Joanne A Labate

Molecular Biologist (Plants)

Plant Genetic Resources Unit
Vegetable Crops Curator
USDA, ARS
630 W. North St., Geneva, NY  14456
315 787 2438 (office)
315 787 2339 (fax)

Overview

I characterize genetic variation in gene bank vegetable collections using molecular tools. At the USDA-ARS Plant Genetic Resources Unit (PGRU) approximately 200 plant species are conserved as collections of seed, including: tomato, onion, broccoli, cauliflower, cabbage, celery, asparagus, tomatillo, ground cherry, winter squash, radish, and buckwheat. We apply molecular, population and quantitative genetic techniques in order to describe, evaluate and better manage the collections. We also perform chemical evaluations in the lab for quality components of vegetables, such as, vitamin C, sugar, acidity and lycopene.

Education

• B.S. in Biology, 1983, Boston College, Chestnut Hill, MA
• Ph.D. in Ecology and Evolution, 1993, SUNY Stony Brook, Stony Brook, NY

Professional Experience

• Molecular Biologist and Lab Director, 1/01 to Present, PGRU, Geneva, NY
• Research Associate, 9/99 to 1/01, Institute for Genomic Diversity, Cornell University, Ithaca, NY
• Research Geneticist (Plants), 7/95 to 8/99, USDA/ARS, Iowa State University, Ames, IA
• Postdoctoral Fellow, 1/94 to 7/95, Center for Agricultural Molecular Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Onion (Allium cepa) psuedoreference genome-()
    Labate, J.A., Glaubitz, J., Havey, M. 2020. Onion (Allium cepa) psuedoreference genome. Dryad Digital Repository. https://doi.org/10.5061/dryad.6wwpzgmwg.
    
  • BioProject number PRJNA650148. Genotyping by sequencing of Allium cepa. BioSamples SAMN15693843-SAMN15694226-()
    
    
  • Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)-(Peer Reviewed Journal)
    Khoury, C.K., Kates, H.R., Carver Jr, D.P., Achicanoy, H.A., van Zonneweld, M., Thomas, E., Heinitz, C.C., Jarret, R.L., Labate, J.A., Reitsma, K., Nabhan, G.P., Greene, S.L. 2019. Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.). Plants, People, Planet. 2(3):269-283. https://doi.org//10.1002/ppp3.10085.
    
  • Population structure and diversity estimates in a geographical core set of radish (Raphanus sativus)-(Abstract Only)
    Arro, J., Labate, J.A. 2019. Population structure and diversity estimates in a geographical core set of radish (Raphanus sativus). Meeting Abstract. 1.
    
  • Characterization of the USDA germplasm collections for watermelon, melon, cucumber and squash using genotyping-by-sequencing-(Abstract Only)
    Fei, Z., Ando, K., Bao, K., Labate, J.A., Levi, A., Mazourek, M., Mccreight, J.D., Patel, T., Ramirez Madera, A., Reddy, U., Reeves, P., Wang, X., Wehner, T., Weng, Y., Wu, S., Grumet, R. 2018. Characterization of the USDA germplasm collections for watermelon, melon, cucumber and squash using genotyping-by-sequencing. American Society of Horticulture Science Meeting. 1.
    
  • Brassica oleracea: the dog of the plant world-(Abstract Only)
    Mabry, M.E., Gallagher, E., Gore, M.A., Labate, J.A., Turner, S.D., Baxter, I.R., Kliebenstein, D.J., Pires, C.J. 2018. Brassica oleracea: the dog of the plant world. Botany 2018 Conference. 1.
    
  • Brassica oleracea; The dog of the plant world-(Abstract Only)
    Mabry, M.E., Gallagher, E., Gore, M.A., Labate, J.A., Turner, S.D., Baxter, I.R., Kliebenstein, D.J., Pires, J.C. 2018. Brassica oleracea; The dog of the plant world. Population, Evolutionary, and Quantitative Genetics Conference. 1.
    
  • Genetic differences in macro-element mineral concentrations among 52 historically important tomato varieties-(Peer Reviewed Journal)
    Labate, J.A., Breksa III, A.P., Robertson, L.D., King, B.A., King, D.E. 2018. Genetic differences in macro-element mineral concentrations among 52 historically important tomato varieties. Plant Genetic Resources: Characterization and Utilization. 16(4):343-351.
    
  • Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L-(Peer Reviewed Journal)
    Bird, K., An, H., Gazave, E., Gore, M., Pires, J., Robertson, L., Labate, J.A. 2017. Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L. Frontiers in Plant Science. 8:321.
    
  • High-throughput genotyping of vegetable crops for germplasm conservation-(Abstract Only)
    Labate, J.A. 2017. High-throughput genotyping of vegetable crops for germplasm conservation. Plant and Animal Genome Conference. 1.
    
  • Characterization of Mineral Nutrients in National Plant Germplasm System (NPGS) Tomato Varieties-(Abstract Only)
    Labate, J.A., Robertson, L.D., Breksa Iii, A.P., King, B.A., King, D.E. 2016. Characterization of Mineral Nutrients in National Plant Germplasm System (NPGS) Tomato Varieties. HortScience. 51:S341.
    
  • Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines -(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D. 2015. Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines. Molecular Breeding. Volume 35(4):106. DOI: 10.1007/s11032-015-0302-9.
    
  • Physicochemical and morphological analysis of ten tomato varieties identifies quality traits more readily manipulated through breeding and traditional selection methods-(Peer Reviewed Journal)
    Breksa Iii, A.P., Robertson, L.D., Labate, J.A., King, B.A., King, D.E. 2015. Physicochemical and morphological analysis of ten tomato varieties identifies quality traits more readily manipulated through breeding and traditional selection methods. Journal of Food Composition and Analysis. 42:16-25. doi: 10.1016/j.jfca.2015.02.011.
    
  • BioProject Number PRJNA254501: Total of 190 sampled plants from Physalis philadelphica (tomatillo) genome sequencing BioSamples SAMN02904339-SAMN02904528-()
    Labate, J.A., Robertson, L.D. 2015. BioProject Number PRJNA254501: Total of 190 sampled plants from Physalis philadelphica (tomatillo) genome sequencing BioSamples SAMN02904339-SAMN02904528. National Center for Biotechnology Information (NCBI). 1.
    
  • Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex-(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D., Strickler, S., Mueller, L. 2014. Genetic structure of the four wil tomato species in the Solanum peruvianum s.l. species complex. Genome. 57:169-180.
    
  • Genomic diversity of four closely related wild tomato species revealed by genotyping-by-sequencing-(Abstract Only)
    Labate, J.A., Robertson, L.D. 2014. Genomic diversity of four closely related wild tomato species revealed by genotyping-by-sequencing. HortScience. 49:S152.
    
  • Multiple loss-of-function 5-O-Glucosyltransferase alleles revealed in Vitis vinifera, but not in other Vitis species-(Abstract Only)
    
    
  • Total of 46 sampled plants from wild tomato species genome sequencing. Study SRP034922, BioProject PRJNA230524 and BioSamples SAMN02436034 - SAMN02436079. -()
    Labate, J.A., Robertson, L.D., Strickler, S., Mueller, L. 2014. Total of 46 sampled plants from wild tomato species genome sequencing. Study SRP034922,BioProject PRJNA230524 and BioSamples SAMN02436034 - SAMN02436079. National Center for Biotechnology Information (NCBI). 1.
    
  • Genetics, Genomics and Breeding of Tomato-()
    Liedl, B., Labate, J.A., Stommel, J.R., Slade, A. 2013. Genetics, Genomics and Breeding of Tomato. Boca Raton, FL: Science Publishers. 520 p.
    
  • A phylogenomic analysis of the grape genus (Vitis) reveals broad reticulation and concurrent diversification during quaternary climate change-(Peer Reviewed Journal)
    Wan, Y., Schwaninger, H.R., Baldo, A.M., Labate, J.A., Simon, C., Zhong, G. 2013. A phylogenomic analysis of the grape genus (Vitis) reveals broad reticulation and concurrent diversification during quaternary climate change. BMC Evlutionary Biology. 13:141.
    
  • Genotype and environmental interaction for fruit quality traits in vintage tomato varieties-(Peer Reviewed Journal)
    Panthee, D., Labate, J.A., Mcgrath, M., Francis, D., Breksa III, A.P., Robertson, L.D. 2013. Genotype and environmental interaction for fruit quality traits in vintage tomato varieties. Euphytica. 193:169-182.
    
  • A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change-(Peer Reviewed Journal)
    Wan, Y., Schwaninger, H.R., Baldo, A.M., Labate, J.A., Zhong, G., Simon, C. 2013. A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. BMC Evolutionary Biology. 13:141.
    
  • Evaluation of tomato germplasm for flavor and flavor contributing components-(Peer Reviewed Journal)
    Panthee, D.R., Labate, J.A., Robertson, L.D. 2013. Evaluation of tomato germplasm for flavor and flavor contributing components. Plant Genetic Resources: Characterization and Utilization. 11:106-113.
    
  • Tomato (Solanum section Lycopersicon spp.) phylogenetic study: aligned genomic sequences for 47 markers used to analyze introgression in domesticated tomato -()
    Labate, J.A., Robertson, L.D. 2012. Tomato (Solanum section Lycopersicon spp.) phylogenetic study: aligned genomic sequences for 47 markers used to analyze introgression in domesticated tomato. European Molecular Biology. European Nucleotide Archive Accessions HE977919-HE978211.
    
  • Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles-(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D. 2012. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. Biomed Central (BMC) Plant Biology. 12:133.
    
  • Mining wild species elleles from introgressed genotypes-(Abstract Only)
    Labate, J.A., Robertson, L.D. 2012. Mining wild species elleles from introgressed genotypes. ASA-CSSA-SSSA Annual Meeting. Paper No. 1.
    
  • Evaluation of tomato germplasm for flavor and flavor-contributing components-(Abstract Only)
    Panthee, D., Labate, J.A., Robertson, L.D. 2012. Evaluation of tomato germplasm for flavor and flavor-contributing components. Proceedings American Society of Horticultural Sciences. Vol. 109, p. 90.
    
  • Magnitude of genotype x environment interactions affecting tomato fruit quality-(Peer Reviewed Journal)
    Panthee, D., Cao, C., Debenport, S., Rodriguez, G., Labate, J.A., Robertson, L.D., Breksa Iii, A.P., Van Der Knaap, E., Mcspadden-Gardener, B. 2012. Magnitude of genotype x environment interactions affecting tomato fruit quality. HortScience. 47:721-726.
    
  • Biochemical evaluation of tomato germplasm part II: evaluation of a core collection-(Abstract Only)
    Labate, J.A., Sheffer, S.M., Panthee, D., Robertson, L.D. 2012. Biochemical evaluation of tomato germplasm part II: evaluation of a core collection. Plant Germplasm Operations Committee Meeting. Vol. 4, P. 1.
    
  • Use of DNA sequence data to interpret diversity in tomato-(Abstract Only)
    Labate, J.A., Robertson, L.D. 2012. Use of DNA sequence data to interpret diversity in tomato. Plant Germplasm Operations Committee Meeting. Vol 4, p. 1..
    
  • Biochemical evaluation of tomato germplasm part I: workflow and methods-(Abstract Only)
    Robertson, L.D., Sheffer, S.M., Labate, J.A. 2012. Biochemical evaluation of tomato germplasm part I: workflow and methods. Plant Germplasm Operations Committee Meeting. Vol. 4, p. 1.
    
  • Phenotypic and molecular variation in 44 vintage tomato varieties-(Proceedings)
    Labate, J.A., Panthee, D., Mcgrath, M., Francis, D., Breksa Iii, A.P., Robertson, L.D. 2011. Phenotypic and molecular variation in 44 vintage tomato varieties. Tomato Breeders Roundtable Proceedings. Vol. 43, p. 10.
    
  • AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis-()
    Baldo, A.M., Francis, D., Caramante, M., Robertson, L.D., Labate, J.A. 2011. AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis. Plant Genetic Resources: Characterization and Utilization. 10: 1-3.
    
  • Diversity and population structure in a geographical sample of tomato (Solanum lycopersicum L.) accessions-(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D., Balch, T., Sheffer, S.M. 2011. Diversity and population structure in a geographical sample of tomato (Solanum lycopersicum L.) accessions. Crop Science. 51:1068-1079.
    
  • Comparing alleles between wild and domesticated tomato-()
    Baldo, A.M., Robertson, L.D., Labate, J.A. 2010. Comparing alleles between wild and domesticated tomato. Plant Genome Conference Proceedings.
    
  • Diversity in a Collection of Heirloom Tomato Varieties-()
    Labate, J.A., Francis, D., Mcgrath, M., Panthee, D., Robertson, L.D. 2010. Diversity in a Collection of Heirloom Tomato Varieties. Annual Meeting Horticultural Society.HortScience 45:S145.
    
  • Single nucleotide polymorphisms (SNPs) in a set of expressed-sequence tag (EST) and conserved ortholog set II (COSII) markers in cultivated tomato (Solanum lycopersicum L.)-()
    Labate, J.A., Robertson, L.D. 2010. Single nucleotide polymorphisms (SNPs) in a set of expressed-sequence tag (EST) and conserved ortholog set II (COSII) markers in cultivated tomato (Solanum lycopersicum L.). National Center for Biotechnology Information (NCBI).
    
  • Characterization of alleles in a diversity panel of tomato-()
    Labate, J.A., Robertson, L.D., Baldo, A.M. 2009. Characterization of alleles in a diversity panel of tomato [abstract]. American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America Int'l Annual Meetings, Pittsburgh, PA. oral presentation 86-6.
    
  • Phenotypic Characterization of a Diversity Panel of Tomato-()
    Robertson, L.D., Balch, T., Sheffer, S.M., Labate, J.A. 2009. Phenotypic Characterization of a Diversity Panel of Tomato. ASA-CSSA-SSSA Int'l Annual Meetings, poster presentation 85-5, Pittsburgh, PA.
    
  • Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)-(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D., Baldo, A.M. 2009. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity 103:257-267.
    
  • EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum)-(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D., Wu, F., Tanksley, S.D., Baldo, A.M. 2009. EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum). Journal of Theoretical and Applied Genetics. 118:1005-1014.
    
  • Tomato-()
    Labate, J.A., Grandillo, S., Fulton, T., Munos, S., Caicedo, A., Peralta, I., Ji, Y., Chetelat, R., Scott, J.W., Gonzalo, M.J., Francis, D., Yang, W., Van Der Knaap, E., Baldo, A.M., Smith-White, B., Mueller, L., Prince, J., Blanchard, N., Storey, D., Stevens, M., Robbins, M., Wang, J., Liedl, B., Oconnell, M., Stommel, J.R., Aoki, K., Iijima, Y., Slade, A., Hurst, S., Loeffler, D., Steine, M., Vafeados, D., Mcguire, C., Freeman, C., Amen, A., Goodstal, J., Facciotti, D., Van Eck, J., Causse, M. 2007. Tomato. Book Chapter. In: Kole, C. editor. Genome mapping and molecular breeding in plants. Volume 5 Vegetables. NY. Springer Publishing Co. p. 1-125.
    
  • The Distribution of Genetic Variation in Cultivated Tomato-(Proceedings)
    
    
  • SNP Validation and Genetic Diversity in Cultivated Tomatoes and Grapes-(Proceedings)
    
    
  • Polymorphism among EST-based markers in tomato-(Abstract Only)
    
    
  • Genetic Resources of Tomato (Lycopersicon esculentum var. esculentum) and Wild Relatives-()
    Robertson, L.D., Labate, J.A. 2007. Genetic Resources of Tomato (Lycopersicon esculentum var. esculentum) and Wild Relatives. Genetic Improvement of Solanaceous Crops, Vol 2: Tomato. p. 25-75.
    
  • HIGHLY POLYMORPHIC GENES IN CULTIVATED TOMATO-(Peer Reviewed Journal)
    Baldo, A.M., Robertson, L.D., Labate, J.A. 2005. Highly polymorphic genes in cultivated tomato. Hortscience. 40:999.
    
  • TOMATO SNP DISCOVERY BY EST MINING AND RESEQUENCING-(Peer Reviewed Journal)
    Labate, J.A., Baldo, A.M. 2005. Tomato snp discovery by est mining and resequencing. Molecular Breeding. 16:343-349.
    
  • HIGH-THROUGHPUT SNP PREDICTION IN TOMATOES BASED ON ESTS-(Proceedings)
    Baldo, A.M., Huntley, D., Robertson, L.D., Labate, J.A. 2005. High-throughput snp prediction in tomatoes based on ests. Tomato Breeders Roundtable Proceedings. p. 7 In Final Abstracts Guide, Plant and Animal Genome XIII, San Diego, Ca.
    
  • USE OF SEQUENCE-BASED POLYMORPHISMS FOR STUDING GENETIC DIVERSITY OF WINTER SQUASH-(Proceedings)
    Robertson, L.D., Baldo, A.M., Sheffer, S.M., Labate, J.A. 2005. Use of sequence-based polymorphisms for studing genetic diversity of winter squash. Meeting Abstract. p. 153 In Final Abstracts Guide, Plant & Animal Genome XII, San Diego, CA.
    
  • DISCOVERY OF HIGHLY POLYMORPHIC GENES IN TOMATO CULTIVARS-(Peer Reviewed Journal)
    Labate, J.A., Baldo, A.M. Discovery of highly polymorphic genes in tomato cultivars. Molecular Breeding. 2005.
    
  • PREDICTION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN DOMESTIC TOMATO: HOW USEFUL IS EST SEQUENCE DIVERSITY?-(Proceedings)
    Baldo, A.M., Labate, J.A., Robertson, L.D., 2004. Prediction of single nucleotide polymorphisms in domestic tomato: how useful is EST sequence diversity?. 12th International Conference on Intelligent Systems for Molecular Biology (ISMB 2004)
    
  • UTILITY OF BOCAL-A AND BOAP1-A GENOTYPES IN IDENTIFYING BROCCOLI AND CAULIFLOWER ACCESSIONS-(Peer Reviewed Journal)
    Labate, J.A., Robertson, L.D., Bjorkman, T. 2004. Utility of bocal-a and boap1-a genotypes in identifying broccoli and cauliflower accessions. Hortscience. 39:773.
    
  • A SEARCH FOR MOLECULAR DIVERSITY IN TOMATO-(Proceedings)
    BALDO, A.M., LABATE, J.A., ROBERTSON, L.D. A SEARCH FOR MOLECULAR DIVERSITY IN TOMATO. PLANT AND ANIMAL GENOME ABSTRACTS. 2004.
    
  • SEQUENCE-BASED AMPLIFIED POLYMORPHISMS ARE USEFUL FOR STUDYING GENETIC DIVERSITY OF WINTER SQUASH-(Proceedings)
    ROBERTSON, L.D., BALDO, A.M., LABATE, J.A. SEQUENCE-BASED AMPLIFIED POLYMORPHISMS ARE USEFUL FOR STUDYING GENETIC DIVERSITY OF WINTER SQUASH. PLANT AND ANIMAL GENOME ABSTRACTS. 2004.
    
  • A SEARCH FOR MOLECULAR DIVERSITY IN TOMATO-(Proceedings)
    BALDO, A.M., LABATE, J.A., ROBERTSON, L.D. A SEARCH FOR MOLECULAR DIVERSITY IN TOMATO. New England Molecular Evoluationary Biologists Meeting, Storrs, CT. 2003. . 2003.
    
  • POLYMORPHISM PREDICTION-(Proceedings)
    BALDO, A.M., LABATE, J.A. POLYMORPHISM PREDICTION. ISMB Intelligent Systems in Molecular Biology. 2003.
    
  • TEMPORAL CHANGES IN ALLELE FREQUENCIES IN TWO DIRECTIONALLY SELECTED MAIZE POPULATIONS-(Peer Reviewed Journal)
    
    
  • POPULATION GENETICS OF INCREASED HYBRID PERFORMANCE BETWEEN TWO MAIZE POPULATIONS UNDER RECIPROCAL RECURRENT SELECTION-(Proceedings)
    
    
  • MOLECULAR VARIATION IN TWO MAIZE POPULATIONS UNDERGOING SELECTION FOR IMPROVED HYBRID PERFORMANCE-(Abstract Only)
    
    
  • GENETIC DIVERSITY AFTER RECIPROCAL RECURRENT SELECTION IN BSSS AND BSCB1 MAIZE POPULATIONS-(Abstract Only)
    
    
  • MOLECULAR GENETIC DIVERSITY AFTER RECIPROCAL RECURRENT SELECTION IN BSSS AND BSCB1 MAIZE POPULATIONS-(Peer Reviewed Journal)
    
    
  • GENOME DUPLICATION IN SOYBEAN (GLYCINE SUBGENUS SOJA)-(Peer Reviewed Journal)
    
    

• Projects

  Conservation and Utilization of Priority Vegetable Crop Genetic Resources and Associated Information In-House Appropriated (D)   Accession Number:434562

  Northern Organic Vegetable Improvement Collaborative II Reimbursable Cooperative Agreement (R)   Accession Number:428202

  Northern Organic Vegetable Improvement Collaborative (NOVIC III) Reimbursable Cooperative Agreement (R)   Accession Number:433387

  Screening Short-Day Onion (Allium cepa L.) Germplasm for Fusarium Basal Rot Resistance Non-Assistance Cooperative Agreement (S)   Accession Number:435000

  Maintenance and Distribution of Wild Species Germplasm at the C.M. Rick Tomato Genetic Resources Center Non-Assistance Cooperative Agreement (S)   Accession Number:435113

  Regeneration of Short-Day Onions Non-Assistance Cooperative Agreement (S)   Accession Number:436542

  Evaluating Non-Heading Leafy Brassica Vegetable Accessions for Their Potential as Baby Greens in Vertical Farming Systems and Beyond Non-Assistance Cooperative Agreement (S)   Accession Number:436833

• ARS News Articles

  	The Search for What Makes a Tasty Tomato
  	Preserving Genetic Variety of Valuable Specialty Crops