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Zhang L, Zhang R, Yan P, Zeng L, Zhao W, Feng H, Mu R, Hou W. PE ( Prickly Eggplant) encoding a cytokinin-activating enzyme responsible for the formation of prickles in eggplant. HORTICULTURE RESEARCH 2024; 11:uhae134. [PMID: 38974191 PMCID: PMC11226868 DOI: 10.1093/hr/uhae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/27/2024] [Indexed: 07/09/2024]
Abstract
Eggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, posing challenges during cultivation, harvesting, and transportation, making them an undesirable agronomic trait. However, the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood, impeding genetic improvements. In this study, genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene, termed PE (Prickly Eggplant). Subsequent bulk segregant RNA-sequencing (BSR-seq) and linkage analysis preliminarily mapped PE to chromosome 6. This locus was then fine mapped to a 9233 bp interval in a segregating population of 1109 plants, harboring only one candidate gene, SmLOG1, which encodes a LONELY GUY (LOG)-family cytokinin biosynthetic enzyme. Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles. CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line 'PI 381159' abolished prickles across all tissues, confirming its critical role in prickle morphogenesis. Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region. We developed a cleaved amplified polymorphic sequences (CAPS) marker from a distinct SNP located at -735-bp within the SmLOG1 promoter, finding significant association with prickle variation in 190 eggplant germplasms. These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection (MAS) for breeding prickleless cultivars.
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Affiliation(s)
- Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Runzhi Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Ping Yan
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Liqian Zeng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Huiqian Feng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Ruyu Mu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
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Li XX, Lai YS. The Development and Application of Vegetable Genomics Increase the Efficiency of Exploring New Gene Resources for Vegetables. Int J Mol Sci 2024; 25:6906. [PMID: 39000015 PMCID: PMC11241489 DOI: 10.3390/ijms25136906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 07/14/2024] Open
Abstract
Vegetables, as indispensable non-staple foods in people's daily diet, provide a variety of essential vitamins, minerals, and other nutrients, as well as special phytochemicals, which are recognized as functional components for human nutritional balance or medicinal purposes [...].
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Affiliation(s)
- Xi-Xiang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu 611100, China
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3
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Zhou Y, Zhao M, Shen Q, Zhang M, Wang C, Zhang Y, Yang Q, Bo Y, Hu Z, Yang J, Zhang M, Lyu X. Genetic mapping reveals a candidate gene CmoFL1 controlling fruit length in pumpkin. FRONTIERS IN PLANT SCIENCE 2024; 15:1408602. [PMID: 38867882 PMCID: PMC11168575 DOI: 10.3389/fpls.2024.1408602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/06/2024] [Indexed: 06/14/2024]
Abstract
Fruit length (FL) is an important economical trait that affects fruit yield and appearance. Pumpkin (Cucurbita moschata Duch) contains a wealth genetic variation in fruit length. However, the natural variation underlying differences in pumpkin fruit length remains unclear. In this study, we constructed a F2 segregate population using KG1 producing long fruit and MBF producing short fruit as parents to identify the candidate gene for fruit length. By bulked segregant analysis (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) approach of fine mapping, we obtained a 50.77 kb candidate region on chromosome 14 associated with the fruit length. Then, based on sequence variation, gene expression and promoter activity analyses, we identified a candidate gene (CmoFL1) encoding E3 ubiquitin ligase in this region may account for the variation of fruit length. One SNP variation in promoter of CmoFL1 changed the GT1CONSENSUS, and DUAL-LUC assay revealed that this variation significantly affected the promoter activity of CmoFL1. RNA-seq analysis indicated that CmoFL1 might associated with the cell division process and negatively regulate fruit length. Collectively, our work identifies an important allelic affecting fruit length, and provides a target gene manipulating fruit length in future pumpkin breeding.
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Affiliation(s)
- Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Meng Zhao
- 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
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Chenhao Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yutong Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinrong Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, 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
- Hainan Institute of Zhejiang University, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Wang B, Chen X, Huang S, Tan J, Zhang H, Wang J, Chen R, Zhang M. Bulk Segregant Analysis Sequencing and RNA-Seq Analyses Reveal Candidate Genes Associated with Sepal Color Phenotype of Eggplant ( Solanum melongena L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1385. [PMID: 38794455 PMCID: PMC11124939 DOI: 10.3390/plants13101385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Eggplant is a highly significant vegetable crop and extensively cultivated worldwide. Sepal color is considered one of the major commercial traits of eggplant. Eggplant sepals develop from petals, and sepals have the ability to change color by accumulating anthocyanins, but whether the eggplants in sepal and their biosynthetic pathways are the same as those in petals is not known. To date, little is known about the underlying mechanisms of sepal color formation. In this study, we performed bulked segregant analysis and transcriptome sequencing using eggplant sepals and obtained 1,452,898 SNPs and 182,543 InDel markers, respectively, as well as 123.65 Gb of clean data using transcriptome sequencing. Through marker screening, the genes regulating eggplant sepals were localized to an interval of 2.6 cM on chromosome 10 by bulked segregant analysis sequencing and transcriptome sequencing and co-analysis, combined with screening of molecular markers by capillary electrophoresis. Eight possible candidate genes were then screened to further interpret the regulatory incentives for the eggplant sepal color.
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Affiliation(s)
| | | | | | | | | | | | | | - Min Zhang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China; (B.W.); (X.C.); (S.H.); (J.T.); (H.Z.); (J.W.); (R.C.)
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5
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Ai J, Wang W, Hu T, Hu H, Wang J, Yan Y, Pang H, Wang Y, Bao C, Wei Q. Identification of Quantitative Trait Loci and Candidate Genes Controlling Seed Dormancy in Eggplant ( Solanum melongena L.). Genes (Basel) 2024; 15:415. [PMID: 38674350 PMCID: PMC11049636 DOI: 10.3390/genes15040415] [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: 03/04/2024] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
Seed dormancy is a life adaptation trait exhibited by plants in response to environmental changes during their growth and development. The dormancy of commercial seeds is the key factor affecting seed quality. Eggplant seed dormancy is controlled by quantitative trait loci (QTLs), but reliable QTLs related to eggplant dormancy are still lacking. In this study, F2 populations obtained through the hybridization of paternally inbred lines with significant differences in dormancy were used to detect regulatory sites of dormancy in eggplant seeds. Three QTLs (dr1.1, dr2.1, and dr6.1) related to seed dormancy were detected on three chromosomes of eggplant using the QTL-Seq technique. By combining nonsynonymous sites within the candidate regions and gene functional annotation analysis, nine candidate genes were selected from three QTL candidate regions. According to the germination results on the eighth day, the male parent was not dormant, but the female parent was dormant. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression of nine candidate genes, and the Smechr0201082 gene showed roughly the same trend as that in the phenotypic data. We proposed Smechr0201082 as the potential key gene involved in regulating the dormancy of eggplant seeds. The results of seed experiments with different concentrations of gibberellin A3 (GA3) showed that, within a certain range, the higher the gibberellin concentration, the earlier the emergence and the higher the germination rate. However, higher concentrations of GA3 may have potential effects on eggplant seedlings. We suggest the use of GA3 at a concentration of 200-250 mg·L-1 to treat dormant seeds. This study provides a foundation for the further exploration of genes related to the regulation of seed dormancy and the elucidation of the molecular mechanism of eggplant seed dormancy and germination.
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Affiliation(s)
- Jiaqi Ai
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
- College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou 310021, China
| | - Wuhong Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
| | - Tianhua Hu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
| | - Haijiao Hu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
| | - Jinglei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
| | - Yaqin Yan
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
| | - Hongtao Pang
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
- College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou 310021, China
| | - Yong Wang
- Zhumadian Academy of Agricultural Sciences, Zhumadian 463000, China;
| | - Chonglai Bao
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
| | - Qingzhen Wei
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.A.); (W.W.); (T.H.); (H.H.); (J.W.); (Y.Y.); (H.P.); (C.B.)
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6
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Xue C, Sun L, Liu W, Gao Y, Pan X, Yang X, Tai P. Decreased cadmium content in Solanum melongena induced by grafting was related to glucosinolates synthesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170115. [PMID: 38232848 DOI: 10.1016/j.scitotenv.2024.170115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Grafting is an effective horticultural method to reduce Cd accumulation in crops. However, the mechanism of grafting inducing the decrease in Cd content in scions remains unclear. This study evaluated the effect of grafting on fruit quality, yield, and Cd content of Solanum melongena, and explored the potential mechanism of grafting reducing Cd content in scions. In the low Cd-contaminated soil, compared with un-grafted (UG) and self-grafted plants (SG), the fruit yield of inter-grafted plants (EG) increased by 38 %, and the fruit quality was not markedly affected. In EG, the decrease in total S and Cd content was not related to organic acids and thiol compounds. The decrease in total S and Cd content in EG leaves and fruits was closely related to the synthesis and transportation of glucosinolates (GSL). The genes encoding GSL synthesis in leaves, such as basic helix-loop-helix, myelocytomatosis proteins, acetyl-CoA, cytochrome P450, and glutathione S-transferases, were significantly downregulated. In EG leaves, the contents of five of the eight amino acids involved in GSL synthesis decreased significantly (P < 0.05). Notably, total GSL in EG stems, leaves, and fruits had a significant linear correlation with total S and Cd. In summary, the decrease in total S and Cd content in scions caused by grafting is closely related to GSL. Our findings provide a theoretical basis for the safe use of Cd-contaminated soil, exploring the long-distance transport of Cd in plants and cultivating crops with low Cd accumulation.
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Affiliation(s)
- Chenyang Xue
- Key Lab of Eco-restoration of Reginal Contaminated Environmental, Shenyang University, Ministry of Education, Shenyang 110044, China; Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lizong Sun
- Key Lab of Eco-restoration of Reginal Contaminated Environmental, Shenyang University, Ministry of Education, Shenyang 110044, China; Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Wanbin Liu
- Dalian Pulandian District Modern Agricultural Production Development Service Center, China
| | - Yingmei Gao
- Shenyang Agricultural University, Shenyang 110016, China
| | - Xiangwen Pan
- Key Laboratory of Molecular Breeding and Design, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xinyao Yang
- Key Lab of Eco-restoration of Reginal Contaminated Environmental, Shenyang University, Ministry of Education, Shenyang 110044, China
| | - Peidong Tai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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7
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Li S, Dong Y, Li D, Shi S, Zhao N, Liao J, Liu Y, Chen H. Eggplant transcription factor SmMYB5 integrates jasmonate and light signaling during anthocyanin biosynthesis. PLANT PHYSIOLOGY 2024; 194:1139-1165. [PMID: 37815242 DOI: 10.1093/plphys/kiad531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 10/11/2023]
Abstract
Low light conditions severely suppress anthocyanin synthesis in fruit skins, leading to compromised fruit quality in eggplant (Solanum melongena L.) production. In this study, we found that exogenous methyl-jasmonate (MeJA) application can effectively rescue the poor coloration of the eggplant pericarp under low light conditions. However, the regulatory relationship between jasmonate and light signaling for regulating anthocyanin synthesis remains unclear. Here, we identified a JA response factor, SmMYB5, as an anthocyanin positive regulator by applying RNA-sequencing and characterization of transgenic plants. Firstly, we resolved that SmMYB5 can interact with TRANSPARENT TESTA8 (SmTT8), an anthocyanin-promoted BASIC HELIX-LOOP-HELIX (bHLH) transcription factor, to form the SmMYB5-SmTT8 complex and activate CHALCONE SYNTHASE (SmCHS), FLAVANONE-3-HYDROXYLASE (SmF3H), and ANTHOCYANIN SYNTHASE (SmANS) promoters by direct binding. Secondly, we revealed that JA signaling repressors JASMONATE ZIM DOMAIN5 (SmJAZ5) and SmJAZ10 can interfere with the stability and transcriptional activity of SmMYB5-SmTT8 by interacting with SmMYB5. JA can partially rescue the transcriptional activation of SmF3H and SmANS promoters by inducing SmJAZ5/10 degradation. Thirdly, we demonstrated that the protein abundance of SmMYB5 is regulated by light. CONSTITUTIVELY PHOTOMORPHOGENIC1 (SmCOP1) interacts with SmMYB5 to trigger SmMYB5 degradation via the 26S proteasome pathway. Finally, we delineated a light-dependent JA-SmMYB5 signaling pathway that promotes anthocyanin synthesis in eggplant fruit skins. These results provide insights into the mechanism of the integration of JA and light signals in regulating secondary metabolite synthesis in plants.
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Affiliation(s)
- Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanxiao Dong
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Na Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jielei Liao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Zheng Y, Liu Q, Shi S, Zhu X, Chen Y, Lin S, Tian H, Huang L, Wei H. Nitrogen Deficiency Enhances Eggplant Defense against Western Flower Thrips via the Induction of the Jasmonate Pathway. PLANTS (BASEL, SWITZERLAND) 2024; 13:273. [PMID: 38256826 PMCID: PMC10820576 DOI: 10.3390/plants13020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 01/13/2024] [Indexed: 01/24/2024]
Abstract
Plant nutrition is connected to defense against insect herbivores, but the exact mechanism underlying the effect of the nitrogen (N) supply on the anti-herbivore capacity of eggplants (Solanum melongena) has not been studied in detail. Therefore, we examined the impact of low (LN, 0.5 mM) and high (HN, 5 mM) nitrate levels on eggplant resistance against the western flower thrips Frankliniella occidentalis (WFT), a major destructive eggplant pest. Our results showed that LN plants displayed enhanced defense responses to WFT compared to HN plants. This included increased transcript levels of key genes in the jasmonic acid (JA) pathway, the accumulation of JA-amido conjugates (jasmonoyl-isoleucine, jasmonoyl-phenylalanine, and jasmonoyl-valine), JA precursor (12-oxophytodienoic acid), and methyl jasmonate, higher transcript levels of defense marker genes (MPK3, MPK7, and WRKY53), and increased activities of polyphenol oxidase and peroxidase upon a WFT attack. Our findings suggest that N deficiency can prime JA-mediated defense responses in eggplants, resulting in increased anti-herbivore resistance.
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Affiliation(s)
- Yueqin Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Qianxia Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
| | - Shuang Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
| | - Xiaowen Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Shuo Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Houjun Tian
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Lanyan Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
| | - Hui Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
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10
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Shen L, Xia X, Zhang L, Yang S, Yang X. Genome-Wide Identification of Catalase Gene Family and the Function of SmCAT4 in Eggplant Response to Salt Stress. Int J Mol Sci 2023; 24:16979. [PMID: 38069301 PMCID: PMC10706941 DOI: 10.3390/ijms242316979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Salinity is an important abiotic stress, damaging plant tissues by causing a burst of reactive oxygen species (ROS). Catalase (CAT) enzyme coded by Catalase (CAT) genes are potent in reducing harmful ROS and hydrogen peroxide (H2O2) produced. Herein, we performed bioinformatics and functional characterization of four SmCAT genes, retrieved from the eggplant genome database. Evolutionary analysis CAT genes revealed that they are divided into subgroups I and II. The RT-qPCR analysis of SmCAT displayed a differential expression pattern in response to abiotic stresses. All the CAT proteins of eggplant were localized in the peroxisome, except for SmCAT4, which localized in the cytomembrane and nucleus. Silencing of SmCAT4 compromised the tolerance of eggplant to salt stress. Suppressed expression levels of salt stress defense related genes SmTAS14 and SmDHN1, as well as increase of H2O2 content and decrease of CAT enzyme activity was observed in the SmCAT4 silenced eggplants. Our data provided insightful knowledge of CAT gene family in eggplant. Positive regulation of eggplant response to salinity by SmCAT4 provides resource for future breeding programs.
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Affiliation(s)
| | | | | | | | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (L.S.); (X.X.); (L.Z.); (S.Y.)
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11
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Gramazio P, Alonso D, Arrones A, Villanueva G, Plazas M, Toppino L, Barchi L, Portis E, Ferrante P, Lanteri S, Rotino GL, Giuliano G, Vilanova S, Prohens J. Conventional and new genetic resources for an eggplant breeding revolution. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.
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Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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12
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Ma W, Du J, Yu X, Chen K, Ming Y, Jiang L, Chen T, Ji D. Genome-Wide Identification and Analysis of Catharanthus roseus Receptor-like Kinase 1-like Proteins in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:3379. [PMID: 37836119 PMCID: PMC10574150 DOI: 10.3390/plants12193379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
As an important member of the plant receptor-like kinases, Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) plays vital roles in plant growth and development, as well as biotic and abiotic stress response. Numerous CrRLK1Ls have been identified and analyzed in various plant species, while our knowledge about eggplant (Solanum melongena L.) CrRLK1Ls is still scarce. Utilizing state-of-the-art genomic data, we conducted the first genome-wide identification and analysis of CrRLK1L proteins in eggplant. In this study, 32 CrRLK1L proteins were identified and analyzed in eggplant. A subsequent gene structure and protein domain analysis showed that the identified eggplant CrRLK1Ls possessed typical features of CrRLK1Ls. A subcellular localization prediction demonstrated that these proteins mostly localized on the plasma membrane. A collinearity analysis showed that some eggplant CrRLK1L genes had predicted intraspecies or interspecies evolutionary duplication events. Promoter analysis suggests that eggplant CrRLK1Ls may be involved in plant hormone signaling, host-pathogen interactions, and environmental responses. Based on transcriptomic gene expression analysis, it is indicated that eggplant CrRLK1Ls may be involved in the resistance response of eggplant to Botrytis cinerea. Together, these results will give us a theoretical foundation and guidance for elaborating the biological functions of CrRLK1Ls in eggplant growth, development, and resistance response.
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Affiliation(s)
- Wenpeng Ma
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Juan Du
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Xinlong Yu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Kai Chen
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Yucheng Ming
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Tong Chen
- 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
- China National Botanical Garden, Beijing 100093, China
| | - Dongchao Ji
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
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13
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Xia D, Guan L, Yin Y, Wang Y, Shi H, Li W, Zhang D, Song R, Hu T, Zhan X. Genome-Wide Analysis of MBF1 Family Genes in Five Solanaceous Plants and Functional Analysis of SlER24 in Salt Stress. Int J Mol Sci 2023; 24:13965. [PMID: 37762268 PMCID: PMC10531278 DOI: 10.3390/ijms241813965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Multiprotein bridging factor 1 (MBF1) is an ancient family of transcription coactivators that play a crucial role in the response of plants to abiotic stress. In this study, we analyzed the genomic data of five Solanaceae plants and identified a total of 21 MBF1 genes. The expansion of MBF1a and MBF1b subfamilies was attributed to whole-genome duplication (WGD), and the expansion of the MBF1c subfamily occurred through transposed duplication (TRD). Collinearity analysis within Solanaceae species revealed collinearity between members of the MBF1a and MBF1b subfamilies, whereas the MBF1c subfamily showed relative independence. The gene expression of SlER24 was induced by sodium chloride (NaCl), polyethylene glycol (PEG), ABA (abscisic acid), and ethrel treatments, with the highest expression observed under NaCl treatment. The overexpression of SlER24 significantly enhanced the salt tolerance of tomato, and the functional deficiency of SlER24 decreased the tolerance of tomato to salt stress. SlER24 enhanced antioxidant enzyme activity to reduce the accumulation of reactive oxygen species (ROS) and alleviated plasma membrane damage under salt stress. SlER24 upregulated the expression levels of salt stress-related genes to enhance salt tolerance in tomato. In conclusion, this study provides basic information for the study of the MBF1 family of Solanaceae under abiotic stress, as well as a reference for the study of other plants.
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Affiliation(s)
- Dongnan Xia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Lulu Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Yue Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Yixi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Hongyan Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Wenyu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Dekai Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Ran Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Tixu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
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14
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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1579-1588. [PMID: 37640880 PMCID: PMC10484786 DOI: 10.1038/s41588-023-01486-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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15
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Yan Y, Wang W, Hu T, Hu H, Wang J, Wei Q, Bao C. Metabolomic and Transcriptomic Analyses Reveal the Effects of Grafting on Nutritional Properties in Eggplant. Foods 2023; 12:3082. [PMID: 37628081 PMCID: PMC10453275 DOI: 10.3390/foods12163082] [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: 07/04/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Grafting has a significant impact on the botany properties, commercial character, disease resistance, and productivity of eggplants. However, the mechanism of phenotypic modulation on grafted eggplants is rarely reported. In this study, a widely cultivated eggplant (Solanum. melongena cv. 'Zheqie No.10') was selected as the scion and grafted, respectively, onto four rootstocks of TOR (S. torvum), Sa (S. aculeatissimum), SS (S. sisymbriifolium), and Sm64R (S. melongena cv. 'Qiezhen No. 64R') for phenotypic screening. Physiological and biochemical analysis showed the rootstock Sm64R could improve the fruit quality with the increasing of fruit size, yield, and the contents of total soluble solid, phenolic acid, total amino acid, total sugar, and vitamin C. To further investigate the improvement of fruit quality on Sm64R, a transcriptome and a metabolome between the Sm64R-grafted eggplant and self-grafted eggplant were performed. Significant differences in metabolites, such as phenolic acids, lipids, nucleotides and derivatives, alkaloids, terpenoids, and amino acids, were observed. Differential metabolites and differentially expressed genes were found to be abundant in three core pathways of nutritional qualities, including biosynthesis of phenylpropanoids, phospholipids, and nucleotide metabolism. Thus, this study may provide a novel insight into the effects of grafting on the fruit quality in eggplant.
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Affiliation(s)
| | | | | | | | | | | | - Chonglai Bao
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China; (Y.Y.); (W.W.); (T.H.); (H.H.); (J.W.); (Q.W.)
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16
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Imbert B, Kreplak J, Flores RG, Aubert G, Burstin J, Tayeh N. Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes. Front Artif Intell 2023; 6:1191122. [PMID: 37601035 PMCID: PMC10435283 DOI: 10.3389/frai.2023.1191122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
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Affiliation(s)
- Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Raphaël-Gauthier Flores
- Université Paris-Saclay, INRAE, URGI, Versailles, France
- Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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17
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Villanueva G, Plazas M, Gramazio P, Moya RD, Prohens J, Vilanova S. Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different gene pools under low N fertilization conditions. HORTICULTURE RESEARCH 2023; 10:uhad141. [PMID: 37575654 PMCID: PMC10421729 DOI: 10.1093/hr/uhad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
The development of new cultivars with improved nitrogen use efficiency (NUE) is key for implementing sustainable agriculture practices. Crop wild relatives (CWRs) provide valuable genetic resources for breeding programs aimed at achieving this goal. In this study, three eggplant (Solanum melongena) accessions together with their advanced backcrosses (ABs; BC3 to BC5 generations) were evaluated for 22 morpho-agronomic, physiological, and NUE traits under low nitrogen (LN) fertilization conditions. The ABs were developed with introgressions from the wild relatives Solanum insanum, Solanum dasyphyllum, and Solanum elaeagnifolium. The AB population comprised a total of 25, 59, and 59 genotypes, respectively, with overall donor wild relative genome coverage percentages of 58.8%, 46.3%, and 99.2%. The three S. melongena recurrent parents were also evaluated under control (normal) N fertilization. Reduction of N fertilization in the parents resulted in decreased chlorophyll content-related traits, aerial biomass, stem diameter, and yield and increased NUE, nitrogen uptake efficiency (NUpE), and nitrogen utilization efficiency (NUtE). However, the decrease in yield was moderate, ranging between 62.6% and 72.6%. A high phenotypic variation was observed within each of the three sets of ABs under LN conditions, with some individuals displaying improved transgressive characteristics over the recurrent parents. Using the single primer enrichment technology 5 k probes platform for high-throughput genotyping, we observed a variable but high degree of recurrent parent genome recovery in the ABs attributable to the lines recombination, allowing the successful identification of 16 quantitative trait loci (QTL). Different allelic effects were observed for the introgressed QTL alleles. Several candidate genes were identified in the QTL regions associated with plant growth, yield, fruit size, and NUE-related parameters. Our results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breeding for a more sustainable agriculture.
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Affiliation(s)
- Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Reyes D Moya
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spains
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18
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Zhang H, Chen H, Tan J, Huang S, Chen X, Dong H, Zhang R, Wang Y, Wang B, Xiao X, Hong Z, Zhang J, Hu J, Zhang M. The chromosome-scale reference genome and transcriptome analysis of Solanum torvum provides insights into resistance to root-knot nematodes. FRONTIERS IN PLANT SCIENCE 2023; 14:1210513. [PMID: 37528971 PMCID: PMC10390315 DOI: 10.3389/fpls.2023.1210513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
Solanum torvum (Swartz) (2n = 24) is a wild Solanaceae plant with high economic value that is used as a rootstock in grafting for Solanaceae plants to improve the resistance to a soil-borne disease caused by root-knot nematodes (RKNs). However, the lack of a high-quality reference genome of S. torvum hinders research on the genetic basis for disease resistance and application in horticulture. Herein, we present a chromosome-level assembly of genomic sequences for S. torvum combining PacBio long reads (HiFi reads), Illumina short reads and Hi-C scaffolding technology. The assembled genome size is ~1.25 Gb with a contig N50 and scaffold N50 of 38.65 Mb and 103.02 Mb, respectively as well as a BUSCO estimate of 98%. GO enrichment and KEGG pathway analysis of the unique S. torvum genes, including NLR and ABC transporters, revealed that they were involved in disease resistance processes. RNA-seq data also confirmed that 48 NLR genes were highly expressed in roots and fibrous roots and that three homologous NLR genes (Sto0288260.1, Sto0201960.1 and Sto0265490.1) in S. torvum were significantly upregulated after RKN infection. Two ABC transporters, ABCB9 and ABCB11 were identified as the hub genes in response to RKN infection. The chromosome-scale reference genome of the S. torvum will provide insights into RKN resistance.
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Affiliation(s)
- Hongyuan Zhang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Hao Chen
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Jie Tan
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Shuping Huang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xia Chen
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Hongxia Dong
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Ru Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Benqi Wang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jihong Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Min Zhang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
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19
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Yang X, Jiang Z, He J, Shen L. iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions. Life (Basel) 2023; 13:1399. [PMID: 37374181 DOI: 10.3390/life13061399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jie He
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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20
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Li Y, Xing M, Yang Q, Wang Y, Jiang J, Zhao Y, Zhao X, Shen A, Feng Y, Zhao X, Zhao Q, Hu C, Wang Y, Zhang B, Zhou S, Gu H, Huang J, Zhang Y. SmCIP7, a COP1 interactive protein, positively regulates anthocyanin accumulation and fruit size in eggplant. Int J Biol Macromol 2023; 234:123729. [PMID: 36801296 DOI: 10.1016/j.ijbiomac.2023.123729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/21/2023]
Abstract
In higher plants, COP1 (Constitutively Photomorphogenic 1) acts as a central regulator of light-signaling networks and globally conditions the target proteins via the ubiquitin-proteasome pathway. However, the function of COP1-interacting proteins in light-regulated fruit coloration and development remains unknown in Solanaceous plants. Here, a COP1-interacting protein-encoding gene, SmCIP7, expressed specifically in the eggplant (Solanum melongena L.) fruit, was isolated. Gene-specific silencing of SmCIP7 using RNA interference (RNAi) significantly altered fruit coloration, fruit size, flesh browning, and seed yield. SmCIP7-RNAi fruits showed evident repression of the accumulation of anthocyanins and chlorophyll, indicating functional similarities between SmCIP7 and AtCIP7. However, the reduced fruit size and seed yield indicated SmCIP7 had evolved a distinctly new function. With the comprehensive application of HPLC-MS, RNA-seq, qRT-PCR, Y2H, BiFC, LCI, and dual-luciferase reporter system (DLR™), it was found that SmCIP7, a COP1 interactive protein in light signaling promoted anthocyanin accumulation, probably by regulating the transcription of SmTT8. Additionally, the drastic up-regulation of SmYABBY1, a homologous gene of SlFAS, might account for the strongly retarded fruit growth in SmCIP7-RNAi eggplant. Altogether, this study proved that SmCIP7 is an essential regulatory gene to modulate fruit coloration and development, serving as a key gene locus in eggplant molecular breeding.
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Affiliation(s)
- Yan Li
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Minghui Xing
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China; State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 475001, Kaifeng, China
| | - Qiu Yang
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Yong Wang
- Henan Engineering Technology Research Center of New Germplasm Creation and Utilization for Solanaceous Vegetable Crops, Zhumadian Academy of Agricultural Sciences, Fuqiang Road 51, Zhumadian 463000, China
| | - Jun Jiang
- Henan Engineering Technology Research Center of New Germplasm Creation and Utilization for Solanaceous Vegetable Crops, Zhumadian Academy of Agricultural Sciences, Fuqiang Road 51, Zhumadian 463000, China
| | - Yingkai Zhao
- Zhengzhou Institute of Vegetable Research, Zhengzhou 450015, China
| | - Xiangmei Zhao
- Zhengzhou Institute of Vegetable Research, Zhengzhou 450015, China
| | - Aimin Shen
- Zhengzhou Institute of Vegetable Research, Zhengzhou 450015, China
| | - Youwei Feng
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Xuejie Zhao
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Qing Zhao
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Chunhua Hu
- Henan Youmei Agricultural Technology Co., Ltd, Zhoukou 466100, China
| | - Yunxing Wang
- Henan Youmei Agricultural Technology Co., Ltd, Zhoukou 466100, China
| | - Bing Zhang
- Henan Vocational College of Agriculture, Zhengzhou, China
| | - Shifeng Zhou
- Henan Vocational College of Agriculture, Zhengzhou, China
| | - Huihui Gu
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
| | - Yanjie Zhang
- School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China.
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21
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Rosa-Martínez E, Bovy A, Plazas M, Tikunov Y, Prohens J, Pereira-Dias L. Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits. FRONTIERS IN PLANT SCIENCE 2023; 14:1135237. [PMID: 37025131 PMCID: PMC10070870 DOI: 10.3389/fpls.2023.1135237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.
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Affiliation(s)
- Elena Rosa-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Arnaud Bovy
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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22
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Zhang F, Qiu F, Zeng J, Xu Z, Tang Y, Zhao T, Gou Y, Su F, Wang S, Sun X, Xue Z, Wang W, Yang C, Zeng L, Lan X, Chen M, Zhou J, Liao Z. Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family. Nat Commun 2023; 14:1446. [PMID: 36922496 PMCID: PMC10017790 DOI: 10.1038/s41467-023-37133-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
Tropane alkaloids (TAs) are widely distributed in the Solanaceae, while some important medicinal tropane alkaloids (mTAs), such as hyoscyamine and scopolamine, are restricted to certain species/tribes in this family. Little is known about the genomic basis and evolution of TAs biosynthesis and specialization in the Solanaceae. Here, we present chromosome-level genomes of two representative mTAs-producing species: Atropa belladonna and Datura stramonium. Our results reveal that the two species employ a conserved biosynthetic pathway to produce mTAs despite being distantly related within the nightshade family. A conserved gene cluster combined with gene duplication underlies the wide distribution of TAs in this family. We also provide evidence that branching genes leading to mTAs likely have evolved in early ancestral Solanaceae species but have been lost in most of the lineages, with A. belladonna and D. stramonium being exceptions. Furthermore, we identify a cytochrome P450 that modifies hyoscyamine into norhyoscyamine. Our results provide a genomic basis for evolutionary insights into the biosynthesis of TAs in the Solanaceae and will be useful for biotechnological production of mTAs via synthetic biology approaches.
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Affiliation(s)
- Fangyuan Zhang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Fei Qiu
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Junlan Zeng
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Zhichao Xu
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Yueli Tang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Tengfei Zhao
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Yuqin Gou
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Fei Su
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Shiyi Wang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Xiuli Sun
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Zheyong Xue
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Weixing Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Chunxian Yang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Lingjiang Zeng
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, Tibetan Collaborative Innovation Centre of Agricultural and Animal Husbandry Resources, Xizang Agricultural and Animal Husbandry College, Nyingchi, Tibet, 860000, China
| | - Min Chen
- College of Pharmaceutical Sciences, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Ministry of Education), Southwest University, Chongqing, 400715, China
| | - Junhui Zhou
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhihua Liao
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China. .,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China.
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23
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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24
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Vegetable biology and breeding in the genomics era. SCIENCE CHINA. LIFE SCIENCES 2023; 66:226-250. [PMID: 36508122 DOI: 10.1007/s11427-022-2248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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25
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Tao T, Hu W, Yang Y, Zou M, Zhou S, Tian S, Wang Y. Transcriptomics reveals the molecular mechanisms of flesh colour differences in eggplant (Solanum melongena). BMC PLANT BIOLOGY 2023; 23:5. [PMID: 36597026 PMCID: PMC9811765 DOI: 10.1186/s12870-022-04002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fruit flesh colour is not only an important commodity attribute of eggplant but is also closely related to maturity. However, very little is known about its formation mechanism in eggplant. RESULTS Two inbred lines of eggplant, green 'NC7' and white 'BL', were used in this study to explain the differences in flesh colour. Transcriptome sequencing results revealed a total of 3304 differentially expressed genes (DEGs) in NC7 vs. BL. Of the DEGs obtained, 2050 were higher and 1254 were lower in BL. These DEGs were annotated to 126 pathways, where porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and photosynthesis-antenna proteins play vital roles in the colour formation of eggplant flesh. At the same time, Gene Ontology (GO) enrichment significance analysis showed that a large number of unigenes involved in the formation of chloroplast structure were lower in BL, which indicated that the formation of chloroplasts in white-fleshed eggplant was blocked. This was confirmed by transmission electron microscopy (TEM), which found only leucoplasts but no chloroplasts in the flesh cells of white-fleshed eggplant. Several genes encoding ERF and bHLH transcription factors were predicted to participate in the regulation of chlorophyll biosynthetic genes. CONCLUSIONS The results of this study indicated that differences in the gene expression of the chlorophyll metabolic pathway were the main cause of the different flesh colour formations. These findings will increase our understanding of the genetic basis in eggplant flesh colors formation mechanism.
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Affiliation(s)
- Tao Tao
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Wei Hu
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Yang Yang
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Min Zou
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Shanshan Zhou
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Shibing Tian
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
| | - Yongqing Wang
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
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26
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He J, Alonge M, Ramakrishnan S, Benoit M, Soyk S, Reem NT, Hendelman A, Van Eck J, Schatz MC, Lippman ZB. Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. THE PLANT CELL 2023; 35:351-368. [PMID: 36268892 PMCID: PMC9806562 DOI: 10.1093/plcell/koac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.
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Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | | | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Subramaniam R, Kumar VS. Allele mining, amplicon sequencing and computational prediction of Solanum melongena L. FT/TFL1 gene homologs uncovers putative variants associated to seed dormancy and germination. PLoS One 2023; 18:e0285119. [PMID: 37134080 PMCID: PMC10156061 DOI: 10.1371/journal.pone.0285119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/16/2023] [Indexed: 05/04/2023] Open
Abstract
The FT/TFL1 gene homolog family plays a crucial role in the regulation of floral induction, seed dormancy and germination in angiosperms. Despite its importance, the FT/TFL1 gene homologs in eggplant (Solanum melongena L.) have not been characterized to date. In this study, we performed a genome-wide identification of FT/TFL1 genes in eggplant using in silico genome mining. The presence of these genes was validated in four economically important eggplant cultivars (Surya, EP-47 Annamalai, Pant Samrat and Arka Nidhi) through Pacbio RSII amplicon sequencing. Our results revealed the presence of 12 FT/TFL1 gene homologs in eggplant, with evidence of diversification among FT-like genes suggesting their possible adaptations towards various environmental stimuli. The amplicon sequencing also revealed the presence of two alleles for certain genes (SmCEN-1, SmCEN-2, SmMFT-1 and SmMFT-2) of which SmMFT-2 was associated with seed dormancy and germination. This association was further supported by the observation that seed dormancy is rarely reported in domesticated eggplant cultivars, but is commonly observed in wild species. A survey of the genetic regions in domesticated cultivars and a related wild species, S. incanum, showed that the alternative allele of S. incanum was present in some members of the Pant Samrat cultivar, but was absent in most other cultivars. This difference could contribute to the differences in seed traits between wild and domesticated eggplants.
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Affiliation(s)
- Ranjita Subramaniam
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
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Li D, Tang X, Dong Y, Wang Y, Shi S, Li S, Liu Y, Ge H, Chen H. Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments. PLANT CELL REPORTS 2022; 41:2213-2228. [PMID: 36001130 DOI: 10.1007/s00299-022-02918-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes (Smechr0202855.1 and Smechr0602431.1) may be involved in anthocyanin synthesis. The Teosinte branched1/Cycloidea/Proliferating cell factors (TCPs), a family of plant-specific transcription factors, plays paramount roles in a plethora of developmental and physiological processes. We here systematically characterized putative TCP genes and their response to abiotic stress in eggplant. In total, 30 SmTCP genes were categorized into two subfamilies based on the classical TCP conserved domains. Chromosomal location analysis illustrated the random distribution of putative SmTCP genes along 12 eggplant chromosomes. Cis-acting elements and miRNA target prediction suggested that versatile and complicated regulatory mechanisms that control SmTCPs gene expression, and 3 miRNAs (miR319a, miR319b, and miR319c-3p) might act as major regulators targeting SmTCPs. Tissue expression profiles indicated divergent spatiotemporal expression patterns of SmTCPs. qRT-PCR assays demonstrated different expression profiles of SmTCP under 4 °C, drought and ABA treatment conditions, suggesting the possible participation of SmTCP genes in multiple signaling pathways. Furthermore, RNA-seq data of eggplant anthocyanin synthesis coupled with yeast one-hybrid and dual-luciferase assays suggested the involvement of SmTCP genes (Smechr0202855.1 and Smechr0602431.1) in the mediation of anthocyanin synthesis. Our study will facilitate further investigation on the putative functional characterization of eggplant TCP genes and lay a solid foundation for the in-depth study of the involvement of SmTCP genes in the regulation of anthocyanin synthesis.
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Affiliation(s)
- Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xin Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yanxiao Dong
- Shanghai Agricultural Science and Technology Service Center, Shanghai, 200335, China
| | - Yingying Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Haiyan Ge
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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Arrones A, Mangino G, Alonso D, Plazas M, Prohens J, Portis E, Barchi L, Giuliano G, Vilanova S, Gramazio P. Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette. FRONTIERS IN PLANT SCIENCE 2022; 13:1025951. [PMID: 36388476 PMCID: PMC9647125 DOI: 10.3389/fpls.2022.1025951] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 06/01/2023]
Abstract
Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.
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Affiliation(s)
- Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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Zhang X, Zhao Y, Kou Y, Chen X, Yang J, Zhang H, Zhao Z, Zhao Y, Zhao G, Li Z. Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae). HORTICULTURE RESEARCH 2022; 10:uhac231. [PMID: 36643751 PMCID: PMC9832869 DOI: 10.1093/hr/uhac231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/01/2022] [Indexed: 06/17/2023]
Abstract
Gynostemma pentaphyllum (Thunb.) Makino is a perennial creeping herbaceous plant in the family Cucurbitaceae, which has great medicinal value and commercial potential, but urgent conservation efforts are needed due to the gradual decreases and fragmented distribution of its wild populations. Here, we report the high-quality diploid chromosome-level genome of G. pentaphyllum obtained using a combination of next-generation sequencing short reads, Nanopore long reads, and Hi-C sequencing technologies. The genome is anchored to 11 pseudo-chromosomes with a total size of 608.95 Mb and 26 588 predicted genes. Comparative genomic analyses indicate that G. pentaphyllum is estimated to have diverged from Momordica charantia 60.7 million years ago, with no recent whole-genome duplication event. Genomic population analyses based on genotyping-by-sequencing and ecological niche analyses indicated low genetic diversity but a strong population structure within the species, which could classify 32 G. pentaphyllum populations into three geographical groups shaped jointly by geographic and climate factors. Furthermore, comparative transcriptome analyses showed that the genes encoding enzyme involved in gypenoside biosynthesis had higher expression levels in the leaves and tendrils. Overall, the findings obtained in this study provide an effective molecular basis for further studies of demographic genetics, ecological adaption, and systematic evolution in Cucurbitaceae species, as well as contributing to molecular breeding, and the biosynthesis and biotransformation of gypenoside.
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Affiliation(s)
- Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yuhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, 030012, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
- College of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yuemei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, 550018, China
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Ro N, Haile M, Kim B, Cho GT, Lee J, Lee YJ, Hyun DY. Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection. PLANTS (BASEL, SWITZERLAND) 2022; 11:2627. [PMID: 36235493 PMCID: PMC9571982 DOI: 10.3390/plants11192627] [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: 09/20/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desired traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and genome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Do Yoon Hyun
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea;
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Identification, Phylogeny, Divergence, Structure, and Expression Analysis of A20/AN1 Zinc Finger Domain Containing Stress-Associated Proteins (SAPs) Genes in Jatropha curcas L. Genes (Basel) 2022; 13:genes13101766. [PMID: 36292651 PMCID: PMC9601316 DOI: 10.3390/genes13101766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/18/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022] Open
Abstract
Jatropha is a small woody perennial biofuel-producing shrub. Stress-associated proteins (SAPs) are novel stress regulatory zinc-finger proteins and are mainly associated with tolerance against various environmental abiotic stresses in Jatropha. In the present study, the JcSAP gene family were analyzed comprehensively in Jatropha curcas and 11 JcSAP genes were identified. Phylogenetic analysis classified the JcSAP genes into four groups based on sequence similarity, similar gene structure features, conserved A20 and/or AN1 domains, and their responsive motifs. Moreover, the divergence analysis further evaluated the evolutionary aspects of the JcSAP genes with the predicted time of divergence from 9.1 to 40 MYA. Furthermore, a diverse range of cis-elements including light-responsive elements, hormone-responsive elements, and stress-responsive elements were detected in the promoter region of JcSAP genes while the miRNA target sites predicted the regulation of JcSAP genes via a candid miRNA mediated post-transcriptional regulatory network. In addition, the expression profiles of JcSAP genes in different tissues under stress treatment indicated that many JcSAP genes play functional developmental roles in different tissues, and exhibit significant differential expression under stress treatment. These results collectively laid a foundation for the functional diversification of JcSAP genes.
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Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. HORTICULTURE RESEARCH 2022; 9:uhac213. [PMID: 36483087 PMCID: PMC9719039 DOI: 10.1093/hr/uhac213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface-The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)-was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.
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Affiliation(s)
| | | | | | | | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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Guan W, Ke C, Tang W, Jiang J, Xia J, Xie X, Yang M, Duan C, Wu W, Zheng Y. Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant. Int J Mol Sci 2022; 23:ijms231810258. [PMID: 36142175 PMCID: PMC9499331 DOI: 10.3390/ijms231810258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 02/08/2023] Open
Abstract
High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F2 plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.
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Affiliation(s)
- Wenxiang Guan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changjiao Ke
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jialong Jiang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Xia
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofang Xie
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Yang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chenfeng Duan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
| | - Yan Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
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Yang T, Li C, Zhang H, Wang J, Xie X, Wen Y. Genome-wide identification and expression analysis of the GRAS transcription in eggplant ( Solanum melongena L.). Front Genet 2022; 13:932731. [PMID: 36118872 PMCID: PMC9478738 DOI: 10.3389/fgene.2022.932731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/11/2022] [Indexed: 01/09/2023] Open
Abstract
GRAS proteins are plant-specific transcription factors and play important roles in plant growth, development, and stress responses. In this study, a total of 48 GRAS genes in the eggplant (S. melongena) genome were identified. These genes were distributed on 11 chromosomes unevenly, with amino acid lengths ranging from 417 to 841 aa. A total of 48 GRAS proteins were divided into 13 subgroups based on the maximum likelihood (ML) model. The gene structure showed that 60.42% (29/48) of SmGRASs did not contain any introns. Nine pairs of SmGRAS appeared to have a collinear relationship, and all of them belonged to segmental duplication. Four types of cis-acting elements, namely, light response, growth and development, hormone response, and stress response, were identified by a cis-acting element predictive analysis. The expression pattern analysis based on the RNA-seq data of eggplant indicated that SmGRASs were expressed differently in various tissues and responded specifically to cold stress. In addition, five out of ten selected SmGRASs (SmGRAS2/28/32/41/44) were upregulated under cold stress. These results provided a theoretical basis for further functional study of GRAS genes in eggplant.
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Affiliation(s)
- Ting Yang
- Fujian Key Laboratory of Crop Breeding By Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng Li
- Institute of Statistics and Applications, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Zhang
- Institute of Statistics and Applications, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingyu Wang
- Institute of Statistics and Applications, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaofang Xie
- Fujian Key Laboratory of Crop Breeding By Design, Fujian Agriculture and Forestry University, Fuzhou, China,College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China,*Correspondence: Xiaofang Xie, ; Yongxian Wen,
| | - Yongxian Wen
- Institute of Statistics and Applications, Fujian Agriculture and Forestry University, Fuzhou, China,College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China,*Correspondence: Xiaofang Xie, ; Yongxian Wen,
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Habe I, Miyatake K. Identification and characterization of resistance quantitative trait loci against bacterial wilt caused by the Ralstonia solanacearum species complex in potato. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:50. [PMID: 37313419 PMCID: PMC10248640 DOI: 10.1007/s11032-022-01321-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) represents one of the most serious diseases affecting potato cultivation. The development of BW-resistant cultivars represents the most efficient strategy to control this disease. The resistance-related quantitative trait loci (QTLs) in plants against different RSSC strains have not been studied extensively. Therefore, we performed QTL analysis for evaluating BW resistance using a diploid population derived from Solanum phureja, S. chacoense, and S. tuberosum. Plants cultivated in vitro were inoculated with different strains (phylotype I/biovar 3, phylotype I/biovar 4, and phylotype IV/biovar 2A) and incubated at 24 °C or 28 °C under controlled conditions. Composite interval mapping was performed for the disease indexes using a resistant parent-derived map and a susceptible parent-derived map consisting of single-nucleotide polymorphism markers. We identified five major and five minor resistance QTLs on potato chromosomes 1, 3, 5, 6, 7, 10, and 11. The major QTLs PBWR-3 and PBWR-7 conferred stable resistance against Ralstonia pseudosolanacearum (phylotype I) and Ralstonia syzygii (phylotype IV), whereas PBWR-6b was a strain-specific major resistance QTL against phylotype I/biovar 3 and was more effective at a lower temperature. Therefore, we suggest that broad-spectrum QTLs and strain-specific QTLs can be combined to develop the most effective BW-resistant cultivars for specific areas. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01321-9.
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Affiliation(s)
- Ippei Habe
- Nagasaki Agriculture and Forestry Technical Development Center, 3118 Kaizu, Isahaya, Nagasaki, 854-0063 Japan
| | - Koji Miyatake
- Institute of Vegetable and Floriculture Science, NARO, Kusawa 360, Mie, Tsu, 514-2392 Japan
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Shen L, Zhao E, Liu R, Yang X. Transcriptome Analysis of Eggplant under Salt Stress: AP2/ERF Transcription Factor SmERF1 Acts as a Positive Regulator of Salt Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:2205. [PMID: 36079586 PMCID: PMC9460861 DOI: 10.3390/plants11172205] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Salt stress, a type of abiotic stress, impedes plant growth and development and strongly reduces crop yield. The molecular mechanisms underlying plant responses to salt stress remain largely unclear. To characterize the enriched pathways and genes that were affected during salt treatment, we performed mRNA sequencing (mRNA-seq) in eggplant roots and identified 8509 differentially expressed genes (DEGs) between the mock and 24 h under salt stress. Among these DEGs, we found that the AP2/ERF transcription factor family member SmERF1 belongs to the plant-pathogen interaction pathway, which was significantly upregulated by salt stress. We found that SmERF1 localizes in the nuclei with transcriptional activity. The results of the virus-induced gene silencing assay showed that SmERF1 silencing markedly enhanced the susceptibility of plants to salt stress, significantly downregulated the transcript expression levels of salt stress defense-related marker genes (9-cis-epoxycarotenoid dioxygenase [SmNCED1, SmNCED2], Dehydrin [SmDHN1], and Dehydrin (SmDHNX1), and reduced the activity of superoxide dismutase and catalase. Silencing SmERF1 promoted the generation of H2O2 and proline. In addition, the transient overexpression of SmERF1 triggered intense cell death in eggplant leaves, as assessed by the darker diaminobenzidine and trypan blue staining. These findings suggest that SmERF1 acts as a positive regulator of eggplant response to salt stress. Hence, our results suggest that AP2/ERF transcription factors play a vital role in the response to salt stress.
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Affiliation(s)
- Lei Shen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Enpeng Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Ruie Liu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201600, China
| | - Xu Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
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Zhang J, Li B, Gao X, Pan X, Wu Y. Integrating Transcriptomic and Metabolomic Analyses to Explore the Effect of Color Under Fruit Calyx on That of Fruit Apex in Eggplant (Solanum melongena L.). Front Genet 2022; 13:889461. [PMID: 35812728 PMCID: PMC9259842 DOI: 10.3389/fgene.2022.889461] [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: 03/04/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
Fruit color is an important commercial characteristic of eggplant (Solanum melongena L.), which affects both the profits of growers and consumer choice. Two eggplant inbred lines were discovered: “Z,” which is a light purple color under the fruit calyx, with purple on the fruit apex; and “L,” fruits of which are green under the calyx and at the apex. To determine the molecular mechanisms underlying the effect of fruit peel color under the calyx on that at the fruit apex, we conducted a combined transcriptomic and metabolomic analyses of the Z and L inbred eggplant lines. Transcriptome analysis of peel samples from three fruit regions (under the calyx, the apex, and the middle surface) of each line was conducted by RNA sequencing, and generated a total of 791,512,404 clean reads from 18 samples (three biological replicates). Differentially expressed genes (DEGs; n = 424) were identified in comparisons of peel samples from the three sites of L line fruits. Gene ontology analysis showed that “catalytic activity” was extremely significantly enriched. Further, DEGs (n = 8) were enriched in the Kyoto Encyclopedia of Genes and Genomes pathway “flavonoid biosynthesis.” Levels of CHI, LDOX, F3′5′H, and dihydroflavonol reductase were higher in the Z line than the L line. In addition, metabolome analysis showed that, 10 differentially accumulated metabolites were detected between peel samples from the apex of L and Z line fruit. The most significant DAM was delphinidin-3-O-rutinoside (Z line content, 34.89 μg/g vs. L line content 0.01 μg/g). Combined transcriptomic and metabolomic analyses indicated that DFR and F3′5′H were closely related to content of the metabolites, cyanidin and delphinidin, and that some downstream metabolites differed significantly between the L and Z lines. Content levels of delphinidin-3-O-rutinoside, delphinidin-3-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside were markedly down-regulated in the L line. Altogether, increased CHI levels could up-regulate the downstream genes, LDOX, F3′5′H, and DFR, which further lead to increasing the content of delphindin. Thus, the uniform purple color was presented at the apex of fruits in Z plants. These findings not only identify key candidate genes, but will also improve understanding of the genetics and the efficiency of breeding for eggplant fruit color.
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Xiao X, Lin W, Feng E, Wu C, Ou X. Genome-Wide Identification of Binding Sites for SmTCP7a Transcription Factors of Eggplant during Bacterial Wilt Resistance by ChIP-Seq. Int J Mol Sci 2022; 23:6844. [PMID: 35743285 PMCID: PMC9224693 DOI: 10.3390/ijms23126844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 12/10/2022] Open
Abstract
Teosinte branched 1/cycloidea/proliferating cell factor (TCP) transcription factors play a key role in the regulation of plant biotic and abiotic stresses. In this study, our results show that SmTCP7a positively regulated bacterial wilt that was caused by Ralstonia solanacearum. ChIP-seq was conducted to analyze the transcriptional regulation mechanism of SmTCP7a before (R0 h) and 48 h after infection (R48 h). SmTCP7a regulated a total of 92 and 91 peak-associated genes in R0 h and R48 h, respectively. A KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis showed that phenylpropanoid biosynthesis, MAPK (mitogen-activated protein kinas) signaling pathway, plant hormone signal transduction and plant-pathogen interactions were involved. The difference in peaks between R0 h and R48 h showed that there were three peak-associated genes that were modulated by infection. A better understanding of the potential target genes of SmTCP7a in response to R. solanacearum will provide a comprehensive understanding of the SmTCP7a regulatory mechanism during the eggplant defense response to bacterial wilt.
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Affiliation(s)
- Xi’ou Xiao
- South Subtropical Crop Research Institute Chinese, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.); (C.W.); (X.O.)
- Key Laboratory for Post-harvest Physiology and Technology of Tropical Horticultural Products of Hainan, Zhanjiang 524091, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang 524091, China
| | - Wenqiu Lin
- South Subtropical Crop Research Institute Chinese, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.); (C.W.); (X.O.)
- Key Laboratory for Post-harvest Physiology and Technology of Tropical Horticultural Products of Hainan, Zhanjiang 524091, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang 524091, China
| | - Enyou Feng
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang 524091, China;
| | - Caiyu Wu
- South Subtropical Crop Research Institute Chinese, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.); (C.W.); (X.O.)
- Key Laboratory for Post-harvest Physiology and Technology of Tropical Horticultural Products of Hainan, Zhanjiang 524091, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang 524091, China
| | - Xiongchang Ou
- South Subtropical Crop Research Institute Chinese, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.); (C.W.); (X.O.)
- Key Laboratory for Post-harvest Physiology and Technology of Tropical Horticultural Products of Hainan, Zhanjiang 524091, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang 524091, China
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The 3D architecture of the pepper genome and its relationship to function and evolution. Nat Commun 2022; 13:3479. [PMID: 35710823 PMCID: PMC9203530 DOI: 10.1038/s41467-022-31112-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/03/2022] [Indexed: 12/21/2022] Open
Abstract
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints. The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.
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41
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Aubriot X, Knapp S. A revision of the "spiny solanums" of Tropical Asia ( Solanum, the Leptostemonum Clade, Solanaceae). PHYTOKEYS 2022; 198:1-270. [PMID: 36760991 PMCID: PMC9849010 DOI: 10.3897/phytokeys.198.79514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/20/2022] [Indexed: 06/18/2023]
Abstract
The Leptostemonum Clade, or the "spiny solanums", is the most species-rich monophyletic clade of the large cosmopolitan genus Solanum (Solanaceae) and represents almost half the species diversity of the genus. Species diversity in the clade is highest in the Americas, but significant clusters of endemic taxa occur in the Eastern Hemisphere. We present here a taxonomic revision of the 51 species of spiny solanums occurring in tropical Asia (excluding the island of New Guinea, and the lowlands of Nepal and Bhutan). Three species are described as new: Solanumkachinense X.Aubriot & S.Knapp, sp. nov. from northern Myanmar, S.peikuoense S.S.Ying, sp. nov. from Taiwan, and S.sulawesi X.Aubriot & S.Knapp, sp. nov. from northern Sulawesi, Indonesia. Of the spiny solanums occurring in the region, 38 are native and 13 are introduced from the Americas or Africa, either as adventive weeds or as cultivated plants. Phylogenetic resolution amongst these taxa is still a work in progress, so we have chosen to treat these taxa in a geographical context to aid with identification and further taxon discovery. For the native species we provide complete nomenclatural details for all recognised species and their synonyms, complete descriptions, distributions including maps, common names and uses, and preliminary conservation assessments. For the introduced taxa that have been treated in detail elsewhere we provide details of types, synonyms based on tropical Asian material, general distributions, and common names for the region. We provide lecto- or neotypifications for 67 names; 63 for native and 4 for introduced taxa. All taxa are discussed and compared to similar species; keys are provided for all taxa. We illustrate all native species with herbarium and field photographs and introduced species with field photographs only. All specimens examined for this treatment are included in Suppl. materials 1-3 as searchable files.
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Affiliation(s)
- Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, FranceThe Natural History MuseumLondonUnited Kingdom
- The Natural History Museum, Cromwell Road, London SW7 5BD, UKUniversité Paris-SaclayParisFrance
| | - Sandra Knapp
- The Natural History Museum, Cromwell Road, London SW7 5BD, UKUniversité Paris-SaclayParisFrance
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Tang D, Jia Y, Zhang J, Li H, Cheng L, Wang P, Bao Z, Liu Z, Feng S, Zhu X, Li D, Zhu G, Wang H, Zhou Y, Zhou Y, Bryan GJ, Buell CR, Zhang C, Huang S. Genome evolution and diversity of wild and cultivated potatoes. Nature 2022; 606:535-541. [PMID: 35676481 PMCID: PMC9200641 DOI: 10.1038/s41586-022-04822-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/28/2022] [Indexed: 12/21/2022]
Abstract
Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1-4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.
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Affiliation(s)
- Dié Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jinzhe Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Lin Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhihong Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuangshuang Feng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijian Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Hongru Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Yao Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, UK
| | - C Robin Buell
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Qian Z, Ji Y, Li R, Lanteri S, Chen H, Li L, Jia Z, Cui Y. Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis. Front Genet 2022; 13:841198. [PMID: 35664340 PMCID: PMC9157640 DOI: 10.3389/fgene.2022.841198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Eggplant (Solanum melongena L.; 2n = 24) is one of the most important Solanaceae vegetables and is primarily cultivated in China (approximately 42% of world production) and India (approximately 39%). Thousand-grain weight (TGW) is an important trait that affects eggplant breeding cost and variety promotion. This trait is controlled by quantitative trait loci (QTLs); however, no quantitative trait loci (QTL) has been reported for TGW in eggplant so far, and its potential genetic basis remain unclear. In this study, two eggplant lines, 17C01 (P1, wild resource, small seed) and 17C02 (P2, cultivar, large seed), were crossed to develop F1, F2 (308 lines), BC1P1 (44 lines), and BC1P2 (44 lines) populations for quantitative trait association analysis. The TGWs of P1, P2 and F1 were determined as 3.00, 3.98 and 3.77 g, respectively. The PG-ADI (polygene-controlled additive-dominance-epistasis) genetic model was identified as the optimal model for TGW and the polygene heritability value in the F2 generation was as high as 80.87%. A high-quality genetic linkage bin map was constructed with resequencing analysis. The map contained 3,918 recombination bins on 12 chromosomes, and the total length was 1,384.62 cM. A major QTL (named as TGW9.1) located on chromosome 9 was identified to be strongly associated with eggplant TGW, with a phenotypic variance explanation of 20.51%. A total of 45 annotated genes were identified in the genetic region of TGW9.1. Based on the annotation of Eggplant genome V3 and orthologous genes in Arabidopsis thaliana, one candidate gene SMEL_009g329850 (SmGTS1, encoding a putative ubiquitin ligase) contains 4 SNPs and 2 Indels consecutive intron mutations in the flank of the same exon in P1. SmGTS1 displayed significantly higher expression in P1 and was selected as a potential candidate gene controlling TGW in eggplant. The present results contribute to shed light on the genetic basis of the traits exploitable in future eggplant marker-assisted selection (MAS) breeding.
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Affiliation(s)
- Zongwei Qian
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yanhai Ji
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Ranhong Li
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Sergio Lanteri
- DISAFA, Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Haili Chen
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Longfei Li
- Jingyan Yinong (Beijing) Seed Sci-Tech Co. Ltd., Beijing, China
| | - Zhiyang Jia
- Jingyan Yinong (Beijing) Seed Sci-Tech Co. Ltd., Beijing, China
| | - Yanling Cui
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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Song X, Liu H, Shen S, Huang Z, Yu T, Liu Z, Yang Q, Wu T, Feng S, Zhang Y, Wang Z, Duan W. Chromosome-level pepino genome provides insights into genome evolution and anthocyanin biosynthesis in Solanaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1128-1143. [PMID: 35293644 DOI: 10.1111/tpj.15728] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Pepino (Solanum muricatum, 2n = 2x = 24), a member of the Solanaceae family, is an important globally grown fruit. Herein, we report high-quality, chromosome-level pepino genomes. The 91.67% genome sequence is anchored to 12 chromosomes, with a total length of 1.20 Gb and scaffold N50 of 87.03 Mb. More than half the genome comprises repetitive sequences. In addition to the shared ancient whole-genome triplication (WGT) event in eudicots, an additional new WGT event was present in the pepino. Our findings suggest that pepinos experienced chromosome rearrangements, fusions, and gene loss after a WGT event. The large number of gene removals indicated the instability of Solanaceae genomes, providing opportunities for species divergence and natural selection. The paucity of disease-resistance genes (NBS) in pepino and eggplant has been explained by extensive loss and limited generation of genes after WGT events in Solanaceae. The outbreak of NBS genes was not synchronized in Solanaceae species, which occurred before the Solanaceae WGT event in pepino, tomato, and tobacco, whereas it was almost synchronized with WGT events in the other four Solanaceae species. Transcriptome and comparative genomic analyses revealed several key genes involved in anthocyanin biosynthesis. Although an extra WGT event occurred in Solanaceae, CHS genes related to anthocyanin biosynthesis in grapes were still significantly expanded compared with those in Solanaceae species. Proximal and tandem duplications contributed to the expansion of CHS genes. In conclusion, the pepino genome and annotation facilitate further research into important gene functions and comparative genomic analysis in Solanaceae.
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Affiliation(s)
- Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Haibin Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shaoqin Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Zhinan Huang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Tong Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Zhuo Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Qihang Yang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Tong Wu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shuyan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yu Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Zhiyuan Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Weike Duan
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
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Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry. Int J Mol Sci 2022; 23:ijms23042259. [PMID: 35216373 PMCID: PMC8875911 DOI: 10.3390/ijms23042259] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023] Open
Abstract
The R2R3-MYB is a large gene family involved in various plant functions, including carotenoid biosynthesis. However, this gene family lacks a comprehensive analysis in wolfberry (Lycium barbarum L.) and other Solanaceae species. The recent sequencing of the wolfberry genome provides an opportunity for investigating the organization and evolutionary characteristics of R2R3-MYB genes in wolfberry and other Solanaceae species. A total of 610 R2R3-MYB genes were identified in five Solanaceae species, including 137 in wolfberry. The LbaR2R3-MYB genes were grouped into 31 subgroups based on phylogenetic analysis, conserved gene structures, and motif composition. Five groups only of Solanaceae R2R3-MYB genes were functionally divergent during evolution. Dispersed and whole duplication events are critical for expanding the R2R3-MYB gene family. There were 287 orthologous gene pairs between wolfberry and the other four selected Solanaceae species. RNA-seq analysis identified the expression level of LbaR2R3-MYB differential gene expression (DEGs) and carotenoid biosynthesis genes (CBGs) in fruit development stages. The highly expressed LbaR2R3-MYB genes are co-expressed with CBGs during fruit development. A quantitative Real-Time (qRT)-PCR verified seven selected candidate genes. Thus, Lba11g0183 and Lba02g01219 are candidate genes regulating carotenoid biosynthesis in wolfberry. This study elucidates the evolution and function of R2R3-MYB genes in wolfberry and the four Solanaceae species.
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Identification and Expression Analysis of Zinc Finger A20/AN1 Stress-Associated Genes SmSAP Responding to Abiotic Stress in Eggplant. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Stress-associated proteins (SAP), a class of zinc-finger proteins, have been identified as novel stress regulatory proteins in stress responses. However, SAP genes in eggplant (SmSAP) have been little reported. It has important significance in identifying SAP members, understanding the molecular mechanisms underlying stress responses, and tolerance. We performed a comprehensive study of the A20/AN1 domains, motifs, gene structures, phylogenetic relationships, chromosomal locations, gene replications, collinearity, cis-acting elements, and expression pattern responses to various abiotic stresses. Twenty-one SAP genes were identified in eggplant (SmSAP) and were localized on 10 chromosomes. A phylogenetic analysis revealed that most of the SmSAP proteins showed a high homology with the tomato SAP members, and 21 members were divided into four groups based on the homology of the SAP members in eggplant, tomato, rice, and Arabidopsis. Further analysis revealed that SmSAP proteins contain the characteristic A20/AN1 domains, the A20 domain composed of motif 2 (ILCINNCGFFGSPATMNLCSKCYKDMJLK). Four pairs of tandem duplications were found in eggplant, and 10 SmSAP genes had collinearity with SAP genes from Arabidopsis, potato, or tomato, but only four SmSAP genes were collinear with SAP genes in the three species mentioned above. Moreover, the promoters of SmSAP genes were predicted to contain many cis-acting elements that respond to abiotic stress and hormones. A qRT-PCR analysis of the four selected SmSAP genes exhibited diverse expression levels in response to various environmental stresses. These results provided a comprehensive analysis of the SmSAP genes and lay a solid foundation for improving the understanding of the functional diversification of SAP genes under various environmental stresses in eggplant.
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Liu Y, Qu J, Shi Z, Zhang P, Ren M. Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum. BMC Genomics 2021; 22:821. [PMID: 34773990 PMCID: PMC8590752 DOI: 10.1186/s12864-021-08109-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
Background The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported. Results In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-β-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm. Conclusions This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08109-9.
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Affiliation(s)
- Yongming Liu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, 610213, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural, Sciences of Zhengzhou University, 450000, Zhengzhou, China.,Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, China
| | - Jingtao Qu
- Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Ziwen Shi
- Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Peng Zhang
- Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, 610213, Chengdu, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural, Sciences of Zhengzhou University, 450000, Zhengzhou, China. .,Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, China.
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Yuan Y, Bayer PE, Batley J, Edwards D. Current status of structural variation studies in plants. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2153-2163. [PMID: 34101329 PMCID: PMC8541774 DOI: 10.1111/pbi.13646] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 05/23/2023]
Abstract
Structural variations (SVs) including gene presence/absence variations and copy number variations are a common feature of genomes in plants and, together with single nucleotide polymorphisms and epigenetic differences, are responsible for the heritable phenotypic diversity observed within and between species. Understanding the contribution of SVs to plant phenotypic variation is important for plant breeders to assist in producing improved varieties. The low resolution of early genetic technologies and inefficient methods have previously limited our understanding of SVs in plants. However, with the rapid expansion in genomic technologies, it is possible to assess SVs with an ever-greater resolution and accuracy. Here, we review the current status of SV studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies.
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Affiliation(s)
- Yuxuan Yuan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
- School of Life Sciences and State Key Laboratory for AgrobiotechnologyThe Chinese University of Hong KongHong Kong SARChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
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Li D, He Y, Li S, Shi S, Li L, Liu Y, Chen H. Genome-wide characterization and expression analysis of AP2/ERF genes in eggplant (Solanum melongena L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:492-503. [PMID: 34425394 DOI: 10.1016/j.plaphy.2021.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 05/20/2023]
Abstract
The AP2/ERF (APETALA2/Ethylene Response Factor) transcription factor superfamily plays crucial roles in a slew of physiological processes, such as plant growth and development, stress response, and secondary metabolites biosynthesis. Eggplant, especially the one rich with anthocyanins, is an economically important horticultural vegetable cultivated worldwide. In this study, we comprehensively analyzed the putative AP2/ERF gene family members and their response to abiotic stress in eggplant. As per the phylogenetic, conserved domains, and motif analysis, 178 AP2/ERF genes in this study belonged to five subfamilies. Chromosomal distributions analysis elucidated stochastic distribution of 178 putative SmAP2/ERF genes across the twelve chromosomes of eggplant. Expression profiles of sixteen selected AP2/ERF genes response to low temperature, drought, salt, abscisic acid, and ethylene treatments were analyzed, which revealed the involvement of SmAP2/ERF genes in diverse signaling pathways. In addition, we integrated RNA-Seq data on anthocyanin biosynthesis in eggplant with yeast one-hybrid and dual-luciferase assays and identified involvement of the SmAP2/ERF genes (Smechr0902114.1 and Smechr1102075.1) in the regulation of anthocyanin biosynthesis. This study will enable further functional characterization of AP2/ERF genes in eggplant and extend the current understanding of the role played by AP2/ERF genes in anthocyanin biosynthesis regulation.
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Affiliation(s)
- Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - YongJun He
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Linzhi Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Berghi ON, Vrinceanu D, Cergan R, Dumitru M, Costache A. Solanum melongena allergy (A comprehensive review). Exp Ther Med 2021; 22:1061. [PMID: 34434275 DOI: 10.3892/etm.2021.10495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
The Solanaceae family, including, among other, eggplants, represents the sixth most widely cultivated crops around the globe. We review the current data regarding allergies to Solanum melongena (eggplants), generating symptoms that range from gastrointestinal to respiratory allergic reactions. Currently, there are more than 4 mechanisms and molecules presumably involved in triggering allergic reactions to Solanum melongena: The lipid transfer protein (LTP) pathway, the profilin pathway, polyphenol oxidase (PPO) mechanism and other molecules. Allergies may be triggered both by pollen respiratory reactions and fruit intake. There is also an important cross-reactivity mechanism revealed by recent studies. Our literature review revealed many case series studies, some with in-depth molecular analysis of the triggering mechanism. However, wide population studies are still scarce. Current geographical distribution of the crops and population migrations should enhance the awareness of allergy and immunology specialists, ENT specialists, emergency physicians and pediatricians to the need for proper routine laboratory testing for possible Solanum allergy.
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Affiliation(s)
- Ovidiu Nicolae Berghi
- Department of Oncologic Dermatology, 'Elias' Emergency University Hospital, 011461 Bucharest, Romania
| | - Daniela Vrinceanu
- ENT Department, Bucharest Emergency University Hospital, 010271 Bucharest, Romania
| | - Romica Cergan
- Department of Anatomy, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Mihai Dumitru
- Department of Anatomy, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Adrian Costache
- Pathology Department, 'Carol Davila' University of Medicine and Pharmacy, 020021 Bucharest, Romania
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