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Tympakianakis S, Trantas E, Avramidou EV, Ververidis F. Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1139647. [PMID: 37180393 PMCID: PMC10169827 DOI: 10.3389/fpls.2023.1139647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.
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Affiliation(s)
- Stylianos Tympakianakis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
| | - Emmanouil Trantas
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organisation “DIMITRA“, Athens, Greece
| | - Filippos Ververidis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
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Park M, Vera D, Kambrianda D, Gajjar P, Cadle-Davidson L, Tsolova V, El-Sharkawy I. Chromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits. HORTICULTURE RESEARCH 2022; 9:uhab011. [PMID: 35040982 PMCID: PMC8769032 DOI: 10.1093/hr/uhab011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/25/2021] [Indexed: 05/29/2023]
Abstract
Vitis has two subgenera: Euvitis, which includes commercially important Vitis vinifera and interspecific hybrid cultivars, and Muscadinia. Of note, the market for Muscadinia grapes remains small, and only Muscadinia rotundifolia is cultivated as a commercial crop. To establish a basis for the study of Muscadinia species, we generated chromosome-level whole-genome sequences of Muscadinia rotundifolia cv. Noble. A total of 393.8 Mb of sequences were assembled from 20 haploid chromosomes, and 26 394 coding genes were identified from the sequences. Comparative analysis with the genome sequence of V. vinifera revealed a smaller size of the M. rotundifolia genome but highly conserved gene synteny. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from breeding populations of M. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 52 quantitative trait nucleotides (QTNs) associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the QTNs with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
| | - Daniel Vera
- Silico LLC, 23 Essex Street #761119, Melrose, MA 02176, USA
| | - Devaiah Kambrianda
- Plant and Soil Sciences, Southern University Agricultural Research and Extension Center, 181 B. A. Little Dr., Baton Rouge, LA 70813, USA
| | - Pranavkumar Gajjar
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
| | - Lance Cadle-Davidson
- USDA-ARS, Grape Genetics Research Unit, 630 West W North St., Geneva, NY, 14456, USA
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
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Pirrello C, Zeilmaker T, Bianco L, Giacomelli L, Moser C, Vezzulli S. Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing. Biomolecules 2021; 11:181. [PMID: 33525704 PMCID: PMC7912118 DOI: 10.3390/biom11020181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes-namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2-in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Tieme Zeilmaker
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Lisa Giacomelli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Silvia Vezzulli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
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Zou C, Karn A, Reisch B, Nguyen A, Sun Y, Bao Y, Campbell MS, Church D, Williams S, Xu X, Ledbetter CA, Patel S, Fennell A, Glaubitz JC, Clark M, Ware D, Londo JP, Sun Q, Cadle-Davidson L. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun 2020; 11:413. [PMID: 31964885 PMCID: PMC6972940 DOI: 10.1038/s41467-019-14280-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Bruce Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Allen Nguyen
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yongming Sun
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yun Bao
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | | | | | | | - Xia Xu
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Craig A Ledbetter
- USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA
| | - Sagar Patel
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Jeffrey C Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Jason P Londo
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
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Yang S, Fresnedo-Ramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark M, Luby J, Manns DC, Sacks G, Mansfield AK, Londo J, Fennell A, Gadoury D, Reisch B, Cadle-Davidson L, Sun Q. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. HORTICULTURE RESEARCH 2016; 3:16002. [PMID: 27257505 PMCID: PMC4879517 DOI: 10.1038/hortres.2016.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 05/07/2023]
Abstract
Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.
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Affiliation(s)
- Shanshan Yang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Minghui Wang
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Linda Cote
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Schweitzer
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth M Takacs
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - James Luby
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - David C Manns
- Department of Food Science, Cornell University, Geneva, NY 14456, USA
| | - Gavin Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Jason Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anne Fennell
- Plant Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - David Gadoury
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
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Houel C, Chatbanyong R, Doligez A, Rienth M, Foria S, Luchaire N, Roux C, Adivèze A, Lopez G, Farnos M, Pellegrino A, This P, Romieu C, Torregrosa L. Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip. BMC PLANT BIOLOGY 2015; 15:205. [PMID: 26283631 PMCID: PMC4539925 DOI: 10.1186/s12870-015-0588-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/06/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci). RESULTS Ten stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered. CONCLUSIONS This study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variation.
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Affiliation(s)
- Cléa Houel
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- INRA, UMR AGAP, F-34060, Montpellier, France.
| | - Ratthaphon Chatbanyong
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- INRA, UMR AGAP, F-34060, Montpellier, France.
| | | | - Markus Rienth
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- INRA, UMR AGAP, F-34060, Montpellier, France.
- Fondation Jean Poupelain, 30 rue Gâte Chien, F-16100, Javrezac, France.
- Changins, Haute Ecole de Viticulture et Oenologie, 1260, Nyon, Switzerland.
| | - Serena Foria
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, I-33100, Udine, Italy.
| | - Nathalie Luchaire
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- Montpellier SupAgro, UMR LEPSE, F- 34060, Montpellier, France.
| | | | | | - Gilbert Lopez
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
| | - Marc Farnos
- INRA, UMR AGAP, F-34060, Montpellier, France.
| | - Anne Pellegrino
- Montpellier SupAgro, UMR LEPSE, F- 34060, Montpellier, France.
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Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L. Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLoS One 2015; 10:e0134880. [PMID: 26244767 PMCID: PMC4526651 DOI: 10.1371/journal.pone.0134880] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.
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Affiliation(s)
- Katie E. Hyma
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
| | - Minghui Wang
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Jason P. Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Charlotte B. Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
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Silva-Junior OB, Faria DA, Grattapaglia D. A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species. THE NEW PHYTOLOGIST 2015; 206:1527-40. [PMID: 25684350 DOI: 10.1111/nph.13322] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/02/2015] [Indexed: 05/23/2023]
Abstract
We used whole genome resequencing of pooled individuals to develop a high-density single-nucleotide polymorphism (SNP) chip for Eucalyptus. Genomes of 240 trees of 12 species were sequenced at 3.5× each, and 46 997 586 raw SNP variants were subject to multivariable filtering metrics toward a multispecies, genome-wide distributed chip content. Of the 60 904 SNPs on the chip, 59 222 were genotyped and 51 204 were polymorphic across 14 Eucalyptus species, providing a 96% genome-wide coverage with 1 SNP/12-20 kb, and 47 069 SNPs at ≤ 10 kb from 30 444 of the 33 917 genes in the Eucalyptus genome. Given the EUChip60K multi-species genotyping flexibility, we show that both the sample size and taxonomic composition of cluster files impact heterozygous call specificity and sensitivity by benchmarking against 'gold standard' genotypes derived from deeply sequenced individual tree genomes. Thousands of SNPs were shared across species, likely representing ancient variants arisen before the split of these taxa, hinting to a recent eucalypt radiation. We show that the variable SNP filtering constraints allowed coverage of the entire site frequency spectrum, mitigating SNP ascertainment bias. The EUChip60K represents an outstanding tool with which to address population genomics questions in Eucalyptus and to empower genomic selection, GWAS and the broader study of complex trait variation in eucalypts.
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Affiliation(s)
- Orzenil B Silva-Junior
- Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, 70790-160, Brasilia, DF, Brazil
| | - Danielle A Faria
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
| | - Dario Grattapaglia
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, 70790-160, Brasilia, DF, Brazil
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
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Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties. PLoS One 2015; 10:e0125628. [PMID: 25973611 PMCID: PMC4431842 DOI: 10.1371/journal.pone.0125628] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/16/2015] [Indexed: 11/19/2022] Open
Abstract
Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.
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Picq S, Santoni S, Lacombe T, Latreille M, Weber A, Ardisson M, Ivorra S, Maghradze D, Arroyo-Garcia R, Chatelet P, This P, Terral JF, Bacilieri R. A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines. BMC PLANT BIOLOGY 2014; 14:229. [PMID: 25179565 PMCID: PMC4167142 DOI: 10.1186/s12870-014-0229-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinifera. The characterisation of polymorphisms in genes underlying the sex-determining chromosomal region may help clarify the history of domestication in grapevine and the evolution of sex chromosomes in plants. In the genus Vitis, sex determination is putatively controlled by one major locus with three alleles, male M, hermaphrodite H and female F, with an allelic dominance M > H > F. Previous genetic studies located the sex locus on chromosome 2. We used DNA polymorphisms of geographically diverse V. vinifera genotypes to confirm the position of this locus, to characterise the genetic diversity and traces of selection in candidate genes, and to explore the origin of hermaphroditism. RESULTS In V. v. sylvestris, a sex-determining region of 154.8 kb, also present in other Vitis species, spans less than 1% of chromosome 2. It displays haplotype diversity, linkage disequilibrium and differentiation that typically correspond to a small XY sex-determining region with XY males and XX females. In male alleles, traces of purifying selection were found for a trehalose phosphatase, an exostosin and a WRKY transcription factor, with strikingly low polymorphism levels between distant geographic regions. Both diversity and network analysis revealed that H alleles are more closely related to M than to F alleles. CONCLUSIONS Hermaphrodite alleles appear to derive from male alleles of wild grapevines, with successive recombination events allowing import of diversity from the X into the Y chromosomal region and slowing down the expansion of the region into a full heteromorphic chromosome. Our data are consistent with multiple domestication events and show traces of introgression from other Asian Vitis species into the cultivated grapevine gene pool.
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Affiliation(s)
- Sandrine Picq
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - Sylvain Santoni
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Thierry Lacombe
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Muriel Latreille
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Audrey Weber
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Morgane Ardisson
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Sarah Ivorra
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - David Maghradze
- />Institute of Horticulture, Viticulture and Oenology, Agrarian University of Georgia, University Campus at Digomi, David Aghmashenebeli Alley, 13-th km. 0159, Tbilisi, Georgia
| | - Rosa Arroyo-Garcia
- />CBGP-INIA. Dpto Biotecnología, Campus de Montegancedo, Autovía M40, km38, 28223 Pozuelo de Alarcón, Madrid Spain
| | - Philippe Chatelet
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Patrice This
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Jean-Frédéric Terral
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
- />Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France
| | - Roberto Bacilieri
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
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11
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Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS One 2013; 8:e78680. [PMID: 24236035 PMCID: PMC3827278 DOI: 10.1371/journal.pone.0078680] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/15/2013] [Indexed: 01/01/2023] Open
Abstract
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction.
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Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 2013; 8:e77022. [PMID: 24155917 PMCID: PMC3796552 DOI: 10.1371/journal.pone.0077022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022] Open
Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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Affiliation(s)
- Sara Montanari
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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13
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Wan Y, Schwaninger HR, Baldo AM, Labate JA, Zhong GY, Simon CJ. A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. BMC Evol Biol 2013; 13:141. [PMID: 23826735 PMCID: PMC3750556 DOI: 10.1186/1471-2148-13-141] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 05/28/2013] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. RESULTS Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 - 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 - 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. CONCLUSIONS Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.
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Affiliation(s)
- Yizhen Wan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Heidi R Schwaninger
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Angela M Baldo
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
- US Department of Agriculture, Agriculture Research Service, Grape Genetic Research Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Joanne A Labate
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Gan-Yuan Zhong
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
- US Department of Agriculture, Agriculture Research Service, Grape Genetic Research Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Charles J Simon
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
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Wong MML, Cannon CH, Wickneswari R. Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data. BMC Genomics 2012; 13:726. [PMID: 23265623 PMCID: PMC3556151 DOI: 10.1186/1471-2164-13-726] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 12/21/2012] [Indexed: 11/22/2022] Open
Abstract
Background Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids. Results We identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100%) compared to the traditional in vitro approach (44%). Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50%) of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively. Conclusion We have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely related species, we converted most SNPs to successful assays. We also demonstrated that Illumina GoldenGate genotyping together with manual clustering can provide high quality genotypes for a non-model species like Acacia. These SNPs markers are not only important for linkage map construction, but will be very useful for hybrid discrimination and genetic diversity assessment of natural germplasms in the future.
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Affiliation(s)
- Melissa M L Wong
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor, Malaysia
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15
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Vezzulli S, Leonardelli L, Malossini U, Stefanini M, Velasco R, Moser C. Pinot blanc and Pinot gris arose as independent somatic mutations of Pinot noir. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6359-69. [PMID: 23095995 PMCID: PMC3504490 DOI: 10.1093/jxb/ers290] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Somatic mutation is a natural mechanism which allows plant growers to develop new cultivars. As a source of variation within a uniform genetic background, it also represents an ideal tool for studying the genetic make-up of important traits and for establishing gene functions. Layer-specific molecular characterization of the Pinot family of grape cultivars was conducted to provide an evolutionary explanation for the somatic mutations that have affected the locus of berry colour. Through the study of the structural dynamics along chromosome 2, a very large deletion present in a single Pinot gris cell layer was identified and characterized. This mutation reveals that Pinot gris and Pinot blanc arose independently from the ancestral Pinot noir, suggesting a novel parallel evolutionary model. This proposed 'Pinot-model' represents a breakthrough towards the full understanding of the mechanisms behind the formation of white, grey, red, and pink grape cultivars, and eventually of their specific enological aptitude.
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Affiliation(s)
- Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele a/Adige (TN), Italy.
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16
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Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 2012; 7:e31745. [PMID: 22363718 PMCID: PMC3283661 DOI: 10.1371/journal.pone.0031745] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/12/2012] [Indexed: 01/07/2023] Open
Abstract
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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Affiliation(s)
- David Chagné
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Mark W. Davey
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Barbara Gilmore
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cindy Lawley
- Illumina Inc., Hayward, California, United States of America
| | - Stijn Vanderzande
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Roger P. Hellens
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Satish Kumar
- Plant and Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Alessandro Cestaro
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - Jasper D. Rees
- Agricultural Research Council, Onderstepoort, South Africa
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Todd Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Susan E. Gardiner
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cameron Peace
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Ollitrault P, Terol J, Garcia-Lor A, Bérard A, Chauveau A, Froelicher Y, Belzile C, Morillon R, Navarro L, Brunel D, Talon M. SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genomics 2012; 13:13. [PMID: 22233093 PMCID: PMC3320530 DOI: 10.1186/1471-2164-13-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/10/2012] [Indexed: 01/18/2024] Open
Abstract
Background With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species. Results Fifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping. Conclusions A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole Citrus gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around C. maxima, C. medica and C. reticulata as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in Citrus and genetic association in C. reticulata.
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Affiliation(s)
- Patrick Ollitrault
- CIRAD, UMR AGAP, Avenue Agropolis, TA A-108/02, 34398 Montpellier, Cedex 5, France.
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Mahanil S, Ramming D, Cadle-Davidson M, Owens C, Garris A, Myles S, Cadle-Davidson L. Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:23-33. [PMID: 21904846 DOI: 10.1007/s00122-011-1684-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 08/12/2011] [Indexed: 05/02/2023]
Abstract
The single, dominant powdery mildew resistance locus Ren4 from Vitis romanetii prevents hyphal growth by Erysiphe necator. Previously, we showed that when introgressed into V. vinifera in the modified BC(2) population 03-3004, Ren4 was linked with the simple sequence repeat marker VMC7f2 on chromosome 18-a marker that is associated with multiple disease resistance and seedlessness. However, in the current study, this marker was monomorphic in related breeding populations 05-3010 and 07-3553. To enhance marker-assisted selection at this locus, we developed multiplexed SNP markers using three approaches: conversion of bulked segregant analysis AFLP markers, sequencing of candidate genes and regions flanking known V. vinifera SNPs, and hybridization to the Vitis9KSNP genotyping array. The Vitis9KSNP array was more cost-efficient than all other approaches tested for marker discovery and genotyping, enabling the genotyping of 1317 informative SNPs within the span of 1 week and at a cost of 11 cents per SNP. From a total of 1,446 high quality, informative markers segregating in 03-3004, we developed a haplotype signature of 15 multiplexed SNP markers linked with Ren4 in 03-3004, 5 of which were linked in 05-3010, and 6 of which were linked in 07-3553. Two of these populations segregated for seedlessness, which was tightly linked with Ren4 in 03-3004 (2 cM) but not in 05-3010 (22 cM). Chromosomal rearrangements were detected among these three populations and the reference genome PN40024. Since this is the first application of the Vitis9KSNP array in a breeding program, some suggestions are provided for application of genotyping arrays. Our results provide novel markers for tracking and pyramiding this unique resistance gene and for further functional characterization of this region on chromosome 18 encoding multiple disease resistance and seedlessness.
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Affiliation(s)
- Siraprapa Mahanil
- USDA-ARS Grape Genetics Research Unit, 630 W. North St, Geneva, NY 14456, USA
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Micheletti D, Troggio M, Zharkikh A, Costa F, Malnoy M, Velasco R, Salvi S. Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. TREE GENETICS & GENOMES 2011; 7:857-868. [PMID: 0 DOI: 10.1007/s11295-011-0380-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P. SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. BMC Bioinformatics 2011; 12:134. [PMID: 21545712 PMCID: PMC3102043 DOI: 10.1186/1471-2105-12-134] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 05/05/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. RESULTS In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates:1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D).Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices.2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. CONCLUSIONS Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies.SNiPlay is available at: http://sniplay.cirad.fr/.
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Affiliation(s)
- Alexis Dereeper
- Diversity, Genetics and Genomics of grapevine, UMR DIAPC, INRA, Montpellier, France.
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Grattapaglia D, Silva-Junior OB, Kirst M, de Lima BM, Faria DA, Pappas GJ. High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC PLANT BIOLOGY 2011; 11:65. [PMID: 21492434 PMCID: PMC3090336 DOI: 10.1186/1471-2229-11-65] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/14/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. RESULTS We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. CONCLUSIONS This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥ 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
- Genomic Sciences Program - Universidade Catolica de Brasília- SGAN, 916 modulo B, 70790-160 Brasília - DF, Brazil
| | - Orzenil B Silva-Junior
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
| | - Matias Kirst
- School of Forest Resources and Conservation, Genetics Institute, University of Florida, PO Box 110410, Gainesville, USA
| | - Bruno Marco de Lima
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
- Department of Genetics - Universidade de São Paulo - ESALQ/USP - Av. Pádua Dias, 11 - Caixa Postal 9 13418-900 Piracicaba, SP, Brazil
| | - Danielle A Faria
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
| | - Georgios J Pappas
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
- Genomic Sciences Program - Universidade Catolica de Brasília- SGAN, 916 modulo B, 70790-160 Brasília - DF, Brazil
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Laucou V, Lacombe T, Dechesne F, Siret R, Bruno JP, Dessup M, Dessup T, Ortigosa P, Parra P, Roux C, Santoni S, Varès D, Péros JP, Boursiquot JM, This P. High throughput analysis of grape genetic diversity as a tool for germplasm collection management. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1233-45. [PMID: 21234742 DOI: 10.1007/s00122-010-1527-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 12/22/2010] [Indexed: 05/20/2023]
Abstract
Using 20 SSR markers well scattered across the 19 grape chromosomes, we analyzed 4,370 accessions of the INRA grape repository at Vassal, mostly cultivars of Vitis vinifera subsp. sativa (3,727), but also accessions of V. vinifera subsp. sylvestris (80), interspecific hybrids (364), and rootstocks (199). The analysis revealed 2,836 SSR single profiles: 2,323 sativa cultivars, 72 wild individuals (sylvestris), 306 interspecific hybrids, and 135 rootstocks, corresponding to 2,739 different cultivars in all. A total of 524 alleles were detected, with a mean of 26.20 alleles per locus. For the 2,323 cultivars of V. vinifera, 338 alleles were detected with a mean of 16.9 alleles per locus. The mean genetic diversity (GDI) was 0.797 and the level of heterozygosity was 0.76, with broad variation from 0.20 to 1. Interspecific hybrids and rootstocks were more heterozygous and more diverse (GDI = 0.839 and 0.865, respectively) than V. vinifera cultivars (GDI = 0.769), Vitis vinifera subsp. sylvestris being the least divergent with GDI = 0.708. Principal coordinates analysis distinguished the four groups. Slight clonal polymorphism was detected. The limit between clonal variation and cultivar polymorphism was set at four allelic differences out of 40. SSR markers were useful as a complementary tool to traditional ampelography for cultivar identification. Finally, a set of nine SSR markers was defined that was sufficient to distinguish 99.8% of the analyzed accessions. This set is suitable for routine characterization and will be valuable for germplasm management.
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Affiliation(s)
- V Laucou
- INRA Montpellier SupAgro, UMR DIAPC, Equipe Génétique de la Vigne, Montpellier, France.
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Genomic resources in horticultural crops: Status, utility and challenges. Biotechnol Adv 2011; 29:199-209. [DOI: 10.1016/j.biotechadv.2010.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 09/04/2010] [Accepted: 09/26/2010] [Indexed: 01/02/2023]
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Houel C, Bounon R, Chaïb J, Guichard C, Péros JP, Bacilieri R, Dereeper A, Canaguier A, Lacombe T, N'Diaye A, Le Paslier MC, Vernerey MS, Coriton O, Brunel D, This P, Torregrosa L, Adam-Blondon AF. Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions. BMC PLANT BIOLOGY 2010; 10:284. [PMID: 21176183 PMCID: PMC3022909 DOI: 10.1186/1471-2229-10-284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 12/22/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the fleshless berry mutation (flb) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication. RESULTS In total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both V. vinifera cv. Chardonnay and a genotype carrying the flb mutation, V. vinifera cv. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that flb could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the flb region, representing 48,874 bp in a highly diverse set of cultivated and wild V. vinifera genotypes, to identify possible signatures of domestication in the cultivated V. vinifera compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the flb region. CONCLUSIONS We observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the flb region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the flb gene in a F2 population when available.
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Affiliation(s)
- Cléa Houel
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Rémi Bounon
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
- Unité INRA Etude du Polymorphisme des Végétaux (EPGV), 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Jamila Chaïb
- CSIRO Plant Industry, PO BOX 350, Glen Osmond SA 5064, Australia
| | - Cécile Guichard
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Jean-Pierre Péros
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Roberto Bacilieri
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Alexis Dereeper
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Aurélie Canaguier
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Thierry Lacombe
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Amidou N'Diaye
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | | | - Marie-Stéphanie Vernerey
- Unité mixte de Recherche Amélioration des Plantes et Biotechnologies Végétales (APBV), INRA Agrocampus Rennes, Plate-forme cytologique moléculaire, 35 653 Le Rheu Cedex, France
- Unité mixte de Recherche Biologie et Génétique des Interactions Plantes-Agents Pathogènes (BGPI), INRA SupAgro CIRAD, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Olivier Coriton
- Unité mixte de Recherche Amélioration des Plantes et Biotechnologies Végétales (APBV), INRA Agrocampus Rennes, Plate-forme cytologique moléculaire, 35 653 Le Rheu Cedex, France
| | - Dominique Brunel
- Unité INRA Etude du Polymorphisme des Végétaux (EPGV), 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Patrice This
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Laurent Torregrosa
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Anne-Françoise Adam-Blondon
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
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Grimplet J, Cramer GR, Dickerson JA, Mathiason K, Van Hemert J, Fennell AY. VitisNet: "Omics" integration through grapevine molecular networks. PLoS One 2009; 4:e8365. [PMID: 20027228 PMCID: PMC2791446 DOI: 10.1371/journal.pone.0008365] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 11/24/2009] [Indexed: 11/25/2022] Open
Abstract
Background Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet). Methodology/Principal Findings The sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 “Metabolic”, 15 “Genetic Information Processing”, 12 “Environmental Information Processing”, 3 “Cellular Processes”, 21 “Transport”, and 80 “Transcription Factors”. The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment. Conclusions/Significance VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage) and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome location can be accessed and downloaded from the VitisNet tab at http://vitis-dormancy.sdstate.org.
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Affiliation(s)
- Jérôme Grimplet
- Horticulture, Forestry, Landscape, and Parks Department, South Dakota State University, Brookings, South Dakota, United States of America
| | - Grant R. Cramer
- Department of Biochemistry, University of Nevada Reno, Reno, Nevada, United States of America
| | - Julie A. Dickerson
- Department of Electrical and Computer Engineering and Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
| | - Kathy Mathiason
- Horticulture, Forestry, Landscape, and Parks Department, South Dakota State University, Brookings, South Dakota, United States of America
| | - John Van Hemert
- Department of Electrical and Computer Engineering and Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
| | - Anne Y. Fennell
- Horticulture, Forestry, Landscape, and Parks Department, South Dakota State University, Brookings, South Dakota, United States of America
- * E-mail:
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