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García-Abadillo J, Barba P, Carvalho T, Sosa-Zuñiga V, Lozano R, Carvalho HF, Garcia-Rojas M, Salazar E, y Sánchez JI. Dissecting the complex genetic basis of pre- and post-harvest traits in Vitis vinifera L. using genome-wide association studies. HORTICULTURE RESEARCH 2024; 11:uhad283. [PMID: 38487297 PMCID: PMC10939405 DOI: 10.1093/hr/uhad283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding. We also mapped novel QTL associated with post-harvest traits across chromosomes 2, 4, 9, 11, 15, 18, and 19, broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior, including decay, shriveling, and weight loss. Leveraging gene ontology annotations, we drew parallels between traits and scrutinized candidate genes, laying a robust groundwork for future trait-feature identification endeavors in plant breeding. We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses, as the use of best linear unbiased estimators (BLUEs) corrections in our study may have led to the suppression of some common QTL in grapevine traits. Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits, offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.
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Affiliation(s)
- Julian García-Abadillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo - Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Paola Barba
- Genetic Resources Unit and Germplasm Bank, La Platina, Instituto de Investigaciones Agropecuarias, Av Santa Rosa 11610, La pintana, Santiago, Chile
- Sun World International, 28994 Gromer Av, Wasco, 93280, California, USA
| | | | - Viviana Sosa-Zuñiga
- Instituto de Ciencias Químicas y Aplicadas (ICQA), Universidad Autónoma de Chile, El Llano Subercaseaux 2801, Santiago, Chile
| | | | - Humberto Fanelli Carvalho
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo - Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Miguel Garcia-Rojas
- Genetic Resources Unit and Germplasm Bank, La Platina, Instituto de Investigaciones Agropecuarias, Av Santa Rosa 11610, La pintana, Santiago, Chile
| | - Erika Salazar
- Genetic Resources Unit and Germplasm Bank, La Platina, Instituto de Investigaciones Agropecuarias, Av Santa Rosa 11610, La pintana, Santiago, Chile
| | - Julio Isidro y Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo - Pozuelo de Alarcón, 28223, Madrid, Spain
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Guzmán-Ardiles RE, Pegoraro C, da Maia LC, Costa de Oliveira A. Genetic changes in the genus Vitis and the domestication of vine. FRONTIERS IN PLANT SCIENCE 2023; 13:1019311. [PMID: 36926258 PMCID: PMC10011507 DOI: 10.3389/fpls.2022.1019311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/28/2022] [Indexed: 06/18/2023]
Abstract
The genus Vitis belongs to the Vitaceae family and is divided into two subgenera: Muscadinia and Vitis, the main difference between these subgenera being the number of chromosomes. There are many hypotheses about the origin of the genus, which have been formed with archaeological studies and lately with molecular analyses. Even though there is no consensus on the place of origin, these studies have shown that grapes have been used by man since ancient times, starting later on its domestication. Most studies point to the Near East and Greece as the beginning of domestication, current research suggests it took place in parallel in different sites, but in all cases Vitis vinifera (L.) subsp. sylvestris [Vitis vinifera (L.) subsp. sylvestris (Gmelin) Hagi] seems to be the species chosen by our ancestors to give rise to the now known Vitis vinifera (L.) subsp. vinifera [=sativa (Hegi)= caucasica (Vavilov)]. Its evolution and expansion into other territories followed the formation of new empires and their expansion, and this is where the historical importance of this crop lies. In this process, plants with hermaphrodite flowers were preferentially selected, with firmer, sweeter, larger fruits of different colors, thus favoring the selection of genes associated with these traits, also resulting in a change in seed morphology. Currently, genetic improvement programs have made use of wild species for the introgression of disease resistance genes and tolerance to diverse soil and climate environments. In addition, the mapping of genes of interest, both linked to agronomic and fruit quality traits, has allowed the use of molecular markers for assisted selection. Information on the domestication process and genetic resources help to understand the gene pool available for the development of cultivars that respond to producer and consumer requirements.
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Huang J, Zhang G, Li Y, Lyu M, Zhang H, Zhang N, Chen R. Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines. PeerJ 2023; 11:e14617. [PMID: 36620751 PMCID: PMC9817954 DOI: 10.7717/peerj.14617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
Background Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. 'Jinzao Wuhe' is a bud sport of the elite cultivar 'Himord Seedless' with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. Methods Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for 'Jinzao Wuhe' and its maternal plant 'Himord Seedless' were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. Results In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between 'Himord Seedless' and 'Jinzao Wuhe' harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. Conclusion Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
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Affiliation(s)
- Jianquan Huang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Guan Zhang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China,College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Yanhao Li
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China,College of Horticulture and Gardening, Tianjin Agricultural University, Tianjin, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - He Zhang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Na Zhang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
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Peng Z, Zhao C, Li S, Guo Y, Xu H, Hu G, Liu Z, Chen X, Chen J, Lin S, Su W, Yang X. Integration of genomics, transcriptomics and metabolomics identifies candidate loci underlying fruit weight in loquat. HORTICULTURE RESEARCH 2022; 9:uhac037. [PMID: 35137085 PMCID: PMC9071381 DOI: 10.1093/hr/uhac037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 05/05/2023]
Abstract
Fruit weight is an integral part of fruit-quality traits and directly influences commodity values and economic returns of fruit crops. Despite its importance, the molecular mechanisms underlying fruit weight remain understudied, especially for perennial fruit tree crops such as cultivated loquat (Eriobotrya japonica Lindl.). Auxin is known to regulate fruit development, whereas its role and metabolism in fruit development remain obscure in loquat. In this study, we applied a multi-omics approach, integrating whole-genome resequencing-based quantitative trait locus (QTL) mapping with an F1 population, population genomics analysis using germplasm accessions, transcriptome analysis, and metabolic profiling to identify the genomic regions potentially associated with fruit weight in loquat. We identified three major loci associated with fruit weight, supported by both QTL mapping and comparative genomic analysis between small- and big-fruited loquat cultivars. Comparison between two genotypes with contrasting fruit weight performance through transcriptomic and metabolic profiling revealed an important role of auxin in regulating fruit development, especially at the fruit enlarging stage. The multi-omics approach identified two homologs of ETHYLENE INSENSITIVE 4 (EjEIN4) and TORNADO 1 (EjTRN1) as promising candidates controlling fruit weight. Moreover, three single nucleotide polymorphism (SNP) markers were closely associated with fruit weight. Results from this study provided insights from multiple perspectives into the genetic and metabolic controls of fruit weight in loquat. The candidate genomic regions, genes, and sequence variants will facilitate understanding the molecular basis of fruit weight and lay a foundation for future breeding and manipulation of fruit weight in loquat.
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Affiliation(s)
- Ze Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Chongbin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Shuqing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yihan Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hongxia Xu
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zongli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiuping Chen
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Junwei Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Shunquan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Wenbing Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
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Rojas B, Suárez-Vega F, Saez-Aguayo S, Olmedo P, Zepeda B, Delgado-Rioseco J, Defilippi BG, Pedreschi R, Meneses C, Pérez-Donoso AG, Campos-Vargas R. Pre-Anthesis Cytokinin Applications Increase Table Grape Berry Firmness by Modulating Cell Wall Polysaccharides. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122642. [PMID: 34961114 PMCID: PMC8708260 DOI: 10.3390/plants10122642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
The use of plant growth regulators (PGRs) is widespread in commercial table grape vineyards. The synthetic cytokinin CPPU is a PGR that is extensively used to obtain higher quality grapes. However, the effect of CPPU on berry firmness is not clear. The current study investigated the effects of pre-anthesis applications (BBCH15 and BBCH55 stages) of CPPU on 'Thompson Seedless' berry firmness at harvest through a combination of cytological, morphological, and biochemical analyses. Ovaries in CPPU-treated plants presented morphological changes related to cell division and cell wall modification at the anthesis stage (BBCH65). Moreover, immunofluorescence analysis with monoclonal antibodies 2F4 and LM15 against pectin and xyloglucan demonstrated that CPPU treatment resulted in cell wall modifications at anthesis. These early changes have major repercussions regarding the hemicellulose and pectin cell wall composition of mature fruits, and are associated with increased calcium content and a higher berry firmness at harvest.
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Affiliation(s)
- Bárbara Rojas
- Centro de Estudios Postcosecha, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8831314, Chile; (B.R.); (P.O.)
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile; (S.S.-A.); (J.D.-R.); (C.M.)
| | - Felipe Suárez-Vega
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Susana Saez-Aguayo
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile; (S.S.-A.); (J.D.-R.); (C.M.)
| | - Patricio Olmedo
- Centro de Estudios Postcosecha, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8831314, Chile; (B.R.); (P.O.)
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile; (S.S.-A.); (J.D.-R.); (C.M.)
| | - Baltasar Zepeda
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, P.O. Box 16, 6700 AA Wageningen, The Netherlands;
| | - Joaquín Delgado-Rioseco
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile; (S.S.-A.); (J.D.-R.); (C.M.)
| | - Bruno G. Defilippi
- INIA La Platina, Instituto de Investigaciones Agropecuarias, Santiago 8831314, Chile;
| | - Romina Pedreschi
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile;
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile; (S.S.-A.); (J.D.-R.); (C.M.)
| | - Alonso G. Pérez-Donoso
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Reinaldo Campos-Vargas
- Centro de Estudios Postcosecha, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8831314, Chile; (B.R.); (P.O.)
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Muñoz-Espinoza C, Di Genova A, Sánchez A, Correa J, Espinoza A, Meneses C, Maass A, Orellana A, Hinrichsen P. Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches. BMC PLANT BIOLOGY 2020; 20:365. [PMID: 32746778 PMCID: PMC7397606 DOI: 10.1186/s12870-020-02564-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/21/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. RESULTS Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. CONCLUSIONS We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.
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Affiliation(s)
- Claudia Muñoz-Espinoza
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
| | - Alex Di Genova
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, Universidad de Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
| | - Alicia Sánchez
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - José Correa
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Alonso Espinoza
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Alejandro Maass
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, Universidad de Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
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Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways. FORESTS 2019. [DOI: 10.3390/f10090738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Plant fruit is an important source of natural active phytonutrients that are profitable for human health. Elm (Ulmus pumila) fruit is considered as natural plant food in China that is rich in nutrients. In the present study, high-throughput RNA sequencing was performed in U. pumila edible fruits and leaves and 11,386 unigenes were filtered as dysregulated genes in fruit samples, including 5231 up- and 6155 downregulated genes. Hundreds of pathways were predicted to participate in seed development and phytonutrient biosynthesis in U. pumila by GO, MapMan, and KEGG enrichment analysis, including “seed maturation”, “glycine, serine, and threonine metabolism” and “phenylpropanoid biosynthesis”. ABA-mediated glucose response-related ethylene-activated signaling pathway (e.g., ABI4) were supposed to associate with elm fruit development; unsaturated fatty acids pathway (e.g., ACX2 and SAD) were predicted to participate in determination of fatty acid composition in elm fruit; flavonoid and coumarins biosynthesis (e.g., CYP98A3 and CCoAOMT1) were demonstrated to correlate with the bioactivity of elm fruits in human cancer and inflammation resistance. To provide more information about fruit developmental status, the qRT-PCR analysis for key genes of “phenylpropanoid biosynthesis” and “alpha-Linolenic acid metabolism” were conducted in samples of young fruits, ripe fruit, old fruit, and leaves. Two biosynthetic pathways for unsaturated fatty acid and Jasmonic acid (JA) were deduced to be involved in fruit development in U. pumila and the phenylpropanoid glycoside, syringin, was speculated to accumulate in the early development stages of elm fruit. Our transcriptome data supports molecular clues for seed development and biologically active substances in elm fruits.
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Kodama M, Brinch-Pedersen H, Sharma S, Holme IB, Joernsgaard B, Dzhanfezova T, Amby DB, Vieira FG, Liu S, Gilbert MTP. Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq. BMC Genomics 2018; 19:811. [PMID: 30409110 PMCID: PMC6225646 DOI: 10.1186/s12864-018-5135-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/01/2018] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix-loop-helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the transcription of structural genes in the anthocyanin pathway. Although black cultivars of carrots (Daucus carota L.) can accumulate large quantities of anthocyanin in their storage roots, the regulatory genes responsible for their biosynthesis are not well characterized. The current study aimed to analyze global transcription profiles based on RNA sequencing (RNA-Seq), and mine MYB, bHLH and WD40 genes that may function as positive or negative regulators in the carrot anthocyanin biosynthesis pathways. RESULTS RNA was isolated from differently colored calli, as well as tissue samples from taproots of various black carrot cultivars across the course of development, and gene expression levels of colored and non-colored tissue and callus samples were compared. The expression of 32 MYB, bHLH and WD40 genes were significantly correlated with anthocyanin content in black carrot taproot. Of those, 11 genes were consistently up- or downregulated in a purple color-specific manner across various calli and cultivar comparisons. The expression of 10 out of these 11 genes was validated using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). CONCLUSIONS The results of this study provide insights into regulatory genes that may be responsible for carrot anthocyanin biosynthesis, and suggest that future focus on them may help improve our overall understanding of the anthocyanin synthesis pathway.
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Affiliation(s)
- Miyako Kodama
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Genome Research and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Brinch-Pedersen
- Research Centre Flakkebjerg, Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | - Shrikant Sharma
- Research Centre Flakkebjerg, Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | - Inger Bæksted Holme
- Research Centre Flakkebjerg, Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | | | | | - Daniel Buchvaldt Amby
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Shanlin Liu
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, 518083 China
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- NTNU University Museum, Erling Skakkes gate 47A, 7012 Trondheim, Norway
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Xie S, Tang Y, Wang P, Song C, Duan B, Zhang Z, Meng J. Influence of natural variation in berry size on the volatile profiles of Vitis vinifera L. cv. Merlot and Cabernet Gernischt grapes. PLoS One 2018; 13:e0201374. [PMID: 30231031 PMCID: PMC6145503 DOI: 10.1371/journal.pone.0201374] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/14/2018] [Indexed: 11/18/2022] Open
Abstract
This study was conducted during the 2014 and 2015 vintages on Vitis vinifera L. cv. Merlot and Cabernet Gernischt to investigate whether natural variation in berry size could affect grape aromatic compounds. Grape berries were separated into three size categories based on their diameter: small, middle and large. The results showed that berry size exerted a significant influence on the volatile profiles of both winegrape varieties. Hierarchical clustering analysis demonstrated that the volatile profiles of middle berries were different from those of large and small berries. Middle berries had the greatest abundance of aroma compounds, followed by small and large berries. Especially, C6/C9 compounds, norisoprenoids, terpenoids showed markedly different concentrations among differently sized Merlot berries and C6/C9 compounds, terpenoids among differently sized Cabernet Gernischt berries. Middle berries of both grape varieties may possess the greatest intensity of fresh-green, fruity and floral aromas due to the high odour activity values (OAVs) of decanal, hexanal, (E)-2-hexenal, (E)-β-damascenone and β-ionone in middle sizes of Merlot berries and the high OAVs of (E)-2-hexenal and (E)-β-damascenone in middle sizes of Cabernet Gernischt berries. This knowledge could be important for winemakers to conduct targeted berry sorting, thereby improving the aromatic quality of grapes.
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Affiliation(s)
- Sha Xie
- College of Enology, Northwest A & F University, Yangling, Shaanxi, China
| | - Yonghong Tang
- College of Enology, Northwest A & F University, Yangling, Shaanxi, China
| | - Peng Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Changzheng Song
- College of Enology, Northwest A & F University, Yangling, Shaanxi, China
| | - Bingbing Duan
- College of Enology, Northwest A & F University, Yangling, Shaanxi, China
| | - Zhenwen Zhang
- College of Enology, Northwest A & F University, Yangling, Shaanxi, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, Shaanxi, China
- * E-mail: (ZZ); (JM)
| | - Jiangfei Meng
- College of Enology, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (ZZ); (JM)
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10
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Das P, Majumder AL. Transcriptome analysis of grapevine under salinity and identification of key genes responsible for salt tolerance. Funct Integr Genomics 2018; 19:61-73. [PMID: 30046943 DOI: 10.1007/s10142-018-0628-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/04/2018] [Accepted: 07/11/2018] [Indexed: 02/02/2023]
Abstract
The negative effects of soil salinity towards grape yield depend upon salt concentration, cultivar type, developmental stage, and rootstock. Thompson Seedless variety of grape plant is considered moderately sensitive to salinity when grown upon its own root stock. In recent epoch, identification of key genes responsive to salinity offers hope to generate salinity-tolerant crop plants by their overexpression through genetic manipulation. In the present report, salt responsive transcriptome analysis of Thompson Seedless grape variety was done to identify vital genes involved in salinity tolerance which could be used further to generate salt liberal grape plant or other crop plants. Transcriptome libraries for control and 150-mM-NaCl-treated grape leaves were sequenced on Illumina platform where 714 genes were found to be differentially expressed. Gene ontology analysis indicated that under salinity conditions, the genes involved in metabolic process were highly enriched. Keto Encyclopedia of Genes and Genomes analysis revealed that, among the top 22 enriched pathways for the salt stress upregulated genes, the carbohydrate metabolism, signal transduction, energy metabolism, amino acid metabolism, biosynthesis of secondary metabolite, and lipid metabolism pathways possessed the largest number of transcripts. Key salinity-induced genes were selected and validated through qRT-PCR analysis which was comparable to RNA-seq results. Real-time PCR analysis also revealed that after 24 days of salinity, the expression of most of the selected key genes was highest. These salinity-induced genes will be characterized further in a model plant and also in Vitis vinifera through transgenic approach to disclose their role towards salt tolerance.
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Affiliation(s)
- Priyanka Das
- Division of Plant Biology, Bose Institute, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India.
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India.
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11
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Cardone MF, D'Addabbo P, Alkan C, Bergamini C, Catacchio CR, Anaclerio F, Chiatante G, Marra A, Giannuzzi G, Perniola R, Ventura M, Antonacci D. Inter-varietal structural variation in grapevine genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:648-661. [PMID: 27419916 DOI: 10.1111/tpj.13274] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 05/10/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties.
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Affiliation(s)
- Maria Francesca Cardone
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, TR-06800, Turkey
| | - Carlo Bergamini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | | | - Fabio Anaclerio
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Giorgia Chiatante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Annamaria Marra
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rocco Perniola
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Donato Antonacci
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
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