1
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Inderbitzin P, Christopoulou M, Lavelle D, Reyes-Chin-Wo S, Michelmore RW, Subbarao KV, Simko I. Correction to: The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. BMC Plant Biol 2019; 19:374. [PMID: 31451107 PMCID: PMC6710860 DOI: 10.1186/s12870-019-1966-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Following publication of the original article [1], the author reported a processing error in Figure 5. This has been corrected in the original article.
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Affiliation(s)
- Patrik Inderbitzin
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
- Present address: Indigo Ag, Charlestown, MA, 02129, USA
| | | | - Dean Lavelle
- Genome Center, University of California, Davis, CA, 95616, USA
| | | | - Richard W Michelmore
- Genome Center, University of California, Davis, CA, 95616, USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA, 95616, USA
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
| | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA.
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Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, Andolfo G, Aprea G, Avanzato C, Bassolino L, Comino C, Molin AD, Ferrarini A, Maor LC, Portis E, Reyes-Chin-Wo S, Rinaldi R, Sala T, Scaglione D, Sonawane P, Tononi P, Almekias-Siegl E, Zago E, Ercolano MR, Aharoni A, Delledonne M, Giuliano G, Lanteri S, Rotino GL. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Sci Rep 2019; 9:11769. [PMID: 31409808 PMCID: PMC6692341 DOI: 10.1038/s41598-019-47985-w] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [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: 11/12/2018] [Accepted: 07/05/2019] [Indexed: 11/30/2022] Open
Abstract
With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.
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Affiliation(s)
- Lorenzo Barchi
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Marco Pietrella
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy.,Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Citrus and Tree Fruit, 47121, Forlì, Italy
| | - Luca Venturini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.,Department of Life Sciences, Natural History Museum, Cromwell Rd, Kensington, London, United Kingdom
| | - Andrea Minio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Laura Toppino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Alberto Acquadro
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy
| | - Carla Avanzato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Cinzia Comino
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Alessandra Dal Molin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Alberto Ferrarini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Louise Chappell Maor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ezio Portis
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Sebastian Reyes-Chin-Wo
- UC Davis Genome Center-GBSF, 451 Health Sciences Drive, University of California, Davis, CA, 95616, USA
| | - Riccardo Rinaldi
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Tea Sala
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Davide Scaglione
- IGA Technology Services, Via J. Linussio, 51, 33100, Udine, Italy
| | - Prashant Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Tononi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Efrat Almekias-Siegl
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elisa Zago
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy.
| | - Sergio Lanteri
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy.
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
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Inderbitzin P, Christopoulou M, Lavelle D, Reyes-Chin-Wo S, Michelmore RW, Subbarao KV, Simko I. The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. BMC Plant Biol 2019; 19:305. [PMID: 31291883 PMCID: PMC6621938 DOI: 10.1186/s12870-019-1905-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 03/04/2019] [Accepted: 06/25/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Verticillium wilt caused by the fungus Verticillium dahliae race 1 is among the top disease concerns for lettuce in the Salinas and Pajaro Valleys of coastal central California. Resistance of lettuce against V. dahliae race 1 was previously mapped to the single dominant Verticillium resistance 1 (Vr1) locus. Lines of tomato resistant to race 1 are known to contain the closely linked Ve1 and Ve2 genes that encode receptor-like proteins with extracellular leucine-rich repeats; the Ve1 and Ve2 proteins act antagonistically to provide resistance against V. dahliae race 1. The Vr1 locus in lettuce contains a cluster of several genes with sequence similarity to the tomato Ve genes. We used genome sequencing and/or PCR screening along with pathogenicity assays of 152 accessions of lettuce to investigate allelic diversity and its relationship to race 1 resistance in lettuce. RESULTS This approach identified a total of four Ve genes: LsVe1, LsVe2, LsVe3, and LsVe4. The majority of accessions, however, contained a combination of only three of these LsVe genes clustered on chromosomal linkage group 9 (within ~ 25 kb in the resistant cultivar La Brillante and within ~ 127 kb in the susceptible cultivar Salinas). CONCLUSIONS A single allele, LsVe1L, was present in all resistant accessions and absent in all susceptible accessions. This allele can be used as a molecular marker for V. dahliae race 1 resistance in lettuce. A PCR assay for rapid detection of race 1 resistance in lettuce was designed based on nucleotide polymorphisms. Application of this assay allows identification of resistant genotypes in early stages of plant development or at seed-level without time- and labor-intensive testing in the field.
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Affiliation(s)
- Patrik Inderbitzin
- Department of Plant Pathology, University of California, Davis, CA 95616 USA
- Present address: Indigo Ag, Charlestown, MA 02129 USA
| | | | - Dean Lavelle
- Genome Center, University of California, Davis, CA 95616 USA
| | | | - Richard W. Michelmore
- Genome Center, University of California, Davis, CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA 95616 USA
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, CA 95616 USA
| | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905 USA
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Fletcher K, Gil J, Bertier LD, Kenefick A, Wood KJ, Zhang L, Reyes-Chin-Wo S, Cavanaugh K, Tsuchida C, Wong J, Michelmore R. Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae. Nat Commun 2019; 10:2645. [PMID: 31201315 PMCID: PMC6570648 DOI: 10.1038/s41467-019-10550-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.
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Affiliation(s)
- Kyle Fletcher
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Juliana Gil
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lien D Bertier
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Aubrey Kenefick
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Kelsey J Wood
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lin Zhang
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Sebastian Reyes-Chin-Wo
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
- Bayer Crop Science, 37437 CA-16, Woodland, CA, 95695, USA
| | - Keri Cavanaugh
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Cayla Tsuchida
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
- Arcadia Biosciences, Davis, CA, 95616, USA
| | - Joan Wong
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
- Pacific Biosciences of California, Inc., Menlo Park, CA, 94025, USA
| | - Richard Michelmore
- Genome Center, University of California, Davis, CA, 95616, USA.
- Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA.
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5
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Fletcher K, Klosterman SJ, Derevnina L, Martin F, Bertier LD, Koike S, Reyes-Chin-Wo S, Mou B, Michelmore R. Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics 2018; 19:851. [PMID: 30486780 PMCID: PMC6264045 DOI: 10.1186/s12864-018-5214-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. RESULTS We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. CONCLUSIONS We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lida Derevnina
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Frank Martin
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lien D. Bertier
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven Koike
- UC Davis Cooperative Extension Monterey County, Salinas, CA 93901 USA
- Present Address: TriCal Diagnostics, Hollister, CA 95023 USA
| | - Sebastian Reyes-Chin-Wo
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Beiquan Mou
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616 USA
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Bielsa B, Hewitt S, Reyes-Chin-Wo S, Dhingra A, Rubio-Cabetas MJ. Identification of water use efficiency related genes in 'Garnem' almond-peach rootstock using time-course transcriptome analysis. PLoS One 2018; 13:e0205493. [PMID: 30308016 PMCID: PMC6181374 DOI: 10.1371/journal.pone.0205493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022] Open
Abstract
Drought is one of the main abiotic stresses with far-reaching ecological and socioeconomic impacts, especially in perennial food crops such as Prunus. There is an urgent need to identify drought resilient rootstocks that can adapt to changes in water availability. In this study, we tested the hypothesis that PEG-induced water limitation stress will simulate drought conditions and drought-related genes, including transcription factors (TFs), will be differentially expressed in response to this stress. 'Garnem' genotype, an almond × peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] was exposed to PEG-6000 solution, and a time-course transcriptome analysis of drought-stressed roots was performed at 0, 2 and 24 h time points post-stress. Transcriptome analysis resulted in the identification of 12,693 unique differentially expressed contigs (DECs) at the 2 h time point, and 7,705 unique DECs at the 24 h time point after initiation of the drought treatment. Interestingly, three drought-induced genes, directly related to water use efficiency (WUE) namely, ERF023 TF; LRR receptor-like serine/threonine-kinase ERECTA; and NF-YB3 TF, were found induced under stress. The RNAseq results were validated with quantitative RT-PCR analysis of eighteen randomly selected differentially expressed contigs (DECs). Pathway analysis in the present study provides valuable information regarding metabolic events that occur during stress-induced signalling in 'Garnem' roots. This information is expected to be useful in understanding the potential mechanisms underlying drought stress responses and drought adaptation strategies in Prunus species.
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Affiliation(s)
- Beatriz Bielsa
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
| | - Seanna Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | | | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - María José Rubio-Cabetas
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
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Kitazaki K, Fukushima A, Nakabayashi R, Okazaki Y, Kobayashi M, Mori T, Nishizawa T, Reyes-Chin-Wo S, Michelmore RW, Saito K, Shoji K, Kusano M. Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs. Sci Rep 2018; 8:7914. [PMID: 29784957 PMCID: PMC5962576 DOI: 10.1038/s41598-018-25686-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [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: 01/18/2018] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m-2·s-1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.
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Affiliation(s)
- Kazuyoshi Kitazaki
- Central Research Institute of Electric Power Industry, Abiko, Chiba, 270-1194, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Kazuhiro Shoji
- Central Research Institute of Electric Power Industry, Abiko, Chiba, 270-1194, Japan.
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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8
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Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO, Truco MJ, Xia R, Zhu S, Xu C, Xu H, Xu X, Cox K, Korf I, Meyers BC, Michelmore RW. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun 2017; 8:14953. [PMID: 28401891 PMCID: PMC5394340 DOI: 10.1038/ncomms14953] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [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: 08/15/2016] [Accepted: 02/15/2017] [Indexed: 01/03/2023] Open
Abstract
Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
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Affiliation(s)
| | | | | | | | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Chi Song
- BGI Shenzhen, Shenzhen 518083, China
| | | | | | | | | | - Rui Xia
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, Missouri 63132, USA
| | | | | | - Huaqin Xu
- UC Davis Genome Center, Davis, California 95616, USA
| | - Xun Xu
- BGI Shenzhen, Shenzhen 518083, China
| | - Kyle Cox
- UC Davis Genome Center, Davis, California 95616, USA
| | - Ian Korf
- UC Davis Genome Center, Davis, California 95616, USA
- Department of Molecular & Cellular Biology, UC Davis, California 95616, USA
| | - Blake C. Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, Missouri 63132, USA
| | - Richard W. Michelmore
- UC Davis Genome Center, Davis, California 95616, USA
- Department of Molecular & Cellular Biology, UC Davis, California 95616, USA
- Department of Plant Sciences, UC Davis, California 95616, USA
- Department of Medical Microbiology & Immunology, UC Davis, California 95616, USA
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9
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Scaglione D, Reyes-Chin-Wo S, Acquadro A, Froenicke L, Portis E, Beitel C, Tirone M, Mauro R, Lo Monaco A, Mauromicale G, Faccioli P, Cattivelli L, Rieseberg L, Michelmore R, Lanteri S. Corrigendum: The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep 2016; 6:25323. [PMID: 27212460 PMCID: PMC4876515 DOI: 10.1038/srep25323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Font i Forcada C, Oraguzie N, Reyes-Chin-Wo S, Espiau MT, Socias i Company R, Fernández i Martí A. Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping. PLoS One 2015; 10:e0127656. [PMID: 26111146 PMCID: PMC4482440 DOI: 10.1371/journal.pone.0127656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 02/20/2015] [Accepted: 04/17/2015] [Indexed: 01/15/2023] Open
Abstract
To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.
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Affiliation(s)
- Carolina Font i Forcada
- Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America
| | - Nnadozie Oraguzie
- Washington State University, Irrigated Agriculture Research and Extension Center, 24106 N Bunn Road, Prosser, WA 99350, United States of America
| | - Sebastian Reyes-Chin-Wo
- Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America
| | - Maria Teresa Espiau
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
| | - Rafael Socias i Company
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
| | - Angel Fernández i Martí
- Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
- * E-mail:
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Pearl SA, Bowers JE, Reyes-Chin-Wo S, Michelmore RW, Burke JM. Genetic analysis of safflower domestication. BMC Plant Biol 2014; 14:43. [PMID: 24502326 PMCID: PMC3925122 DOI: 10.1186/1471-2229-14-43] [Citation(s) in RCA: 12] [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: 09/19/2013] [Accepted: 01/28/2014] [Indexed: 05/31/2023]
Abstract
BACKGROUND Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family.We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and its wild progenitor, Carthamus palaestinus Eig. Also, we compared QTL positions in safflower against those that have been previously identified in cultivated x wild sunflower crosses to identify instances of colocalization. RESULTS We mapped 61 QTL, the vast majority of which (59) exhibited minor or moderate phenotypic effects. The two large-effect QTL corresponded to one each for flower color and leaf spininess. A total of 14 safflower QTL colocalized with previously reported sunflower QTL for the same traits. Of these, QTL for three traits (days to flower, achene length, and number of selfed seed) had cultivar alleles that conferred effects in the same direction in both species. CONCLUSIONS As has been observed in sunflower, and unlike many other crops, our results suggest that the genetics of safflower domestication is quite complex. Moreover, our comparative mapping results indicate that safflower and sunflower exhibit numerous instances of QTL colocalization, suggesting that parallel trait transitions during domestication may have been driven, at least in part, by parallel genotypic evolution at some of the same underlying genes.
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Affiliation(s)
- Stephanie A Pearl
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - John E Bowers
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
| | | | | | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
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Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, Truco MJ, Kozik A, Michelmore RW, Van Deynze A. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip. PLoS One 2013; 8:e56200. [PMID: 23409153 PMCID: PMC3568043 DOI: 10.1371/journal.pone.0056200] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [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: 03/16/2012] [Accepted: 01/10/2013] [Indexed: 11/19/2022] Open
Abstract
The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.
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Affiliation(s)
- Theresa A. Hill
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Sebastian Reyes-Chin-Wo
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
- Genome Center, University of California Davis, Davis, California, United States of America
| | - JiQiang Yao
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
| | - Kevin Stoffel
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Maria-Jose Truco
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Alexander Kozik
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Richard W. Michelmore
- Genome Center, University of California Davis, Davis, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
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Yarnes SC, Ashrafi H, Reyes-Chin-Wo S, Hill TA, Stoffel KM, Van Deynze A. Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population. Genome 2013; 56:61-74. [PMID: 23379339 DOI: 10.1139/gen-2012-0083] [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] [Indexed: 11/22/2022]
Abstract
Quantitative trait loci (QTL) analyses in pepper are common for horticultural, disease resistance, and fruit quality traits; although none of the studies to date have used sequence-based markers associated with genes. In this study we measured plant architectural, phenological, and fruit quality traits in a pepper mapping population consisting of 92 recombinant inbred lines derived from a cross between Capsicum frutescens acc. 2814-6 and C. annuum var. NuMexRNAKY. Phenotypic measurements were correlated to loci in a high-density EST-based genetic map. In total, 96 QTL were identified for 38 traits, including 12 QTL associated with capsaicinoid levels. Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper.
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Affiliation(s)
- Shawn C Yarnes
- Seed Biotechnology Center, University of California, Davis, CA 95616, USA
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Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco MJ, Michelmore RW, Van Deynze A. Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics 2012; 13:185. [PMID: 22583801 PMCID: PMC3490809 DOI: 10.1186/1471-2164-13-185] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 11/14/2011] [Accepted: 02/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
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Affiliation(s)
- Kevin Stoffel
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | - Hans van Leeuwen
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
- Nunhems Netherlands B.V., P.O. Box 4005, 6080, AA, Haelen, The Netherlands
| | - Alexander Kozik
- Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - David Caldwell
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
- Monsanto, Molecular Breeding Technology, 700 Chesterfield Pkwy W, BB34, Chesterfield, MO, 63017, England
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | - Xinping Cui
- Department of Statistics, University of California, Riverside, CA, 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Xiaoping Tan
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
| | | | - Maria-Jose Truco
- Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Richard W Michelmore
- Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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15
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Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco MJ, Michelmore RW, Van Deynze A. Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics 2012. [PMID: 22583801 DOI: 10.1186/1471‐2164‐13‐185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
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Affiliation(s)
- Kevin Stoffel
- Seed Biotechnology Center, University of California-Davis, CA 95616, USA
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