34722000 PMCID: PMC8533027 DOI: 10.7717/peerj.12343] [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: 04/30/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS). METHODS The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS). RESULTS Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values.
Collapse
Affiliation(s)
- Vijay Joshi
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas, United States
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Qiushuo Song
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
| | - Venkata Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Amnon Levi
- Vegetable Laboratory, USDA-ARS, Charleston, South Carolina, United States
| | - Kevin Crosby
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
| | - Umesh K. Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| |
Collapse
|
23
|
Sorokina M, McCaffrey KS, Deaton EE, Ma G, Ordovás JM, Perkins-Veazie PM, Steinbeck C, Levi A, Parnell LD. A Catalog of Natural Products Occurring in Watermelon- Citrullus lanatus. Front Nutr 2021; 8:729822. [PMID: 34595201 PMCID: PMC8476801 DOI: 10.3389/fnut.2021.729822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Sweet dessert watermelon (Citrullus lanatus) is one of the most important vegetable crops consumed throughout the world. The chemical composition of watermelon provides both high nutritional value and various health benefits. The present manuscript introduces a catalog of 1,679 small molecules occurring in the watermelon and their cheminformatics analysis for diverse features. In this catalog, the phytochemicals are associated with the literature describing their presence in the watermelon plant, and when possible, concentration values in various plant parts (flesh, seeds, leaves, roots, rind). Also cataloged are the chemical classes, molecular weight and formula, chemical structure, and certain physical and chemical properties for each phytochemical. In our view, knowing precisely what is in what we eat, as this catalog does for watermelon, supports both the rationale for certain controlled feeding studies in the field of precision nutrition, and plant breeding efforts for the development of new varieties with enhanced concentrations of specific phytochemicals. Additionally, improved and comprehensive collections of natural products accessible to the public will be especially useful to researchers in nutrition, cheminformatics, bioinformatics, and drug development, among other disciplines.
Collapse
Affiliation(s)
- Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
| | | | - Erin E. Deaton
- Department of Horticulture, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Guoying Ma
- Department of Horticulture, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - José M. Ordovás
- Nutrition and Genomics Laboratory, Jean Mayer-United States Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| | - Penelope M. Perkins-Veazie
- Department of Horticulture, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
| | - Amnon Levi
- United States Department of Agriculture (USDA), Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Laurence D. Parnell
- United States Department of Agriculture (USDA), Agricultural Research Service, Nutrition and Genomics Laboratory, Jean Mayer-United States Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| |
Collapse
|
24
|
Yu X, Ali MM, Li B, Fang T, Chen F. Transcriptome data-based identification of candidate genes involved in metabolism and accumulation of soluble sugars during fruit development in 'Huangguan' plum. J Food Biochem 2021; 45:e13878. [PMID: 34337770 DOI: 10.1111/jfbc.13878] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/19/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022]
Abstract
Fruit sweetness being an important factor of organoleptic quality directly affects the consumers' preferences for fresh fruit consumption, and is influenced by the composition and quantity of sugars. In this study, four soluble sugars (sucrose, fructose, glucose, and sorbitol) were identified and quantified in plum fruits cv. 'Huangguan' at four different maturity stages (fruitlet, green, veraison, and mature stage). The results revealed that sucrose and glucose are major soluble sugar components at the fruitlet and mature stages, respectively. RNA-Seq analysis was carried out and 6,778 differentially expressed genes (DEGs) were identified, including 121 genes involved in sugar metabolism. Furthermore, a total of 39 transcripts of 8 gene families encoding key enzymes related to the metabolism and accumulation of soluble sugars were separately identified. ERD6L (gene 103322904) was involved in keeping a balance of glucose between the inside and outside of vacuole. SS (gene 103333990) and SDH (gene 103335104) regulated the accumulation of fructose at the green stage. SDH (gene 103335104) controlled the degradation of sorbitol at the green stage. SS (gene 103333990) and PFK (gene 103333391) regulated the degradation of sucrose at the early stages of fruit development. Moreover, NINV (gene 103331108) regulated the accumulation of total sugar in plum. Genes 103321334 and 103335689 were important bZIP transcription factors that regulate the accumulation of glucose and fructose in fruits. Twelve DEGs were selected and validated to observe the relative accuracy of transcriptome sequencing data using qRT-PCR. Gene expression patterns were consistent between qRT-PCR and RNA-Seq data, indicating the reliability of RNA-Seq data. PRACTICAL APPLICATIONS: The results of this study provided new insights into comprehensive understanding of the genetic control of sugar metabolism and accumulation in plum fruits.
Collapse
Affiliation(s)
- Xinmiao Yu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Moaaz Ali
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binqi Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Fang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Subtropical Fruits, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
25
|
Yuan P, Umer MJ, He N, Zhao S, Lu X, Zhu H, Gong C, Diao W, Gebremeskel H, Kuang H, Liu W. Transcriptome regulation of carotenoids in five flesh-colored watermelons (Citrullus lanatus). BMC PLANT BIOLOGY 2021; 21:203. [PMID: 33910512 PMCID: PMC8082968 DOI: 10.1186/s12870-021-02965-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/07/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluating the appearance quality and a key contributor influencing consumers' preferences. But the molecular mechanism of this intricate trait remains largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed. RESULTS A total of 13 carotenoids and 16,781 differentially expressed genes (DEGs), including 1295 transcription factors (TFs), were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted the hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be the hub genes and may play an essential role in yellow flesh formation. CONCLUSIONS The composition and contents of carotenoids in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting candidate genes and molecular basis governing flesh color formation in watermelon fruit.
Collapse
Affiliation(s)
- Pingli Yuan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Weinan Diao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Haileslassie Gebremeskel
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Hanhui Kuang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
| |
Collapse
|
26
|
Kou J, Zhao Z, Zhang Q, Wei C, Ference CM, Guan J, Wang W. Comparative transcriptome analysis reveals the mechanism involving ethylene and cell wall modification related genes in Diospyros kaki fruit firmness during ripening. Genomics 2021; 113:552-563. [PMID: 33460734 DOI: 10.1016/j.ygeno.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/29/2020] [Accepted: 01/11/2021] [Indexed: 01/24/2023]
Abstract
Rapid loss of firmness is a major handicap for persimmon (Diospyros kaki Thunb.) transportation and retail. The present study employed a comparative transcriptomic approach to elucidate the mechanism involving ethylene and cell wall modification related genes in fruit firmness control of two cultivars during post harvest ripening. In contrast to the short shelf life cultivar (Mopan), the long shelf life cultivar (Yoho) kept high firmness during ripening. Extensive loss of firmness in Mopan drove an intense transcriptional activity. Globally, Mopan and Yoho shared very few common differentially expressed structural genes and regulators. Yoho strongly repressed the expression of ACC synthase and several classes of cell wall degradation genes at the onset of ripening and only induced them during late ripening period. Various ERF, WRKY, MYB, bHLH transcription factors were found highly active during fruit ripening. Overall, this study generates novel gene resources as important tools for extending persimmon shelf life.
Collapse
Affiliation(s)
- Jingjing Kou
- College of Horticulture, Hebei Agricultural University, Baoding 071000, PR China
| | - Zhihui Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, PR China; Research Center of Chinese Jujube, Hebei Agricultural University, 071001 Baoding, Hebei, PR China.
| | - Qiong Zhang
- Research Center of Chinese Jujube, Hebei Agricultural University, 071001 Baoding, Hebei, PR China; Shandong Institute of pomology, Tai'an, Shandong 271000, PR China
| | - Chuangqi Wei
- Institute of Genetics and Physiology, Hebei Academy of Agricultural and Forestry Science, Shijia Zhuang 050051, PR China
| | - Christopher M Ference
- Department of Plant Pathology, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
| | - Junfeng Guan
- Institute of Genetics and Physiology, Hebei Academy of Agricultural and Forestry Science, Shijia Zhuang 050051, PR China
| | - Wenjiang Wang
- Mountainous Area Research Institute of Hebei Province, Hebei Agricultural University, Baoding 071000, PR China; National Engineering Research Center for Agriculture in Northern Mountainous Areas, Hebei Agricultural University, Baoding 071000, PR China; Agricultural Technology Innovation Center in Mountainous Areas of Hebei Province, Hebei Agricultural University, Baoding 071000, PR China.
| |
Collapse
|
27
|
Gong C, Diao W, Zhu H, Umer MJ, Zhao S, He N, Lu X, Yuan P, Anees M, Yang D, Kaseb MO, Liu W. Metabolome and Transcriptome Integration Reveals Insights Into Flavor Formation of 'Crimson' Watermelon Flesh During Fruit Development. FRONTIERS IN PLANT SCIENCE 2021; 12:629361. [PMID: 34054886 PMCID: PMC8153042 DOI: 10.3389/fpls.2021.629361] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/29/2021] [Indexed: 05/15/2023]
Abstract
Metabolites have been reported as the main factor that influences the fruit flavor of watermelon. But the comprehensive study on the dynamics of metabolites during the development of watermelon fruit is not up-to-date. In this study, metabolome and transcriptome datasets of 'Crimson' watermelon fruit at four key developmental stages were generated. A total of 517 metabolites were detected by ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry and gas chromatography-solid-phase microextraction-mass spectrometry. Meanwhile, by K-means clustering analysis, the total differentially expressed genes were clustered in six classes. Integrating transcriptome and metabolome data revealed similar expression trends of sugars and genes involved in the glycolytic pathway, providing molecular insights into the formation of taste during fruit development. Furthermore, through coexpression analysis, we identified five differentially expressed ADH (alcohol dehydrogenase) genes (Cla97C01G013600, Cla97C05G089700, Cla97C01G001290, Cla97C05G095170, and Cla97C06G118330), which were found to be closely related to C9 alcohols/aldehydes, providing information for the formation of fruit aroma. Our findings establish a metabolic profile during watermelon fruit development and provide insights into flavor formation.
Collapse
|
28
|
Umer MJ, Bin Safdar L, Gebremeskel H, Zhao S, Yuan P, Zhu H, Kaseb MO, Anees M, Lu X, He N, Gong C, Liu W. Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles. HORTICULTURE RESEARCH 2020; 7:193. [PMID: 33328462 PMCID: PMC7705761 DOI: 10.1038/s41438-020-00416-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 05/03/2023]
Abstract
The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents, which undergo considerable variations during development and maturation. The molecular mechanisms underlying these variations remain unclear. In this study, we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism. We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids. Within these modules, based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction (RT-qPCR), we identified 7 genes involved in the metabolism of sugars and organic acids. Among these genes, Cla97C01G000640, Cla97C05G087120 and Cla97C01G018840 (r2 = 0.83 with glucose content) were identified as sugar transporters (SWEET, EDR6 and STP) and Cla97C03G064990 (r2 = 0.92 with sucrose content) was identified as a sucrose synthase from information available for other crops. Similarly, Cla97C07G128420, Cla97C03G068240 and Cla97C01G008870, having strong correlations with malic (r2 = 0.75) and citric acid (r2 = 0.85), were annotated as malate and citrate transporters (ALMT7, CS, and ICDH). The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon. These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.
Collapse
Affiliation(s)
- Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Luqman Bin Safdar
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Haileslassie Gebremeskel
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Pingli Yuan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - M O Kaseb
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou, China.
| |
Collapse
|
29
|
Chen T, Qin G, Tian S. Regulatory network of fruit ripening: current understanding and future challenges. THE NEW PHYTOLOGIST 2020; 228:1219-1226. [PMID: 32729147 DOI: 10.1111/nph.16822] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/07/2020] [Indexed: 05/19/2023]
Abstract
Fruit ripening is a developmental process that is spatio-temporally tuned at multiple levels. Molecular dissections of the mechanisms underlying the ripening process have revealed a network encompassed by hormones, transcriptional regulators, epigenomic modifications and other regulatory elements that directly determine fruit quality and the postharvest commodity of fresh produce. Many studies have addressed the important roles of ethylene, abscisic acid (ABA) and other hormones in regulating fruit ripening. Recent studies have shown that some spontaneous mutants for tomato transcription factors (TFs) have resulted from loss-of-function or dominant-negative mutations. Unlike in DNA methylation variation, the histone mark H3K27me3 may be conserved and prevents the transcriptional feedback circuit from generating autocatalytic ethylene. These observations of a network of partially redundant component indicate the need to improve our current understanding. Here, we focussed on the recent advances and future challenges in investigations of the molecular mechanisms of fruit ripening. We also identified several issues that still need to be addressed in future studies.
Collapse
Affiliation(s)
- Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
30
|
Wang L, Xu JY, Jia W, Chen Z, Xu ZC. Chloride salinity in a chloride-sensitive plant: Focusing on photosynthesis, hormone synthesis and transduction in tobacco. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 153:119-130. [PMID: 32498010 DOI: 10.1016/j.plaphy.2020.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/28/2020] [Accepted: 05/20/2020] [Indexed: 05/28/2023]
Abstract
Chloride (Cl-) is a micronutrient and a beneficial ion for plant growth, but excess Cl- easily leads to Cl- salinity. As a species sensitive to Cl-, tobacco experiences serious damage when encountering excessive Cl-. However, the molecular mechanism by which excess Cl- delays plant growth and development remain largely unknown. In this study, physiological, biochemical and genetic responses were determined in tobacco plants exposed to 12 h, 24 h and 48 h of Cl- salinity. Compared with the control, Cl- salinity increased the content of Cl- and decreased the relative water content (RWC) in tobacco, which severely limited the photosynthetic capacity and reduced photosynthetic products, resulting in decreased levels of auxin (IAA) and gibberellin (GA3). In addition, tobacco increased the content of starch, total phenol and increased phenylalanine ammonia-lyase (PAL) activity in response to Cl- salinity. Multi-omics results revealed that a total of 15,445 genes and 1983 proteins were differentially abundant in response to Cl- salinity. Two metabolic pathways, phenylalanine metabolism and starch and sucrose metabolism, were specifically enriched in the transcriptomic and proteomic data, respectively. In addition, our conjoint analysis of RNA-Seq and proteomics data revealed that 734 differentially abundant genes/proteins were enriched mainly in plant hormone signal transduction, photosynthesis and photosynthesis-antenna protein pathways. Our work presented here not only provides new insights into the molecular response of tobacco to Cl- salinity but also offers important guidance for the improvement of Cl- sensitive crops.
Collapse
Affiliation(s)
- Lin Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jia-Yang Xu
- Agronomy and Biotechnology College, China Agricultural University, Beijing, 100083, China.
| | - Wei Jia
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Zheng Chen
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Zi-Cheng Xu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
31
|
Lawson T, Lycett GW, Mayes S, Ho WK, Chin CF. Transcriptome-wide identification and characterization of the Rab GTPase family in mango. Mol Biol Rep 2020; 47:4183-4197. [PMID: 32444976 DOI: 10.1007/s11033-020-05519-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
The Rab GTPase family plays a vital role in several plant physiological processes including fruit ripening. Fruit softening during ripening involves trafficking of cell wall polymers and enzymes between cellular compartments. Mango, an economically important fruit crop, is known for its delicious taste, exotic flavour and nutritional value. So far, there is a paucity of information on the mango Rab GTPase family. In this study, 23 genes encoding Rab proteins were identified in mango by a comprehensive in silico approach. Sequence alignment and similarity tree analysis with the model plant Arabidopsis as a reference enabled the bona fide assignment of the deduced mango proteins to classify into eight subfamilies. Expression analysis by RNA-Sequencing (RNA-Seq) showed that the Rab genes were differentially expressed in ripe and unripe mangoes suggesting the involvement of vesicle trafficking during ripening. Interaction analysis showed that the proteins involved in vesicle trafficking and cell wall softening were interconnected providing further evidence of the involvement of the Rab GTPases in fruit softening. Correlation analyses showed a significant relationship between the expression level of the RabA3 and RabA4 genes and fruit firmness at the unripe stage of the mango varieties suggesting that the differences in gene expression level might be associated with the contrasting firmness of these varieties. This study will not only provide new insights into the complexity of the ripening-regulated molecular mechanism but also facilitate the identification of potential Rab GTPases to address excessive fruit softening.
Collapse
Affiliation(s)
- Tamunonengiyeofori Lawson
- School of Biosciences, Faculty of Science, The University of Nottingham, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.,Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,Crops for the Future (CFF) Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Grantley W Lycett
- Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Sean Mayes
- Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,Crops for the Future (CFF) Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Wai Kuan Ho
- School of Biosciences, Faculty of Science, The University of Nottingham, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.,Crops for the Future (CFF) Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Chiew Foan Chin
- School of Biosciences, Faculty of Science, The University of Nottingham, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
32
|
Abbas HMK, Huang HX, Wang AJ, Wu TQ, Xue SD, Ahmad A, Xie DS, Li JX, Zhong YJ. Metabolic and transcriptomic analysis of two Cucurbita moschata germplasms throughout fruit development. BMC Genomics 2020; 21:365. [PMID: 32414328 PMCID: PMC7227267 DOI: 10.1186/s12864-020-6774-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/06/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quality. RESULTS Two pumpkin germplasms, CMO-X and CMO-E, were analyzed regarding the essential quality traits such as dry weight, soluble solids, organic acids, carotenoids and sugar contents. For the comparison of fruit development in these two germplasms, fruit transcriptome was analyzed at 5 different developmental stages from 0 d to 40 d in a time course manner. Putative pathways for carotenoids biosynthesis and sucrose metabolism were developed in C. moschata fruit and homologs were identified for each key gene involved in the pathways. Gene expression data was found consistent with the accumulation of metabolites across developmental stages and also between two germplasms. PSY, PDS, ZEP, CRTISO and SUS, SPS, HK, FK were found highly correlated with the accumulation of carotenoids and sucrose metabolites, respectively, at different growth stages of C. moschata as shown by whole transcriptomic analysis. The results of qRT-PCR analysis further confirmed the association of these genes. CONCLUSION Developmental regulation of the genes associated with the metabolite accumulation can be considered as an important factor for the determination of C. moschata fruit quality. This research will facilitate the investigation of metabolic profiles in other cultivars.
Collapse
Affiliation(s)
- Hafiz Muhammad Khalid Abbas
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - He-Xun Huang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - An-Jun Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ting-Quan Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shu-Dan Xue
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aqeel Ahmad
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Da-Sen Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun-Xing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yu-Juan Zhong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| |
Collapse
|
33
|
Wang C, Dong Y, Zhu L, Wang L, Yan L, Wang M, Zhu Q, Nan X, Li Y, Li J. Comparative transcriptome analysis of two contrasting wolfberry genotypes during fruit development and ripening and characterization of the LrMYB1 transcription factor that regulates flavonoid biosynthesis. BMC Genomics 2020; 21:295. [PMID: 32272876 PMCID: PMC7147035 DOI: 10.1186/s12864-020-6663-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/10/2020] [Indexed: 11/25/2022] Open
Abstract
Background Lycium barbarum and L. ruthenicum have been used as traditional medicinal plants in China and other Asian counties for centuries. However, the molecular mechanisms underlying fruit development and ripening, as well as the associated production of medicinal and nutritional components, have been little explored in these two species. Results A competitive transcriptome analysis was performed to identify the regulators and pathways involved in the fruit ripening of red wolfberry (L. barbarum) and black wolfberry (L. ruthenicum) using an Illumina sequencing platform. In total, 155,606 genes and 194,385 genes were detected in red wolfberry (RF) and black wolfberry (BF), respectively. Of them, 20,335, 24,469, and 21,056 genes were differentially expressed at three different developmental stages in BF and RF. Functional categorization of the differentially expressed genes revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, anthocyanin biosynthesis, and sugar metabolism were the most differentially regulated processes during fruit development and ripening in the RF and BF. Furthermore, we also identified 38 MYB transcription factor-encoding genes that were differentially expressed during black wolfberry fruit development. Overexpression of LrMYB1 resulted in the activation of structural genes for flavonoid biosynthesis and led to an increase in flavonoid content, suggesting that the candidate genes identified in this RNA-seq analysis are credible and might offer important utility. Conclusion This study provides novel insights into the molecular mechanism of Lycium fruit development and ripening and will be of value to novel gene discovery and functional genomic studies.
Collapse
Affiliation(s)
- Cuiping Wang
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China. .,Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
| | - Yan Dong
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lizhen Zhu
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Libin Wang
- Biochip Research Center, the General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Li Yan
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Mengze Wang
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Qiang Zhu
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Xiongxiong Nan
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Yonghua Li
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Jian Li
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| |
Collapse
|
34
|
Aslam A, Zhao S, Azam M, Lu X, He N, Li B, Dou J, Zhu H, Liu W. Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development. PeerJ 2020; 8:e8259. [PMID: 31934503 PMCID: PMC6951286 DOI: 10.7717/peerj.8259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/20/2019] [Indexed: 02/05/2023] Open
Abstract
Grafting has been reported as a factor that influences fruit quality. However, a comprehensive study of the metabolic profile related to fruit quality and the underlying molecular mechanism in grafted watermelon has not been carried out. Metabolomics and transcriptome analysis were performed on both pumpkin-grafted watermelon and ungrafted watermelon at different developmental stages. In total, 56 primary metabolites were identified with either high or low abundance between ungrafted and pumpkin-grafted watermelon. The results indicated that ornithine, arginine, lysine (amino acids), glucose, sucrose, glucosamine (sugars), malic acid, fumaric acid and succinic acid (organic acids) were among the dominant metabolites influencing fruit quality. Additionally, comparative RNA sequence analysis on grafted and ungrafted watermelon yielded 729, 174, 128 and 356 differentially expressed genes at 10, 18, 26 and 34 days after pollination (DAP), respectively. Functional annotations of these genes indicated that grafting significantly altered the biological and metabolic processes related to fruit quality. Our comparative metabolomics and transcriptome analysis revealed that FBA2, FK, SuSy, SPS, IAI, AI and sugar transporter gene (SWT3b) might play a central role in the accumulation of glucose and sucrose, whereas higher malic acid content was attributed to high down regulation of ALMT13 and ALMT8 in pumpkin-grafted watermelon. Changes in the ornithine, glutamine, alanine, tyrosine, valine, asparagine, phenylalanine, arginine and tryptophan contents were consistent with the transcript level of their metabolic genes such as NAOD, GS, AGT, TaT, aDH1, OGDH, aDC, 4CL 1, PaL, CaT and two nitrate transporter genes (NRT1) in pumpkin-grafted watermelon. This study provides the basis for understanding the graft-responsive changes in the metabolic profile and regulatory mechanism related to fruit quality.
Collapse
Affiliation(s)
- Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Muhammad Azam
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| |
Collapse
|
35
|
Sun L, Zhang Y, Cui H, Zhang L, Sha T, Wang C, Fan C, Luan F, Wang X. Linkage Mapping and Comparative Transcriptome Analysis of Firmness in Watermelon ( Citrullus lanatus). FRONTIERS IN PLANT SCIENCE 2020; 11:831. [PMID: 32612625 PMCID: PMC7308538 DOI: 10.3389/fpls.2020.00831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/25/2020] [Indexed: 05/20/2023]
Abstract
Watermelon fruit texture and quality are determined by flesh firmness. As a quality trait, flesh firmness is controlled by multigenes. Defining the key regulatory factors of watermelon flesh firmness is of great significance for watermelon genetic breeding. In this study, the hard-flesh egusi seed watermelon PI186490 was used as the male parent, the soft-flesh cultivated watermelon W1-1 was used as the female parent, and 175 F2 generations were obtained from selfing F1. Primary mapping of the major genes controlling center flesh firmness was achieved by bulked-segregant analysis (BSA)-Seq analysis and molecular marker technology. Finally, major genes were delimited in the physical interval between 6,210,787 and 7,742,559 bp on chromosome 2 and between 207,553 and 403,137 bp on chromosome 8. The content of each cell wall component and hormone was measured, and comparative transcriptome analysis was performed during fruit development in watermelon. The protopectin, cellulose, hemicellulose, indole-3-acetic acid (IAA) and abscisic acid (ABA) contents were measured, and paraffin sections were made during the three fruit developmental stages. The results revealed that protopectin, celluloses, and hemicelluloses exhibited similar trends for flesh firmness, while the IAA and ABA concentrations continued to decrease with fruit ripening. Paraffin sections showed that PI186490 cells were more numerous, were more tightly packed, had clearer cell wall edges and had thicker cell walls than W1-1 cells at every developmental stage. Comparative transcriptome analysis was conducted on RNA samples of flesh during fruit development and ripening in W1-1 and PI186490. The results from the localization interval transcriptome analysis showed that Cla016033 (DUF579 family member), which may influence the cell wall component contents to adjust the flesh firmness in watermelon fruit, was different in W1-1 and PI186490 and that Cla012507 (MADS-box transcription factor) may be involved in the regulation of fruit ripening and affect the hardness of watermelon fruit.
Collapse
Affiliation(s)
- Lei Sun
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
- *Correspondence: Lei Sun,
| | - Yushu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Haonan Cui
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Lupeng Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Tongyun Sha
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Chaonan Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Chao Fan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
- Feishi Luan,
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, China
- Xuezheng Wang,
| |
Collapse
|
36
|
Garcia-Lozano M, Dutta SK, Natarajan P, Tomason YR, Lopez C, Katam R, Levi A, Nimmakayala P, Reddy UK. Transcriptome changes in reciprocal grafts involving watermelon and bottle gourd reveal molecular mechanisms involved in increase of the fruit size, rind toughness and soluble solids. PLANT MOLECULAR BIOLOGY 2020; 102:213-223. [PMID: 31845303 DOI: 10.1007/s11103-019-00942-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/04/2019] [Indexed: 05/07/2023]
Abstract
Transcriptome landscape reveals the molecular mechanisms involved in the improvement of fruit traits by the grafting of watermelon and bottle gourd. Grafting has been used as a sustainable alternative for watermelon breeding to control soil-borne pathogens and to increase tolerance to various abiotic stresses. However, some reports have shown that grafting can negatively affect the quality of fruits. Despite several field studies on the effects of grafting on fruit quality, the regulation of this process at the molecular level has not been revealed. The aim of this study was to elucidate various molecular mechanisms involved in different tissues of heterografted watermelon and bottle gourd plants. Grafting with bottle gourd rootstock increased the size and rind thickness of watermelon fruits, whereas that with watermelon rootstock produced bottle gourd fruits with higher total soluble solid content and thinner rinds. Correspondingly, genes related to ripening, softening, cell wall strengthening, stress response and disease resistance were differentially expressed in watermelon fruits. Moreover, genes associated mainly with sugar metabolism were differentially expressed in bottle gourd fruits. RNA-seq revealed more than 400 mobile transcripts across the heterografted sets. More than half of these were validated from PlaMoM, a database for plant mobile macromolecules. In addition, some of these mobile transcripts contained a transfer RNA-like structure. Other RNA motifs were also enriched in these transcripts, most with a biological role based on GO analysis. This transcriptome study provided a comprehensive understanding of various molecular mechanisms underlying grafted tissues in watermelon.
Collapse
Affiliation(s)
- Marleny Garcia-Lozano
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Sudip Kumar Dutta
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Yan R Tomason
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Carlos Lopez
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Ramesh Katam
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL, 32317, USA
| | - Amnon Levi
- USDA, ARS, U.S. Vegetable Lab, 2700 Savannah Highway, Charleston, SC, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA.
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA.
| |
Collapse
|
37
|
Shi T, Joshi V, Joshi M, Vitha S, Gibbs H, Wang K, Okumoto S. Broad-Spectrum Amino Acid Transporters ClAAP3 and ClAAP6 Expressed in Watermelon Fruits. Int J Mol Sci 2019; 20:E5855. [PMID: 31766598 PMCID: PMC6928636 DOI: 10.3390/ijms20235855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022] Open
Abstract
Watermelon fruit contains a high percentage of amino acid citrulline (Cit) and arginine (Arg). Cit and Arg accumulation in watermelon fruit are most likely mediated by both de novo synthesis from other amino acids within fruits and direct import from source tissues (leaves) through the phloem. The amino acid transporters involved in the import of Cit, Arg, and their precursors into developing fruits of watermelon have not been reported. In this study, we have compiled the list of putative amino acid transporters in watermelon and characterized transporters that are expressed in the early stage of fruit development. Using the yeast complementation study, we characterized ClAAP3 (Cla023187) and ClAAP6 (Cla023090) as functional amino acid transporters belonging to the family of amino acid permease (AAP) genes. The yeast growth and uptake assays of radiolabeled amino acid suggested that ClAAP3 and ClAAP6 can transport a broad spectrum of amino acids. Expression of translational fusion proteins with a GFP reporter in Nicotiana benthamiana leaves confirmed the ER- and plasma membrane-specific localization, suggesting the role of ClAAP proteins in the cellular import of amino acids. Based on the gene expression profiles and functional characterization, ClAAP3 and ClAAP6 are expected to play a major role in regulation of amino acid import into developing watermelon fruits.
Collapse
Affiliation(s)
- Tianran Shi
- Department of Soil and Crop, Texas A&M, College Station, TX 77843, USA;
- College of Grassland Science and Technology, China Agricultural University, Beijing 100083, China;
| | - Vijay Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA; (V.J.); (M.J.)
| | - Madhumita Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA; (V.J.); (M.J.)
| | - Stanislav Vitha
- Microscopy and Imaging Center, Texas A&M, College Station, TX, 77843, USA; (S.V.); (H.G.)
| | - Holly Gibbs
- Microscopy and Imaging Center, Texas A&M, College Station, TX, 77843, USA; (S.V.); (H.G.)
| | - Kehua Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100083, China;
| | - Sakiko Okumoto
- Department of Soil and Crop, Texas A&M, College Station, TX 77843, USA;
| |
Collapse
|
38
|
Subburaj S, Lee K, Jeon Y, Tu L, Son G, Choi S, Lim YP, McGregor C, Lee GJ. Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content. PLoS One 2019; 14:e0223441. [PMID: 31596903 PMCID: PMC6785133 DOI: 10.1371/journal.pone.0223441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Cultivated watermelon (Citrullus lanatus) is one of the most important food crops in the Cucurbitaceae family. Diversification after domestication has led cultivated watermelons to exhibit diverse fruit flesh colors, including red, yellow, and orange. Recently, there has been increased interest in red-fleshed watermelons because they contain the antioxidant cis-isomeric lycopene. We performed whole genome resequencing (WGRS) of 24 watermelons with different flesh colors to identify single-nucleotide polymorphisms (SNPs) related to high lycopene content. The resequencing data revealed 203,894-279,412 SNPs from read mapping between inbred lines and the 97103 reference genome. In total, 295,065 filtered SNPs were identified, which had an average polymorphism information content of 0.297. Most of these SNPs were intergenic (90.1%) and possessed a transversion (Tv) rate of 31.64%. Overall, 2,369 SNPs were chosen at 0.5 Mb physical intervals to analyze genetic diversity across the 24 inbred lines. A neighbor-joining dendrogram and principal coordinate analysis (PCA) based on the 2,369 SNPs revealed that the 24 inbred lines could be grouped into high and low lycopene-type watermelons. In addition, we analyzed SNPs that could discriminate high lycopene content, red-fleshed watermelon from low lycopene, yellow or orange watermelon inbred lines. For validation, 19 SNPs (designated as WMHL1-19) were chosen randomly, and cleavage amplified polymorphic sequence (CAPS) markers were designed. Genotyping of the above 24 lines and 12 additional commercial cultivars using WMHL1-19 CAPS markers resulted in match rates of over 0.92 for most validated markers in correlation with the flesh color phenotypes. Our results provide valuable genomic information regarding the high lycopene content phenotype of red-fleshed cultivated watermelons, and the identified SNPs will be useful for the development of molecular markers in the marker-assisted breeding of watermelons with high lycopene content.
Collapse
Affiliation(s)
- Saminathan Subburaj
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Kayoun Lee
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Yongsam Jeon
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Luhua Tu
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Gilwoo Son
- Breeding Institute, Hyundai Seed Co Ltd., Yeoju, Gyeonggi, Republic of Korea
| | - SuBok Choi
- Asia Seed, Co., Ltd., Seoul, Republic of Korea
| | - Yong-Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA, United States of America
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| |
Collapse
|
39
|
Dos Santos CP, Batista MC, da Cruz Saraiva KD, Roque ALM, de Souza Miranda R, Alexandre E Silva LM, Moura CFH, Alves Filho EG, Canuto KM, Costa JH. Transcriptome analysis of acerola fruit ripening: insights into ascorbate, ethylene, respiration, and softening metabolisms. PLANT MOLECULAR BIOLOGY 2019; 101:269-296. [PMID: 31338671 DOI: 10.1007/s11103-019-00903-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The first transcriptome coupled to metabolite analyses reveals major trends during acerola fruit ripening and shed lights on ascorbate, ethylene signalling, cellular respiration, sugar accumulation, and softening key regulatory genes. Acerola is a fast growing and ripening fruit that exhibits high amounts of ascorbate. During ripening, the fruit experience high respiratory rates leading to ascorbate depletion and a quickly fragile and perishable state. Despite its growing economic importance, understanding of its developmental metabolism remains obscure due to the absence of genomic and transcriptomic data. We performed an acerola transcriptome sequencing that generated over 600 million reads, 40,830 contigs, and provided the annotation of 25,298 unique transcripts. Overall, this study revealed the main metabolic changes that occur in the acerola ripening. This transcriptional profile linked to metabolite measurements, allowed us to focus on ascorbate, ethylene, respiration, sugar, and firmness, the major metabolism indicators for acerola quality. Our results suggest a cooperative role of several genes involved in AsA biosynthesis (PMM, GMP1 and 3, GME1 and 2, GGP1 and 2), translocation (NAT3, 4, 6 and 6-like) and recycling (MDHAR2 and DHAR1) pathways for AsA accumulation in unripe fruits. Moreover, the association of metabolites with transcript profiles provided a comprehensive understanding of ethylene signalling, respiration, sugar accumulation and softening of acerola, shedding light on promising key regulatory genes. Overall, this study provides a foundation for further examination of the functional significance of these genes to improve fruit quality traits.
Collapse
Affiliation(s)
- Clesivan Pereira Dos Santos
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Mathias Coelho Batista
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Federal Institute of Education, Science and Technology of Paraíba, Campus Princesa Isabel, Princesa Isabel, Paraíba, Brazil
| | - André Luiz Maia Roque
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | | | | | | | | | | | - José Hélio Costa
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil.
| |
Collapse
|
40
|
Joshi V, Joshi M, Silwal D, Noonan K, Rodriguez S, Penalosa A. Systematized biosynthesis and catabolism regulate citrulline accumulation in watermelon. PHYTOCHEMISTRY 2019; 162:129-140. [PMID: 30884257 DOI: 10.1016/j.phytochem.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/20/2019] [Accepted: 03/02/2019] [Indexed: 05/22/2023]
Abstract
Citrulline, a non-protein amino acid, is present in large amounts in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai Cucurbitaceae) fruits. Amino acid profiling of various tissues of cv. Charleston Gray during plant development confirmed progressive accumulation of citrulline only in the fruit flesh and rind tissues. Citrulline content was positively correlated with precursor (ornithine) and by-product (arginine) amino acids during fruit ripening. Genetic variation in the partitioning of citrulline and related amino acids in the flesh and rind tissues was confirmed in a sub-set of watermelon cultivars. No correlation was established between morphological fruit traits (size and rind properties) and citrulline content. To understand the regulation of citrulline accumulation, we investigated the expression of genes associated with its biosynthesis and catabolism in flesh and rind tissues during fruit development. The expression of ornithine carbamoyltransferase (OTC) involved in the ultimate step of citrulline synthesis remained steady in both tissues. The expression of N-acetylornithine aminotransferase (N-AOA) involved in the production of N-acetylornithine and N-acetylornithine deacetylase (AOD-3) involved in ornithine synthesis coincided with increasing accumulation of citrulline in flesh and rind tissues during fruit development. Down-regulation N-acetylornithine-glutamate acetyltransferase (N-AOGA) suggests the subordinate role of the non-cyclic pathway in citrulline synthesis. Eccentricity between citrulline accumulation and expression of carbamoyl phosphate synthases (CPS-1, CPS-2) during fruit development suggest that the localized synthesis of carbamoyl phosphates may not be required for citrulline synthesis. Most genes involved in citrulline break-down (Argininosuccinate synthases - ASS-1, ASS-2, and ASS-3, Argininosuccinate lyases - ASL-1, Ornithine decarboxylase - ODC, Arginine decarboxylase - ADC) were consistently down-regulated during fruit development.
Collapse
Affiliation(s)
- Vijay Joshi
- Texas A&M AgriLife Research Center, Texas A&M University, Uvalde, TX, 78801, USA.
| | - Madhumita Joshi
- Texas A&M AgriLife Research Center, Texas A&M University, Uvalde, TX, 78801, USA
| | - Diwas Silwal
- Department of Horticultural Sciences, College Station, TX, 77843, USA
| | - Kayce Noonan
- NovoThelium, San Antonio Technology Center, Texas, 78229, USA
| | | | | |
Collapse
|
41
|
Gao L, Zhao S, Lu X, He N, Zhu H, Dou J, Liu W. Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon. PLoS One 2018; 13:e0190096. [PMID: 29324867 PMCID: PMC5764247 DOI: 10.1371/journal.pone.0190096] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/08/2017] [Indexed: 01/06/2023] Open
Abstract
Soluble sugars and organic acids are important components of fruit flavor and have a strong impact on the overall organoleptic quality of watermelon (Citrullus lanatus) fruit. Several studies have analyzed the expression levels of the genes related to soluble sugar accumulation and the dynamic changes in their content during watermelon fruit development and ripening. Nevertheless, to date, there have been no reports on the organic acid content in watermelon or the genes regulating their synthesis. In this study, the soluble sugars and organic acids in watermelon were measured and a comparative transcriptome analysis was performed to identify the key genes involved in the accumulation of these substances during fruit development and ripening. The watermelon cultivar '203Z' and its near-isogenic line (NIL) 'SW' (in the '203Z' background) were used as experimental materials. The results suggested that soluble sugar consist of fructose, glucose and sucrose while malic-, citric-, and oxalic acids are the primary organic acids in watermelon fruit. Several differentially expressed genes (DEGs) related to soluble sugar- and organic acid accumulation and metabolism were identified. These include the DEGs encoding raffinose synthase, sucrose synthase (SuSy), sucrose-phosphate synthase (SPSs), insoluble acid invertases (IAI), NAD-dependent malate dehydrogenase (NAD-cyt MDH), aluminum-activated malate transporter (ALMT), and citrate synthase (CS). This is the first report addressing comparative transcriptome analysis via NILs materials in watermelon fruit. These findings provide an important basis for understanding the molecular mechanism that leads to soluble sugar and organic acid accumulation and metabolism during watermelon fruit development and ripening.
Collapse
Affiliation(s)
- Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| |
Collapse
|
42
|
Li X, An M, Xia Z, Bai X, Wu Y. Transcriptome analysis of watermelon (Citrullus lanatus) fruits in response to Cucumber green mottle mosaic virus (CGMMV) infection. Sci Rep 2017; 7:16747. [PMID: 29196660 PMCID: PMC5711961 DOI: 10.1038/s41598-017-17140-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/22/2017] [Indexed: 11/22/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) belongs to the Tobamovirus genus and is a major global plant virus on cucurbit plants. It causes severe disease symptoms on infected watermelon plants (Citrullus lanatus), particularly inducing fruit decay. However, little is known about the molecular mechanism of CGMMV-induced watermelon fruit decay. For this study, comparative analysis of transcriptome profiles of CGMMV-inoculated and mock-inoculated watermelon fruits were conducted via RNA-Seq. A total of 1,621 differently expressed genes (DEGs) were identified in CGMMV-inoculated watermelon, among which 1,052 were up-regulated and 569 were down-regulated. Functional annotation analysis showed that several DEGs were involved in carbohydrate metabolism, hormone biosynthesis and signaling transduction, secondary metabolites biosynthesis, and plant-pathogen interactions. We furthermore found that some DEGs were related to cell wall components and photosynthesis, which may directly be involve in the development of the symptoms associated with diseased watermelons. To confirm the RNA-Seq data, 15 DEGs were selected for gene expression analysis by qRT-PCR. The results showed a strong correlation between these two sets of data. Our study identified many candidate genes for further functional studies during CGMMV-watermelon interactions, and will furthermore help to clarify the understanding of pathogenic mechanism underlying CGMMV infection in cucurbit plants.
Collapse
Affiliation(s)
- Xiaodong Li
- Plant Virus Laboratory of Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Mengnan An
- Plant Virus Laboratory of Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zihao Xia
- Plant Virus Laboratory of Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaojiao Bai
- Plant Virus Laboratory of Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuanhua Wu
- Plant Virus Laboratory of Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China.
| |
Collapse
|
43
|
Rhee SJ, Kwon T, Seo M, Jang YJ, Sim TY, Cho S, Han SW, Lee GP. De novo-based transcriptome profiling of male-sterile and fertile watermelon lines. PLoS One 2017; 12:e0187147. [PMID: 29095876 PMCID: PMC5667795 DOI: 10.1371/journal.pone.0187147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/14/2017] [Indexed: 12/23/2022] Open
Abstract
The whole-genome sequence of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), a valuable horticultural crop worldwide, was released in 2013. Here, we compared a de novo-based approach (DBA) to a reference-based approach (RBA) using RNA-seq data, to aid in efforts to improve the annotation of the watermelon reference genome and to obtain biological insight into male-sterility in watermelon. We applied these techniques to available data from two watermelon lines: the male-sterile line DAH3615-MS and the male-fertile line DAH3615. Using DBA, we newly annotated 855 watermelon transcripts, and found gene functional clusters predicted to be related to stimulus responses, nucleic acid binding, transmembrane transport, homeostasis, and Golgi/vesicles. Among the DBA-annotated transcripts, 138 de novo-exclusive differentially-expressed genes (DEDEGs) related to male sterility were detected. Out of 33 randomly selected newly annotated transcripts and DEDEGs, 32 were validated by RT-qPCR. This study demonstrates the usefulness and reliability of the de novo transcriptome assembly in watermelon, and provides new insights for researchers exploring transcriptional blueprints with regard to the male sterility.
Collapse
Affiliation(s)
- Sun-Ju Rhee
- Department of Integrative Plant Science, Chung-Ang University, Ansung, Republic of Korea
| | - Taehyung Kwon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minseok Seo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak Gu, Seoul, Republic of Korea
- CHO&KIM Genomics, C-1008, H Business Park, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea
| | - Yoon Jeong Jang
- Department of Integrative Plant Science, Chung-Ang University, Ansung, Republic of Korea
| | - Tae Yong Sim
- Department of Integrative Plant Science, Chung-Ang University, Ansung, Republic of Korea
| | - Seoae Cho
- CHO&KIM Genomics, C-1008, H Business Park, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea
| | - Sang-Wook Han
- Department of Integrative Plant Science, Chung-Ang University, Ansung, Republic of Korea
- * E-mail: (SWH); (GPL)
| | - Gung Pyo Lee
- Department of Integrative Plant Science, Chung-Ang University, Ansung, Republic of Korea
- * E-mail: (SWH); (GPL)
| |
Collapse
|
44
|
Joshi V, Fernie AR. Citrulline metabolism in plants. Amino Acids 2017; 49:1543-1559. [PMID: 28741223 DOI: 10.1007/s00726-017-2468-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/17/2017] [Indexed: 11/28/2022]
Abstract
Citrulline was chemically isolated more than 100 years ago and is ubiquitous in animals, plants, bacteria, and fungi. Most of the research on plant citrulline metabolism and transport has been carried out in Arabidopsis thaliana and the Cucurbitaceae family, particularly in watermelon which accumulates this non-proteinogenic amino acid to very high levels. Industrially, citrulline is produced via specially optimized microbial strains; however, the amounts present in watermelon render it an economically viable source providing that other high-value compounds can be co-extracted. In this review, we provide an overview of our current understanding of citrulline biosynthesis, transport, and catabolism in plants additionally pointing out significant gaps in our knowledge which need to be closed by future experimentation. This includes the identification of further potential enzymes of citrulline metabolism as well as obtaining a far better spatial resolution of both sub-cellular and long-distance partitioning of citrulline. We further discuss what is known concerning the biological function of citrulline in plants paying particular attention to the proposed roles in scavenging of excess NH4+ and as a compatible solute.
Collapse
Affiliation(s)
- Vijay Joshi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Uvalde, TX, 78801, USA.
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam-Golm, Germany
| |
Collapse
|
45
|
Gupta S, Yadav BS, Raj U, Freilich S, Varadwaj PK. Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency. FRONTIERS IN PLANT SCIENCE 2017; 8:1025. [PMID: 28690617 PMCID: PMC5479913 DOI: 10.3389/fpls.2017.01025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/29/2017] [Indexed: 05/11/2023]
Abstract
Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data. A set of 435 statistically significant probes encoding 398 Nutrient Deficiency Response Genes (NRGs) responding at-least one nutrients deficiency (ND) were identified. Out of them 55 NRGs were found to response to minimum two ND. Singular Enrichment Analysis (SEA) predicts ontological based classifications and functional analysis of NRGs in different cellular/molecular pathways involved in root development and growth. Functional annotation and reaction mechanism of differentially expressed genes, proteins/enzymes in the different metabolic pathway through MapMan analysis were explored. Further the meta-analysis was performed to revels the active involvement each NRGs in distinct tissues and their comparative potential expression analysis in different stress conditions. The study results in exploring the role of major acting candidate genes such as Non-specific serine/threonine protein kinase, Xyloglucan endotransglucosylase/hydrolase, Peroxides, Glycerophosphoryl diester phosphodiesterase, S-adenosylmethionine decarboxylase proenzyme, Dehydrin family proteins, Transcription factors, Membrane Proteins, Metal binding proteins, Photosystem proteins, Transporter and Transferase associated in different metabolic pathways. Finally, the differences of transcriptional responses in the soil-grown root of T. aestivum cv. and in-vitro grown model plants under nutrients deficiency were summarized.
Collapse
Affiliation(s)
- Saurabh Gupta
- Department of Bioinformatics, Indian Institute of Information TechnologyAllahabad, Allahabad, India
| | - Brijesh S. Yadav
- Department of Molecular Biology and Ecology of Plants, Tel Aviv UniversityTel Aviv, Israel
| | - Utkarsh Raj
- Department of Bioinformatics, Indian Institute of Information TechnologyAllahabad, Allahabad, India
| | - Shiri Freilich
- Institute of Plant Sciences, Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
| | - Pritish K. Varadwaj
- Department of Bioinformatics, Indian Institute of Information TechnologyAllahabad, Allahabad, India
- *Correspondence: Pritish K. Varadwaj
| |
Collapse
|