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Shavrukov Y, Hinrichsen P, Watanabe S. Editorial: Plant genotyping: from traditional markers to modern technologies. Front Plant Sci 2024; 15:1419798. [PMID: 38745928 PMCID: PMC11093220 DOI: 10.3389/fpls.2024.1419798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Affiliation(s)
- Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
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Mathias-Ramwell M, Pavez V, Meneses M, Fernández F, Valdés A, Lobos I, Silva M, Saldaña R, Hinrichsen P. Phenotypic and genetic characterization of an Avena sativa L. germplasm collection of diverse origin: implications for food-oat breeding in Chile. Front Plant Sci 2023; 14:1298591. [PMID: 38179484 PMCID: PMC10764548 DOI: 10.3389/fpls.2023.1298591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024]
Abstract
Oats are known for their nutritional value and also for their beneficial properties on human health, such as the reduction of cholesterol levels and risk of coronary heart disease; they are an important export product for Chile. During the last decade (2010-2022) over 90% of the oat cultivated area in Chile has been covered with Avena sativa L. cv. Supernova INIA. This lack of genetic diversity in a context of climate change could limit the long-term possibility of growing oats in Chile. The present study is a phenotypic and genetic analysis of 132 oat cultivars and pure lines of diverse origin that can be considered as potential breeding material. The germplasm was evaluated for 28 traits and analyzed with 14 SSR markers. The effects of genotypes on phenotype were significant over all traits (P ≤ 0.05). Most traits exhibited moderate to high broad-sense heritability with exceptions such as yield (H2 = 0.27) and hulls staining (H2 = 0.32). Significant undesirable correlations between traits were generally of small biological importance, which is auspicious for achieving breeding objectives. Some of the heritability data and correlations provided here have not been previously reported. The overall phenotypic diversity was high (H' = 0.68 ± 0.18). The germplasm was grouped into three phenotypic clusters, differing in their qualities for breeding. Twenty-six genotypes outperforming Supernova INIA were identified for breeding of conventional food-oats. The genetic diversity of the germplasm was moderate on average (He = 0.58 ± 0.03), varying between 0.32 (AM22) and 0.77 (AME178). Two genetic subpopulations supported by the Structure algorithm exhibited a genetic distance of 0.24, showing low divergence of the germplasm. The diversity and phenotypic values found in this collection of oat genotypes are promising with respect to obtaining genetic gain in the short term in breeding programs. However, the similar genetic diversity, higher phenotypic diversity, and better phenotypic performance of the germplasm created in Chile compared to foreign germplasm suggest that germplasm harboring new genetic diversity will be key to favor yield and quality in new oat cultivars in the long term.
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Affiliation(s)
- Mónica Mathias-Ramwell
- Programa de mejoramiento genético de avena, Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Carillanca, Temuco, Chile
| | - Valentina Pavez
- Laboratorio de Análisis Genético, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La Platina, Santiago, Chile
| | - Marco Meneses
- Laboratorio de Análisis Genético, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La Platina, Santiago, Chile
| | - Feledino Fernández
- Programa de mejoramiento genético de avena, Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Carillanca, Temuco, Chile
| | - Adriana Valdés
- Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Iris Lobos
- Laboratorio de Espectroscopía Infrarrojo Cercano, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Remehue, Osorno, Chile
| | - Mariela Silva
- Laboratorio de Espectroscopía Infrarrojo Cercano, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Remehue, Osorno, Chile
| | - Rodolfo Saldaña
- Laboratorio de Nutrición Animal y Medio Ambiente, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Remehue, Osorno, Chile
| | - Patricio Hinrichsen
- Laboratorio de Análisis Genético, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La Platina, Santiago, Chile
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Muñoz-Espinoza C, Meneses M, Hinrichsen P. Transcriptomic Approach for Global Distribution of SNP/Indel and Plant Genotyping. Methods Mol Biol 2023; 2638:147-164. [PMID: 36781640 DOI: 10.1007/978-1-0716-3024-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Single Nucleotide Polymorphisms (SNPs) are the most common structural variants found in any genome. They have been used for different genetic studies, from the understanding of genetic structure of populations to the development of breeding selection markers. In this chapter we present the use of transcriptomic data obtained from contrasting phenotypes for a target trait, in searching of SNPs and insertions/deletions (InDels). This approach has the advantage that the identified markers are in or close to differentially expressed genes, and so they have higher chances to tag the genes underlying the phenotypic expression of a particular trait.
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Affiliation(s)
| | - Marco Meneses
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile.
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Correa F, Beltrán MF, Millas P, Moreno Z, Hinrichsen P, Meza P, Sagredo B. Genome Sequence Resources of Pseudomonas syringae Strains Isolated from Sweet Cherry Orchards in Chile. Mol Plant Microbe Interact 2022; 35:933-937. [PMID: 36176216 DOI: 10.1094/mpmi-04-22-0092-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Francisco Correa
- Instituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile
| | - M Francisca Beltrán
- Instituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile
| | - Paz Millas
- Instituto de Investigaciones Agropecuarias (INIA), INIA Quilamapu. Avenida Vicente Méndez 515, Chillán, Chile
| | - Zoe Moreno
- Instituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias (INIA), INIA La Platina. Avenida Santa Rosa 11610, La Pintana, Santiago, Chile
| | - Pablo Meza
- Instituto de Investigaciones Agropecuarias (INIA), INIA La Platina. Avenida Santa Rosa 11610, La Pintana, Santiago, Chile
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile
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Aguirre C, Sánchez E, Olivares N, Hinrichsen P. Multiplex TaqMan Real-Time PCR Assay for Sensitive Detection of Two Weevil Species (Coleoptera: Curculionidae). J Econ Entomol 2021; 114:90-99. [PMID: 33155656 DOI: 10.1093/jee/toaa251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Indexed: 06/11/2023]
Abstract
Rapid and cost-efficient identification of Naupactus species is becoming a key process for the exportation of citrus fruit from Chile and other countries, considering the quarantine regulations for some species of the cosmopolitan genus Naupactus. This study deals with the development of a fast and sensitive detection protocol for Naupactus cervinus (Coleoptera: Curculionidae) (Boheman) and Naupactus xanthographus (Coleoptera: Curculionidae) (Germar) based on multiplex TaqMan Real-time polymerase chain reaction. Both N. cervinus and N. xanthographus primer and probe sets achieved species-specific detection in a linear range from 1 pg/μl to 1 × 10-6 pg/μl, allowing detection of as few as 160 copies of template DNA. Non-target amplifications were not detected and a panel composed of 480 test samples had 100% coincidence with the respective morphological identification.
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Affiliation(s)
- Carlos Aguirre
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11,610, Santiago, Chile
| | - Evelyn Sánchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - Natalia Olivares
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, Chorrillos 86, La Cruz, Quillota, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11,610, Santiago, Chile
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Aguirre C, Olivares N, Hinrichsen P. An Efficient Duplex PCR Method for Sex Identification of the European Grapevine Moth Lobesia botrana (Lepidoptera: Tortricidae) at Any Developmental Stage. J Econ Entomol 2020; 113:2505-2510. [PMID: 32676656 DOI: 10.1093/jee/toaa155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 06/11/2023]
Abstract
Many genetic studies in insects require sex identification of individuals in all developmental stages. The most common sex chromosome system in lepidopterans is WZ/ZZ; the W chromosome is present only in females. Based on two W chromosome-specific short sequences (CpW2 and CpW5) described in Cydia pomonella (L.) (Lepidoptera: Tortricidae), we identified homologous female-specific sequences in Lobesia botrana Den. & Schiff, a polyphagous and very harmful species present in Chile since 2008. From this starting point, we extended the sequence information using the inverse PCR method, identifying the first W-specific sequences described up to now for the moth. Finally, we developed a duplex PCR method for rapid and sensitive determination of sex in L. botrana from larva to adult. The method showed a detection limit of 1 pg of genomic DNA; a blind panel of samples exhibited exact correspondence with the morphological identification. These results will be very useful for studies requiring sex-specific analyses at any developmental stage, contributing also to the understanding of gene expression in the insect, as well as to the eventual development of control protocols against the moth, such as the development of genetic sexing strains for the implementation of the sterile insect technique.
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Affiliation(s)
- Carlos Aguirre
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | - Natalia Olivares
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, La Cruz, Quillota, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
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Álvarez Á, Yáñez J, Neira Y, Castillo-Felices R, Hinrichsen P. Simple distinction of grapevine (Vitis vinifera L.) genotypes by direct ATR-FTIR. Food Chem 2020; 328:127164. [DOI: 10.1016/j.foodchem.2020.127164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 05/14/2020] [Accepted: 05/25/2020] [Indexed: 10/24/2022]
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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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Meneses M, García-Rojas M, Muñoz-Espinoza C, Carrasco-Valenzuela T, Defilippi B, González-Agüero M, Meneses C, Infante R, Hinrichsen P. Transcriptomic study of pedicels from GA 3-treated table grape genotypes with different susceptibility to berry drop reveals responses elicited in cell wall yield, primary growth and phenylpropanoids synthesis. BMC Plant Biol 2020; 20:66. [PMID: 32041534 PMCID: PMC7011282 DOI: 10.1186/s12870-020-2260-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/20/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Gibberellins (GA3) are the most sprayed growth regulator for table grape production worldwide, increasing berry size of seedless varieties through pericarp cell expansion. However, these treatments also exacerbate berry drop, which has a detrimental effect on the postharvest quality of commercialized clusters. Several studies have suggested that pedicel stiffening caused by GA3 would have a role in this disorder. Nevertheless, transcriptional and phenotypic information regarding pedicel responses to GA3 is minimal. RESULTS Characterization of responses to GA3 treatments using the lines L23 and Thompson Seedless showed that the former was up to six times more susceptible to berry drop than the latter. GA3 also increased the diameter and dry matter percentage of the pedicel on both genotypes. Induction of lignin biosynthesis-related genes by GA3 has been reported, so the quantity of this polymer was measured. The acetyl bromide method detected a decreased concentration of lignin 7 days after GA3 treatment, due to a higher cell wall yield of the isolated fractions of GA3-treated pedicel samples which caused a dilution effect. Thus, an initial enrichment of primary cell wall components in response to GA3 was suggested, particularly in the L23 background. A transcriptomic profiling was performed to identify which genes were associated with these phenotypic changes. This analysis identified 1281 and 1787 genes differentially upregulated by GA3 in L23 and cv. Thompson Seedless, respectively. Concomitantly, 1202 and 1317 downregulated genes were detected in L23 and cv. Thompson Seedless (FDR < 0.05). Gene ontology analysis of upregulated genes showed enrichment in pathways including phenylpropanoids, cell wall metabolism, xylem development, photosynthesis and the cell cycle at 7 days post GA3 application. Twelve genes were characterized by qPCR and striking differences were observed between genotypes, mainly in genes related to cell wall synthesis. CONCLUSIONS High levels of berry drop are related to an early strong response of primary cell wall synthesis in the pedicel promoted by GA3 treatment. Genetic backgrounds can produce similar phenotypic responses to GA3, although there is considerable variation in the regulation of genes in terms of which are expressed, and the extent of transcript levels achieved within the same time frame.
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Affiliation(s)
- Marco Meneses
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santiago, Chile
| | - Miguel García-Rojas
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Tomás Carrasco-Valenzuela
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Bruno Defilippi
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | | | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Infante
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile.
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Ravest G, León‐Lobos P, Aguirre C, Hernández J, Bolados G, Castro MH, Silva S, Hinrichsen P. New microsatellites for the Atacama Desert endemic Balsamocarpon brevifolium (Fabaceae). Appl Plant Sci 2019; 7:e11271. [PMID: 31236318 PMCID: PMC6580986 DOI: 10.1002/aps3.11271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Algarrobilla (Balsamocarpon brevifolium, Fabaceae) is an endemic xerophytic shrub restricted to the Atacama Desert in northern Chile. Extensive utilization of the region for coal production has endangered this species. Conservation efforts are underway, with genetic diversity analyses being key to the restoration of these populations. METHODS AND RESULTS Fifteen new microsatellite markers were developed for B. brevifolium and used to analyze three populations from the Atacama and Coquimbo regions in Chile. Microsatellites were highly polymorphic, with an average of 5.77 alleles per marker and an average level of expected heterozygosity of 0.72. These markers were evaluated and cross-amplified on two related species (Senna cumingii and Caesalpinia angulata) with partial success. CONCLUSIONS The development of this set of markers permits an extensive study of B. brevifolium populations for conservation purposes.
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Affiliation(s)
- Gonzalo Ravest
- Instituto de Investigaciones Agropecuarias (INIA) La PlatinaSanta Rosa11610SantiagoChile
| | - Pedro León‐Lobos
- Instituto de Investigaciones Agropecuarias (INIA) La PlatinaSanta Rosa11610SantiagoChile
| | - Carlos Aguirre
- Instituto de Investigaciones Agropecuarias (INIA) La PlatinaSanta Rosa11610SantiagoChile
| | | | | | - María Herminia Castro
- Instituto de Investigaciones Agropecuarias (INIA) La PlatinaSanta Rosa11610SantiagoChile
| | | | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias (INIA) La PlatinaSanta Rosa11610SantiagoChile
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Del Pozo T, Miranda S, Latorre M, Olivares F, Pavez L, Gutiérrez R, Maldonado J, Hinrichsen P, Defilippi BG, Orellana A, González M. Comparative Transcriptome Profiling in a Segregating Peach Population with Contrasting Juiciness Phenotypes. J Agric Food Chem 2019; 67:1598-1607. [PMID: 30632375 DOI: 10.1021/acs.jafc.8b05177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cold storage of fruit is one of the methods most commonly employed to extend the postharvest lifespan of peaches ( Prunus persica (L.) Batsch). However, fruit quality in this species is affected negatively by mealiness, a physiological disorder triggered by chilling injury after long periods of exposure to low temperatures during storage and manifested mainly as a lack of juiciness, which ultimately modifies the organoleptic properties of peach fruit. The aim of this study was to identify molecular components and metabolic processes underlying mealiness in susceptible and nonsusceptible segregants. Transcriptome and qRT-PCR profiling were applied to individuals with contrasting juiciness phenotypes in a segregating F2 population. Our results suggest that mealiness is a multiscale phenomenon, because juicy and mealy fruit display distinctive reprogramming processes affecting translational machinery and lipid, sugar, and oxidative metabolism. The candidate genes identified may be useful tools for further crop improvement.
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Affiliation(s)
- Talía Del Pozo
- Centro Tecnológico de Recursos Vegetales, Faculty of Sciences , Universidad Mayor , Santiago, Chile, Camino La Pirámide 5750 , Huechuraba , Santiago , Chile
- Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile
| | - Simón Miranda
- Centro Tecnológico de Recursos Vegetales, Faculty of Sciences , Universidad Mayor , Santiago, Chile, Camino La Pirámide 5750 , Huechuraba , Santiago , Chile
- Laboratorio de Genética Molecular Vegetal , INTA, Universidad de Chile , Av. El Líbano 5524 , Macul , Santiago , Chile
| | - Mauricio Latorre
- Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile
- FONDAP Center for Genome Regulation, Av. Blanco Encalada 2085 , Santiago , Chile
- Instituto de Ingeniería , Universidad de O'Higgins , Av. Libertador Bernardo O'Higgins 611 , Rancagua , Chile
- Mathomics, Center for Mathematical Modeling , Universidad de Chile , Av. Almirante Beauchef 851, Seventh Floor , Santiago , Chile
| | - Felipe Olivares
- Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile
| | - Leonardo Pavez
- Instituto de Ciencias Naturales , Universidad de Las Américas , Av. Manuel Montt 948 , Santiago , Chile
- Departamento de Ciencias Químicas y Biológicas , Universidad Bernardo O'Higgins , General Gana 1702 , Santiago , Chile
| | - Ricardo Gutiérrez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) , University of Cologne , Cologne , Germany
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile
| | - Patricio Hinrichsen
- Laboratorio de Biotecnología , Instituto de Investigaciones Agropecuarias , INIA La Platina, Santa Rosa 11610 , Santiago , Chile
| | - Bruno G Defilippi
- Unidad de Poscosecha , Instituto de Investigaciones Agropecuarias , INIA La Platina, Santa Rosa 11610 , Santiago , Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Av. Blanco Encalada 2085 , Santiago , Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida , Universidad Andrés Bello , Santiago , Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile
- FONDAP Center for Genome Regulation, Av. Blanco Encalada 2085 , Santiago , Chile
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García-Rojas M, Meneses M, Oviedo K, Carrasco C, Defilippi B, González-Agüero M, León G, Hinrichsen P. Exogenous gibberellic acid application induces the overexpression of key genes for pedicel lignification and an increase in berry drop in table grape. Plant Physiol Biochem 2018; 126:32-38. [PMID: 29499433 DOI: 10.1016/j.plaphy.2018.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/10/2018] [Accepted: 02/08/2018] [Indexed: 05/22/2023]
Abstract
Most table grape (Vitis vinifera L.) varieties require gibberellic acid (GA3) applications to obtain an adequate berry size in order to satisfy market requirements. However, GA3 treatments also produce severe berry drop in some cultivars, which occurs mainly after a cold storage period during post-harvest. Berry drop in bunches treated with GA3 has been related to the hardening and thickening of the pedicel produced by the over-accumulation of cellulose and its lignification. The main goal of this study was to compare the morphology and gene expression in pedicel samples of genotypes contrasting for berry drop susceptibility. These genotypes are Thompson Seedless, which exhibits a low incidence of berry drop, and a genetic line (Line #23) of INIA's breeding program that is very susceptible to berry drop at harvest and after storage in bunches sprayed with GA3. The parameters measured to study this phenomenon during fruit growth and post-harvest storage included fruit detachment force (FDF), hardness and thickness of the pedicel and berry drop frequency. Histological analyses of pedicel structures at harvest showed an increase in cell size and deposition of lignin in the cortex zone in both contrasting genotypes treated with GA3. The expression profile in both genotypes of the key lignin biosynthesis genes Vv4CL4, VvCCR1L and VvCAD1 analyzed by quantitative real time PCR (qPCR) revealed evident changes in response to GA3 treatments. In particular, gene VvCAD1 is overexpressed (100X) in pedicels of line #23 treated with GA3 after 30 and 45 days in cold storage compared to control. Moreover, the frequency of berry drop was higher for Line #23 treated with GA3 than for the control (23% vs. 1%). Our results suggest that gibberellic acid regulates the expression of the biosynthesis of lignin genes, generating changes in cell wall composition and pedicel structure that result in an increase in berry drop.
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Affiliation(s)
- Miguel García-Rojas
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | - Marco Meneses
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile; Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santiago, Chile
| | - Kristen Oviedo
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | - Carlos Carrasco
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | - Bruno Defilippi
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | | | - Gabriel León
- Centro de Biotecnología Vegetal, Facultad de Ciencia Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile.
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Bustamante L, Sáez V, Hinrichsen P, Castro MH, Vergara C, von Baer D, Mardones C. Differences in Vvufgt and VvmybA1 Gene Expression Levels and Phenolic Composition in Table Grape (Vitis vinifera L.) 'Red Globe' and Its Somaclonal Variant 'Pink Globe'. J Agric Food Chem 2017; 65:2793-2804. [PMID: 28274120 DOI: 10.1021/acs.jafc.6b04817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel 'Red Globe' (RG)-derived grape variety, 'Pink Globe' (PG), was described and registered as a new genotype, with earlier ripening and sweeter taste than those of RG. Microsatellite analysis revealed that PG and RG are undifferentiable; however, the PG VvmybA1c contains six single-nucleotide polymorphisms within the coding and noncoding region, possibly related to the reduced VvmybA1 expression levels. Conversely, HPLC-DAD-ESI-MS/MS analysis showed significantly lower anthocyanin content in PG skin than in RG skin, and PG had no detectable trihydroxylated anthocyanins. Total flavonols did not differ between the variants, although some quercetin derivate concentrations were lower in PG. HPLC-FLD analysis revealed slightly higher concentrations of epicatechin and a procyanidin dimer in PG seeds, although the antioxidant capacity of crude extracts from either variety did not differ significantly. These differences, particularly in monomeric anthocyanin content, can be attributed to altered activity of a MYB-type transcription factor, reducing Vvufgt expression.
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Affiliation(s)
- Luis Bustamante
- Instrumental Analysis Department, Faculty of Pharmacy, University of Concepción , P.O. Box 160-C, Concepción, Chile
| | - Vania Sáez
- Instrumental Analysis Department, Faculty of Pharmacy, University of Concepción , P.O. Box 160-C, Concepción, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA La Platina , Santa Rosa 11610 La Pintana, Santiago, Chile
| | - María H Castro
- Instituto de Investigaciones Agropecuarias, INIA La Platina , Santa Rosa 11610 La Pintana, Santiago, Chile
| | - Carola Vergara
- Instrumental Analysis Department, Faculty of Pharmacy, University of Concepción , P.O. Box 160-C, Concepción, Chile
| | - Dietrich von Baer
- Instrumental Analysis Department, Faculty of Pharmacy, University of Concepción , P.O. Box 160-C, Concepción, Chile
| | - Claudia Mardones
- Instrumental Analysis Department, Faculty of Pharmacy, University of Concepción , P.O. Box 160-C, Concepción, Chile
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Muñoz-Espinoza C, Di Genova A, Correa J, Silva R, Maass A, González-Agüero M, Orellana A, Hinrichsen P. Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. BMC Plant Biol 2016; 16:104. [PMID: 27118480 PMCID: PMC4845426 DOI: 10.1186/s12870-016-0789-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/18/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6-8 mm berries (B68) phenological stages. RESULTS A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. CONCLUSIONS We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.
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Affiliation(s)
- Claudia Muñoz-Espinoza
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. Repúbica 217, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Alex Di Genova
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, University of Chile, Av. Blanco Encalada 2120, 7th Floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - José Correa
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile
| | - Romina Silva
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile
| | - Alejandro Maass
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, University of Chile, Av. Blanco Encalada 2120, 7th Floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Mauricio González-Agüero
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. Repúbica 217, 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 11, 610, Santiago, Chile.
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Guajardo V, Hinrichsen P, Muñoz C. Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model. Chilean J Agric Res 2015. [PMID: 0 DOI: 10.4067/s0718-58392015000300003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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16
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Guajardo V, Solís S, Sagredo B, Gainza F, Muñoz C, Gasic K, Hinrichsen P. Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS). PLoS One 2015; 10:e0127750. [PMID: 26011256 PMCID: PMC4444190 DOI: 10.1371/journal.pone.0127750] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/17/2015] [Indexed: 11/18/2022] Open
Abstract
Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a ‘Rainier’ x ‘Rivedel’ (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in ‘Rainier’, ‘Rivedel’ and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for ‘Rainier’, ‘Rivedel’ and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both ‘Rainier’ and ‘Rivedel’ maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.
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Affiliation(s)
- Verónica Guajardo
- Centro de Estudios Avanzados en Fruticultura (CEAF), Los Choapinos, Rengo, Chile
| | - Simón Solís
- Centro de Estudios Avanzados en Fruticultura (CEAF), Los Choapinos, Rengo, Chile
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias, INIA Rayentué, Rengo, Chile
| | - Felipe Gainza
- Centro de Estudios Avanzados en Fruticultura (CEAF), Los Choapinos, Rengo, Chile
| | - Carlos Muñoz
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Ksenija Gasic
- Department of Agricultural and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
- * E-mail:
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17
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Aguirre C, Olivares N, Luppichini P, Hinrichsen P. A PCR-Based Diagnostic System for Differentiating Two Weevil Species (Coleoptera: Curculionidae) of Economic Importance to the Chilean Citrus Industry. J Econ Entomol 2015; 108:107-113. [PMID: 26470110 DOI: 10.1093/jee/tou041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/14/2014] [Indexed: 06/05/2023]
Abstract
A PCR-based method was developed to identify Naupactus cervinus (Boheman) and Naupactus xanthographus (Germar), two curculionids affecting the citrus industry in Chile. The quarantine status of these two species depends on the country to which fruits are exported. This identification method was developed because it is not possible to discriminate between these two species at the egg stage. The method is based on the species-specific amplification of sequences of internal transcribed spacers, for which we cloned and sequenced these genome fragments from each species. We designed an identification system based on two duplex-PCR reactions. Each one contains the species-specific primer set and a second generic primer set that amplify a short 18S region common to coleopterans, to avoid false negatives. The marker system is able to differentiate each Naupactus species at any life stage, and with a diagnostic sensitivity to 0.045 ng of genomic DNA. This PCR kit was validated by samples collected from different citrus production areas throughout Chile and showed 100% accuracy in differentiating the two Naupactus species.
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Affiliation(s)
- C Aguirre
- Biotechnology Lab, La Platina Experimental Center, Instituto de Investigaciones Agropecuarias (INIA), Santa Rosa 11,610, Santiago, 8820000, Chile. Doctoral Program in Agricultural and Veterinary Sciences, Universidad de Chile, Santa Rosa 11,315, Santiago, 8820000, Chile
| | - N Olivares
- La Cruz Experimental Center, Instituto de Investigaciones Agropecuarias (INIA), Chorrillos 86, La Cruz, Quillota, 2260000, Chile
| | - P Luppichini
- La Cruz Experimental Center, Instituto de Investigaciones Agropecuarias (INIA), Chorrillos 86, La Cruz, Quillota, 2260000, Chile
| | - P Hinrichsen
- Biotechnology Lab, La Platina Experimental Center, Instituto de Investigaciones Agropecuarias (INIA), Santa Rosa 11,610, Santiago, 8820000, Chile.
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18
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Correa J, Mamani M, Muñoz-Espinoza C, Laborie D, Muñoz C, Pinto M, Hinrichsen P. Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L.). Theor Appl Genet 2014; 127:1143-62. [PMID: 24556794 DOI: 10.1007/s00122-014-2286-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 02/04/2014] [Indexed: 05/18/2023]
Abstract
We have identified 19 QTLs for rachis architecture, a key and complex trait for grapevine production. Fifty out of 1,173 genes underlying these QTLs are candidates to be further explored. In the table grape industry, the rachis architecture has economic and management implications. Therefore, understanding the genetics of this trait is key for its breeding. The aim of this work was to identify genetic determinants of traits associated with the cluster architecture. Characterisations of eight traits was performed on a 'Ruby Seedless' × 'Sultanina' crossing (F1: n = 137) during three seasons, with and without gibberellic acid (GA3) applications. The genotypic effects and the genotype × GA3 interactions were significant for several traits. Rachis length (rl), lateral shoulder length and node number along the central axis were the most prominent traits. On average, the heritability of these traits was ~71 %, with heritability of rl being 76 % as estimated under different seasons. Quantitative trait loci (QTLs) analyses showed that linkage group 5 (LG5) and LG18 harboured the largest number of QTLs for these traits. According to the variance explained, the main QTL (corresponding to rl) was found on LG9. These QTLs were supported mainly by a paternal additive effect and revealed possible pleiotropic effects. Based on the grapevine reference genome, we identified 1,173 genes located under these QTL confidence intervals. Fifty of the 891 annotated genes of this list were selected for their further characterisation because of their possible participation in the rachis architecture. In conclusion, the QTLs detected indicate that these traits and their GA3 responsiveness have a clear genetic basis. Due to the percentage of the total variance explained, they are good candidates to participate in the genetic determination of the cluster architecture.
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Affiliation(s)
- J Correa
- Facultad de Agronomía, Universidad de Chile, Santiago, Chile
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19
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Di Genova A, Almeida AM, Muñoz-Espinoza C, Vizoso P, Travisany D, Moraga C, Pinto M, Hinrichsen P, Orellana A, Maass A. Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants. BMC Plant Biol 2014; 14:7. [PMID: 24397443 PMCID: PMC3890619 DOI: 10.1186/1471-2229-14-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/27/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. 'Sultanina' plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome. RESULTS Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in 'Sultanina' and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes. CONCLUSIONS This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes.
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Affiliation(s)
- Alex Di Genova
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
| | - Andrea Miyasaka Almeida
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. República 237, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. República 237, Santiago, Chile
| | - Paula Vizoso
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. República 237, Santiago, Chile
| | - Dante Travisany
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
| | - Carol Moraga
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. República 237, Santiago, Chile
| | - Manuel Pinto
- Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, Santiago, La Pintana, Chile
| | - Patricio Hinrichsen
- Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, Santiago, La Pintana, Chile
| | - Ariel Orellana
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. República 237, Santiago, Chile
| | - Alejandro Maass
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
- Department of Mathematical Engineering, University of Chile, Av. Blanco Encalada 2120, 5th floor, Santiago, Chile
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20
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González-Agüero M, García-Rojas M, Di Genova A, Correa J, Maass A, Orellana A, Hinrichsen P. Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data. BMC Genomics 2013; 14:878. [PMID: 24330674 PMCID: PMC3878734 DOI: 10.1186/1471-2164-14-878] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 12/02/2013] [Indexed: 11/10/2022] Open
Abstract
Background Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and experimental errors occurring during sample preparation and expression measurements. However, the transcription level of the most commonly used reference genes can vary considerably in samples obtained from different individuals, tissues, developmental stages and under variable physiological conditions, resulting in a misinterpretation of the performance of the target gene(s). This issue has been scarcely approached in woody species such as grapevine. Results A statistical criterion was applied to select a sub-set of 19 candidate reference genes from a total of 242 non-differentially expressed (NDE) genes derived from a RNA-Seq experiment comprising ca. 500 million reads obtained from 14 table-grape genotypes sampled at four phenological stages. From the 19 candidate reference genes, VvAIG1 (AvrRpt2-induced gene) and VvTCPB (T-complex 1 beta-like protein) were found to be the most stable ones after comparing the complete set of genotypes and phenological stages studied. This result was further validated by qPCR and geNorm analyses. Conclusions Based on the evidence presented in this work, we propose to use the grapevine genes VvAIG1 or VvTCPB or both as a reference tool to normalize RNA expression in qPCR assays or other quantitative method intended to measure gene expression in berries and other tissues of this fruit crop, sampled at different developmental stages and physiological conditions.
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Affiliation(s)
| | | | | | | | | | | | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias (INIA -Chile), La Platina Research Centre, Santiago, Chile, Av, Santa Rosa 11, 610, P,O, Box 439-3, Santiago, Chile.
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21
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Nilo-Poyanco R, Olivares D, Orellana A, Hinrichsen P, Pinto M. Proteomic analysis of grapevine (Vitis vinifera L.) leaf changes induced by transition to autotrophy and exposure to high light irradiance. J Proteomics 2013; 91:309-30. [PMID: 23933133 DOI: 10.1016/j.jprot.2013.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 06/25/2013] [Accepted: 07/02/2013] [Indexed: 01/08/2023]
Abstract
UNLABELLED Using a proteomics approach, we evaluated the response of heterotrophic and autotrophic leaves of grapevine when exposed to high light irradiation. From a total of 572 protein spots detected on two-dimensional gels, 143 spots showed significant variation caused by changes in the trophic state. High light treatment caused variation in 90 spots, and 51 spots showed variation caused by the interaction between both factors. Regarding the trophic state of the leaf, most of the proteins detected in the heterotrophic stage decreased in abundance when the leaf reached the autotrophic stage. Major differences induced by high light were detected in autotrophic leaves. In the high-light-treated autotrophic leaves several proteins involved in the oxidative stress response were up-regulated. This pattern was not observed in the high-light-treated heterotrophic leaves. This indicates that in these types of leaves other mechanisms different to the protein antioxidant system are acting to protect young leaves against the excess of light. This also suggests that these protective mechanisms rely on other sets of proteins or non-enzymatic molecules, or that differences in protein dynamics between the heterotrophic and autotrophic stages makes the autotrophic leaves more prone to the accumulation of oxidative stress response proteins. BIOLOGICAL SIGNIFICANCE Transition from a heterotrophic to an autotrophic state is a key period during which the anatomical, physiological and molecular characteristics of a leaf are defined. In many aspects the right functioning of a leaf at its mature stage depends on the conditions under what this transition occurs. This because apart of the genetic control, environmental factors like mineral nutrition, temperature, water supply, light etc. are also important in its control. Many anatomical and physiological changes have been described in several plant species, however in grapevine molecular data regarding changes triggered by this transition or by light stress are still scarce. In this study, we identify that the transition from heterotrophic to autotrophic state in grapevine triggers major changes in the leaf proteome, which are mainly related to processes such as protein synthesis, protein folding and degradation, photosynthesis and chloroplast development. With the exception of proteins involved in carbon fixation, that increased in abundance, most of the proteins detected during the heterotrophic stage decreased in abundance when the leaf reached its autotrophic stage. This is most likely because leaves have reached their full size and from now they have to work as a carbon source for sink organs located in other parts of the plant. Despite the potential control of this transition by light, to date, no studies using a proteomics approach have been conducted to gain a broader view of the effects of short-term high light stress. Our results indicate that short-term high light exposure has a major impact on the proteome of the autotrophic leaves, and trigger a differential accumulation of several proteins involved in the oxidative stress response. Surprisingly, heterotrophic leaves do not display this pattern which can be attributed to a lower sensitivity of these leaves to high light stimulus. In fact we discovered that heterotrophic leaves are more tolerant to light stress than autotrophic leaves. This finding is of high biological significance because it helps to understand how young leaves are able to evolve to autotrophy in areas where high light intensities are predominant. This also reveals in this type of leaves the existence of alternative mechanisms to address this stressful condition. These observations provide new insights into the molecular changes occurring during transition of leaves to autotrophy particularly when this transition occurs under high light intensities. This for example occurs during the springtime when the grapevine buds burst and the young leaves are suddenly exposed to high light intensities.
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Affiliation(s)
- R Nilo-Poyanco
- FONDAP Centre for Genome Regulation, Núcleo Milenio en Biotecnología Celular Vegetal, Universidad Andrés Bello, Santiago, Chile
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Varas B, Castro MH, Rodriguez R, von Baer D, Mardones C, Hinrichsen P. Identification and characterization of microsatellites from calafate (Berberis microphylla, Berberidaceae). Appl Plant Sci 2013; 1:apps1200003. [PMID: 25202561 PMCID: PMC4103124 DOI: 10.3732/apps.1200003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/06/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Southern barberry or calafate (Berberis microphylla) is a shrub species endemic to the Patagonian region of South America that is used for human consumption. The fruit is very rich in vitamin C and anthocyanins and has a very high antioxidant capacity. There have been only a few genetic studies of this and other closely related species. • METHODS AND RESULTS Here we present the first 18 microsatellite markers of B. microphylla that were characterized using 66 accessions of calafate from Patagonia. On average, they had 7.6 alleles per marker, with an expected heterozygosity of 0.688. The informativeness of these markers was also evaluated in another 15 Berberis species, including most of the native and endemic Chilean species. • CONCLUSIONS The results confirm that these new simple sequence repeat markers are very polymorphic and potentially useful in genetic studies in any species of the genus Berberis.
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Affiliation(s)
- Benjamín Varas
- Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias (INIA), Santa Rosa 11,610, Santiago, Chile
| | - María H. Castro
- Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias (INIA), Santa Rosa 11,610, Santiago, Chile
| | - Roberto Rodriguez
- Depto. de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Dietrich von Baer
- Depto. de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Claudia Mardones
- Depto. de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Patricio Hinrichsen
- Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias (INIA), Santa Rosa 11,610, Santiago, Chile
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Ruiz A, Mardones C, Vergara C, Hermosín-Gutiérrez I, von Baer D, Hinrichsen P, Rodriguez R, Arribillaga D, Dominguez E. Analysis of hydroxycinnamic acids derivatives in calafate (Berberis microphylla G. Forst) berries by liquid chromatography with photodiode array and mass spectrometry detection. J Chromatogr A 2013; 1281:38-45. [PMID: 23398997 DOI: 10.1016/j.chroma.2013.01.059] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 01/07/2013] [Accepted: 01/11/2013] [Indexed: 02/05/2023]
Abstract
Calafate (Berberis microphylla G. Forst) is a Patagonian barberry very rich in anthocyanins and one of the fruits with the highest levels of these polyphenols. Other phenolic compounds have also been described in calafate berries. However, to the best of our knowledge there is no available information on hydroxycinnamic acid derivatives. The complexity of hydroxycinnamic acids determination in calafate berries, due to their structure similarities and the interference of high anthocyanin concentration is addressed by means of solid liquid extraction, followed by solid phase extraction clean-up on MCX columns and HPLC-DAD-ESI-MS/MS. The optimized extraction, clean-up and HPLC separation method allowed the assignation of identity and quantification of 20 hydroxycinnamic acids from calafate fruits. 5-Caffeoylquinic acid was the main compound found in all the studied samples. Other 13 hydroxycinnamoyl quinic acids and 6 caffeic acid esters with aldaric acid derivatives assigned as glucaric acid were also identified. Moreover, the glucaric-based hydroxycinnamic acid derivatives accounted for almost the half of total content of this kind of phenolic compounds. The total concentration of hydroxycinnamic acids derivatives ranged between 0.32±0.00 μmol/g and 8.28±0.01 μmol/g. Effect of ripening and geographical location on hydroxycinnamic acid profiles and concentrations are also evaluated. The methodology allows the determination of hydroxycinnamic acids from calafate despite of the high anthocyanin concentrations, showing a much higher concentration of these acids than other widely consumed berries. Thus suggesting that calafate could be considered a very interesting fruit from the point of view of their nutraceutical composition. However, geographical location and ripening have incidence in levels of studied compounds.
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Affiliation(s)
- Antonieta Ruiz
- Instrumental Analysis Department, Faculty of Pharmacy, University of Concepción, PO Box 160-C, Concepción, Chile
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A'Hara SW, Amouroux P, Argo EE, Avand-Faghih A, Barat A, Barbieri L, Bert TM, Blatrix R, Blin A, Bouktila D, Broome A, Burban C, Capdevielle-Dulac C, Casse N, Chandra S, Cho KJ, Cottrell JE, Crawford CR, Davis MC, Delatte H, Desneux N, Djieto-Lordon C, Dubois MP, El-Mergawy RAAM, Gallardo-Escárate C, Garcia M, Gardiner MM, Guillemaud T, Haye PA, Hellemans B, Hinrichsen P, Jeon JH, Kerdelhué C, Kharrat I, Kim KH, Kim YY, Kwan YS, Labbe EM, LaHood E, Lee KM, Lee WO, Lee YH, Legoff I, Li H, Lin CP, Liu SS, Liu YG, Long D, Maes GE, Magnoux E, Mahanta PC, Makni H, Makni M, Malausa T, Matura R, McKey D, McMillen-Jackson AL, Méndez MA, Mezghani-Khemakhem M, Michel AP, Paul M, Muriel-Cunha J, Nibouche S, Normand F, Palkovacs EP, Pande V, Parmentier K, Peccoud J, Piatscheck F, Puchulutegui C, Ramos R, Ravest G, Richner H, Robbens J, Rochat D, Rousselet J, Saladin V, Sauve M, Schlei O, Schultz TF, Scobie AR, Segovia NI, Seyoum S, Silvain JF, Tabone E, Van Houdt JKJ, Vandamme SG, Volckaert FAM, Wenburg J, Willis TV, Won YJ, Ye NH, Zhang W, Zhang YX. Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2011-30 September 2011. Mol Ecol Resour 2011; 12:185-9. [PMID: 22136175 DOI: 10.1111/j.1755-0998.2011.03088.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra gotyla, Hippodamia convergens, Linnaea borealis, Menippe mercenaria, Menippe adina, Parus major, Pinus densiflora, Portunus trituberculatus, Procontarinia mangiferae, Rhynchophorus ferrugineus, Schizothorax richardsonii, Scophthalmus rhombus, Tetraponera aethiops, Thaumetopoea pityocampa, Tuta absoluta and Ugni molinae. These loci were cross-tested on the following species: Barilius bendelisis, Chiromantes haematocheir, Eriocheir sinensis, Eucalyptus camaldulensis, Eucalyptus cladocalix, Eucalyptus globulus, Garra litaninsis vishwanath, Garra para lissorhynchus, Guindilla trinervis, Hemigrapsus sanguineus, Luma chequen. Guayaba, Myrceugenia colchagüensis, Myrceugenia correifolia, Myrceugenia exsucca, Parasesarma plicatum, Parus major, Portunus pelagicus, Psidium guayaba, Schizothorax richardsonii, Scophthalmus maximus, Tetraponera latifrons, Thaumetopoea bonjeani, Thaumetopoea ispartensis, Thaumetopoea libanotica, Thaumetopoea pinivora, Thaumetopoea pityocampa ena clade, Thaumetopoea solitaria, Thaumetopoea wilkinsoni and Tor putitora. This article also documents the addition of nine EPIC primer pairs for Euphaea decorata, Euphaea formosa, Euphaea ornata and Euphaea yayeyamana.
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Affiliation(s)
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- Forest Research, Northern Research Station, Roslin, Midlothian, Scotland EH25 9SY, UK
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Mejía N, Soto B, Guerrero M, Casanueva X, Houel C, de los Ángeles Miccono M, Ramos R, Le Cunff L, Boursiquot JM, Hinrichsen P, Adam-Blondon AF. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC Plant Biol 2011; 11:57. [PMID: 21447172 PMCID: PMC3076230 DOI: 10.1186/1471-2229-11-57] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 03/29/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. RESULTS Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development.Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation.For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. CONCLUSION We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.
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Affiliation(s)
- Nilo Mejía
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Braulio Soto
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Marcos Guerrero
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Ximena Casanueva
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Cléa Houel
- UMR INRA CNRS University of Evry on Plant Genomics, 2 rue Gaston Crémieux, BP 5708, 91057, Evry, France
| | | | - Rodrigo Ramos
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Loïc Le Cunff
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Jean-Michel Boursiquot
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Patricio Hinrichsen
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
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Meza P, Hinrichsen P, Aballay E. Molecular and morphological characterisation of species within the Xiphinema americanum-group (Dorylaimida: Longidoridae) from the central valley of Chile. NEMATOLOGY 2011. [DOI: 10.1163/138855410x518498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Pelsy F, Hocquigny S, Moncada X, Barbeau G, Forget D, Hinrichsen P, Merdinoglu D. An extensive study of the genetic diversity within seven French wine grape variety collections. Theor Appl Genet 2010; 120:1219-31. [PMID: 20062965 DOI: 10.1007/s00122-009-1250-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 12/14/2009] [Indexed: 05/21/2023]
Abstract
The process of vegetative propagation used to multiply grapevine varieties produces, in most cases, clones genetically identical to the parental plant. Nevertheless, spontaneous somatic mutations can occur in the regenerative cells that give rise to the clones, leading to consider varieties as populations of clones that conform to a panel of phenotypic traits. Using two sets of nuclear microsatellite markers, the present work aimed at evaluating and comparing the intravarietal genetic diversity within seven wine grape varieties: Cabernet franc, Cabernet Sauvignon, Chenin blanc, Grolleau, Pinot noir, Riesling, Savagnin, comprising a total number of 344 accessions of certified clones and introductions preserved in French repositories. Ten accessions resulted in being either self-progeny, possible offspring of the expected variety or misclassified varieties. Out of the 334 remaining accessions, 83 displayed genotypes different from the varietal reference, i.e., the microsatellite profile shared by the larger number of accessions. They showed a similarity value ranging from 0.923 to 0.992, and thus were considered as polymorphic monozygotic clones. The fraction of polymorphic clones ranged from 2 to 75% depending on the variety and the set of markers, the widest clonal diversity being observed within the Savagnin. Among the 83 polymorphic clones, 29 had unique genotype making them distinguishable; others were classified in 21 groups sharing the same genotype. All microsatellite markers were not equally efficient to show diversity within clone collections and a standard set of five microsatellite markers (VMC3a9, VMC5g7, VVS2, VVMD30, and VVMD 32) relevant to reveal clonal polymorphism is proposed.
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Rojas G, Méndez MA, Muñoz C, Lemus G, Hinrichsen P. Identification of a minimal microsatellite marker panel for the fingerprinting of peach and nectarine cultivars. ELECTRON J BIOTECHN 2008. [DOI: 10.2225/vol11-issue5-fulltext-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Moncada X, Pelsy F, Merdinoglu D, Hinrichsen P. Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers. Genome 2006; 49:1459-72. [PMID: 17426761 DOI: 10.1139/g06-102] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intravarietal genetic diversification associated with geographical dispersal of a vegetatively propagated species was studied using grapevine Vitis vinifera L. ‘Cabernet Sauvignon’ as a model. Fifty-nine clonal samples obtained from 7 countries (France, Chile, Spain, Australia, Hungary, USA, and Italy) were analyzed using 84 microsatellite markers. Eighteen polymorphic microsatellite loci (21.4%) were detected, finding 22 different genotypes in the population analyzed with a genetic similarity of over 97%. The presence of chimeric clones was evidenced at locus VMC5g7 by means of a segregation analysis of descendants by self-pollination of a triallelic Chilean clone and by somatic embryogenesis analysis, showing a mutation in L2 cell layer. Only 2 clones (obtained from France and Australia) presented the ancestral genotype, and the most divergent genotype was exhibited by another French clone, which had accumulated 5 somatic mutations. The 2 largest populations considered (from France and Chile) showed a clear divergency in the polymorphisms detected. These antecedents enabled the tracing of geographical dispersal with a phylogenetic hypothesis supporting France as the center of origin of diversification of Cabernet Sauvignon. The results obtained could help to explain diversification processes in other grapevine cultivars. The possibility that this kind of genetic variability occurs in other vegetatively propagated species is discussed, focusing on possible fingerprinting applications.
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Affiliation(s)
- Ximena Moncada
- Laboratorio de Biotecnología, Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias, INIA, Chile, PO Box 439-3 Santiago, Chile
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Moncada X, Muñoz L, Merdinoglu D, Castro M, Hinrichsen P. CLONAL POLYMORPHISM IN THE RED WINE CULTIVARS ´CARMENÉRE´ AND ´CABERNET SAUVIGNON´. ACTA ACUST UNITED AC 2005. [DOI: 10.17660/actahortic.2005.689.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hinrichsen P, Reyes M, Castro A, Araya S, Garnier M, Prieto H, Reyes F, Muñoz C, Dell'Orto P, Moynihan M. GENETIC TRANSFORMATION OF GRAPEVINES WITH TRICHODERMA HARZIANUM AND ANTIMICROBIAL PEPTIDE GENES FOR IMPROVEMENT OF FUNGAL TOLERANCE. ACTA ACUST UNITED AC 2005. [DOI: 10.17660/actahortic.2005.689.56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Mejía N, Hinrichsen P. A NEW, HIGHLY ASSERTIVE SCAR MARKER POTENTIALLY USEFUL TO ASSIST SELECTION FOR SEEDLESSNESS IN TABLE GRAPE BREEDING. ACTA ACUST UNITED AC 2003. [DOI: 10.17660/actahortic.2003.603.74] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Prieto H, Bruna A, Hinrichsen P, Muñoz C. Isolation and Molecular Characterization of a Chilean Isolate of Zucchini yellow mosaic virus. Plant Dis 2001; 85:644-648. [PMID: 30823033 DOI: 10.1094/pdis.2001.85.6.644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) was described in 1981 affecting squash, melon, and other cultivated cucurbits with severe stunting and yellowing symptoms. It was reported to be present in most countries where cucurbits are grown, and in Chile since 1995, from surveys using enzyme-linked immunosorbent assay (ELISA) but without further characterization. A potyvirus was isolated from ELISA-positive symptomatic plants. The results indicate that this virus is ZYMV based on symptoms on herbaceous indicators, immunospecific electron microscopy of the purified particle, and sequencing of 395 bases of the 3' end of the coat protein gene. The virus was detected in melon, watermelon, and squash plants. In agreement with previous descriptions for ZYMV, the Chilean isolate is a flexuous filamentous particle 740 nm long with one main protein of approximately 36 kDa. Nucleotide sequence comparisons of the 3' portion of the coat protein gene revealed a high similarity to the Connecticut and California strains.
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Affiliation(s)
- H Prieto
- Biotechnology Laboratory, Instituto de Investigaciones Agropecuarias (INIA) - Centro Regional de Investigación La Platina, Santiago, Chile
| | - A Bruna
- Biotechnology Laboratory, Instituto de Investigaciones Agropecuarias (INIA) - Centro Regional de Investigación La Platina, Santiago, Chile
| | - P Hinrichsen
- Biotechnology Laboratory, Instituto de Investigaciones Agropecuarias (INIA) - Centro Regional de Investigación La Platina, Santiago, Chile
| | - C Muñoz
- Biotechnology Laboratory, Instituto de Investigaciones Agropecuarias (INIA) - Centro Regional de Investigación La Platina, Santiago, Chile
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Affiliation(s)
- V Obreque
- INIA-La Platina, Laboratory de Biotecnología, Santiago, Chile
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Obreque V, Coogle L, Henney PJ, Bailey E, Mancilla R, García-Huidobro J, Hinrichsen P, Cothran EG. Characterization of 10 polymorphic alpaca dinucleotide microsatellites. Anim Genet 1998; 29:461-2. [PMID: 9883512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- V Obreque
- INIA-La Platina, Lab. de Biotecnología, Santiago, Chile
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Abstract
The gene (bzl) encoding benzaldehyde lyase (BL) from Pseudomonas fluorescens biovar I has been cloned and characterized. The nucleotide sequence contains an open reading frame encoding a protein of 563 amino acids. The deduced BL protein shares little homology with proteins contained in the NBRF-PIR data bank. However, the higher homologies (up to about 28%) were obtained with enzymes that also utilize thiamine pyrophosphate as a cofactor.
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Affiliation(s)
- P Hinrichsen
- Laboratorio de Bioquímica, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago
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Hinrichsen P, Vicuña R. Possible initial steps in the catabolism of 1,2-diphenylethanone (deoxybenzoin) by Pseudomonas fluorescens DB-5. Appl Environ Microbiol 1993; 59:3477-9. [PMID: 8250568 PMCID: PMC182477 DOI: 10.1128/aem.59.10.3477-3479.1993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A natural bacterial strain, identified as Pseudomonas fluorescens DB-5, was isolated in enrichment cultures containing 1,2-diphenylethanone as the only source of carbon and energy. On the basis of characteristic features observed in the mass spectra of degradation intermediates, it is proposed that metabolism of 1,2-diphenylethanone is initiated by two hydroxylations on the benzyl ring. Phenol, presumably arising from the benzoyl ring, was transiently detected as a catabolic intermediate.
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Affiliation(s)
- P Hinrichsen
- Laboratorio de Bioquímica, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago
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Breuer H, Fincham J, Hinrichsen P, Uys CJ, Weich H, Reichart B. Coronary artery plaque rapidly induced by local electromagnetic stimulation in the baboon. Eur Surg Res 1989; 21:123-8. [PMID: 2767087 DOI: 10.1159/000129012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A reliable method has been developed to produce stenosis of the right coronary artery of baboons as a consequence of electrostimulation of the vessel at a chosen position. At that site a pair of electrodes were implanted and activated with a train of 9-volt pulses (length: 10 ms, separation: 100 ms) for 30 min, 5 days/week, up to 6 weeks. 13 animals were included in the experiment, 2 of those served as controls. Pathohistologically the structure of the artificially produced constrictions is similar to atherosclerotic lesions. On average the stenoses occupied 55% of the available lumen; total occlusion and no stenosis were observed in 1 case each.
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Affiliation(s)
- H Breuer
- Department of Cardiothoracic Surgery, University of Cape Town, South Africa
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Abstract
1. Yeast pyruvate kinase was purified to near homogeneity and subjected to chemical modification by trinitrobenzenesulfonate and by P1, P2-bis (5' pyridoxal) diphosphate. 2. Labeled peptides were isolated and their amino acid composition was determined. 3. The results suggest that yeast pyruvate kinase has an essential lysine residue, and that this residue is in a location equivalent to an essential lysine described in the muscle enzyme. 4. Protection experiments indicate that this lysine is located at the nucleotide binding site.
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Affiliation(s)
- M Imarai
- Laboratoiro de Bioquímica, Facultad de Ciencias Biològicas, Pontifica Universidad Católica de Chile, Santiago
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