1
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Yocca AE, Platts A, Alger E, Teresi S, Mengist MF, Benevenuto J, Ferrão LFV, Jacobs M, Babinski M, Magallanes-Lundback M, Bayer P, Golicz A, Humann JL, Main D, Espley RV, Chagné D, Albert NW, Montanari S, Vorsa N, Polashock J, Díaz-Garcia L, Zalapa J, Bassil NV, Munoz PR, Iorizzo M, Edger PP. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. Hortic Res 2023; 10:uhad202. [PMID: 38023484 PMCID: PMC10673653 DOI: 10.1093/hr/uhad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/01/2023] [Indexed: 12/01/2023]
Abstract
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
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Affiliation(s)
- Alan E Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, United States
| | - Adrian Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, United States
| | - Elizabeth Alger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
| | - Scott Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, United States
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC United States
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Luis Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States
| | - Michal Babinski
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
| | | | - Philipp Bayer
- University of Western Australia, Perth 6009Australia
| | | | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA, 99163, United States
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, United States
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019United States
| | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019United States
| | - Luis Díaz-Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, United States
| | - Juan Zalapa
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, United States
| | - Nahla V Bassil
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR 97333, United States
| | - Patricio R Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NCUnited States
- Department of Horticulture, North Carolina State University, Kannapolis, NCUnited States
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, United States
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, United States
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2
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Yocca AE, Platts A, Alger E, Teresi S, Mengist MF, Benevenuto J, Ferrão LFV, Jacobs M, Babinski M, Magallanes-Lundback M, Bayer P, Golicz A, Humann JL, Main D, Espley RV, Chagné D, Albert NW, Montanari S, Vorsa N, Polashock J, Díaz-Garcia L, Zalapa J, Bassil NV, Munoz PR, Iorizzo M, Edger PP. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. bioRxiv 2023:2023.07.31.551392. [PMID: 37577683 PMCID: PMC10418200 DOI: 10.1101/2023.07.31.551392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
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Affiliation(s)
- Alan E. Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Elizabeth Alger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Molla F. Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Luis Felipe V. Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Michal Babinski
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Philipp Bayer
- University of Western Australia, Perth 6009 Australia
| | | | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Richard V. Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Luis Díaz-Garcia
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Juan Zalapa
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Patricio R. Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticulture, North Carolina State University, Kannapolis, NC USA
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
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Lopez-Moreno H, Basurto-Garduño AC, Torres-Meraz MA, Diaz-Valenzuela E, Arellano-Arciniega S, Zalapa J, Sawers RJH, Cibrián-Jaramillo A, Diaz-Garcia L. Genetic analysis and QTL mapping of domestication-related traits in chili pepper ( Capsicum annuum L .). Front Genet 2023; 14:1101401. [PMID: 37255716 PMCID: PMC10225550 DOI: 10.3389/fgene.2023.1101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 06/01/2023] Open
Abstract
Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.
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Affiliation(s)
- Hector Lopez-Moreno
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Ana Celia Basurto-Garduño
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | | | - Eric Diaz-Valenzuela
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Sergio Arellano-Arciniega
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
| | - Juan Zalapa
- Department of Horticulture, University of WI-Madison, Madison, WI, United States
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture University of WI-Madison, Madison, WI, United States
| | - Ruairidh J. H. Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, United States
| | - Angelica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
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4
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Albert NW, Iorizzo M, Mengist MF, Montanari S, Zalapa J, Maule A, Edger PP, Yocca AE, Platts AE, Pucker B, Espley RV. Vaccinium as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit. Plant Physiol 2023:7147756. [PMID: 37129240 DOI: 10.1093/plphys/kiad250] [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] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops including blueberry, cranberry, bilberry and lingonberry. Consumption of Vaccinium berries is strongly associated with various potential health and many of these benefits are attributed to the relatively high concentrations of flavonoids, including the anthocyanins that provide the attractive red and blue berry colours. Since these phytochemicals are increasingly appealing to consumers, they have become a crop breeding target. There has been substantial recent progress in Vaccinium genomics and genetics together with new functional data on the transcriptional regulation of flavonoids. This is helping to unravel the developmental control of flavonoids and to identify genetic regions and genes that can be selected for, to further improve Vaccinium crops, and advance our understanding of flavonoid regulation and biosynthesis across a broader range of fruit crops. In this update we consider the recent progress in understanding flavonoid regulation in fruit crops, using Vaccinium as an example, and highlighting the significant gains in both genomic tools and functional analysis.
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Affiliation(s)
- Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NCUSA
- Department of Horticultural Science, North Carolina State University, Raleigh, NCUSA
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NCUSA
- Department of Horticultural Science, North Carolina State University, Raleigh, NCUSA
| | | | - Juan Zalapa
- USDA-ARS, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin-Madison, WI, 53706, USA
| | - Andrew Maule
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NCUSA
- Department of Horticultural Science, North Carolina State University, Raleigh, NCUSA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, AL, 35806, USA
| | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, AL, 35806, USA
| | - Boas Pucker
- Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
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5
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Neyhart JL, Kantar MB, Zalapa J, Vorsa N. Genomic-environmental associations in wild cranberry (Vaccinium macrocarpon Ait.). G3 (Bethesda) 2022; 12:jkac203. [PMID: 35944211 PMCID: PMC9526045 DOI: 10.1093/g3journal/jkac203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/01/2022] [Indexed: 06/01/2023]
Abstract
Understanding the genetic basis of local adaptation in natural plant populations, particularly crop wild relatives, may be highly useful for plant breeding. By characterizing genetic variation for adaptation to potentially stressful environmental conditions, breeders can make targeted use of crop wild relatives to develop cultivars for novel or changing environments. This is especially appealing for improving long-lived woody perennial crops such as the American cranberry (Vaccinium macrocarpon Ait.), the cultivation of which is challenged by biotic and abiotic stresses. In this study, we used environmental association analyses in a collection of 111 wild cranberry accessions to identify potentially adaptive genomic regions for a range of bioclimatic and soil conditions. We detected 126 significant associations between SNP marker loci and environmental variables describing temperature, precipitation, and soil attributes. Many of these markers tagged genes with functional annotations strongly suggesting a role in adaptation to biotic or abiotic conditions. Despite relatively low genetic variation in cranberry, our results suggest that local adaptation to divergent environments is indeed present, and the identification of potentially adaptive genetic variation may enable a selective use of this germplasm for breeding more stress-tolerant cultivars.
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Affiliation(s)
- Jeffrey L Neyhart
- USDA, Agricultural Research Service, Genetic Improvement for Fruits & Vegetables Laboratory, Chatsworth, NJ 08019, USA
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Juan Zalapa
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Nicholi Vorsa
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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6
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Edger PP, Iorizzo M, Bassil NV, Benevenuto J, Ferrão LFV, Giongo L, Hummer K, Lawas LMF, Leisner CP, Li C, Munoz PR, Ashrafi H, Atucha A, Babiker EM, Canales E, Chagné D, DeVetter L, Ehlenfeldt M, Espley RV, Gallardo K, Günther CS, Hardigan M, Hulse-Kemp AM, Jacobs M, Lila MA, Luby C, Main D, Mengist MF, Owens GL, Perkins-Veazie P, Polashock J, Pottorff M, Rowland LJ, Sims CA, Song GQ, Spencer J, Vorsa N, Yocca AE, Zalapa J. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Hortic Res 2022; 9:uhac083. [PMID: 35611183 PMCID: PMC9123236 DOI: 10.1093/hr/uhac083] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/22/2022] [Indexed: 06/02/2023]
Abstract
The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Nahla V Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Luis Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Lara Giongo
- Fondazione Edmund Mach - Research and Innovation CentreItaly
| | - Kim Hummer
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Lovely Mae F Lawas
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Changying Li
- Phenomics and Plant Robotics Center, College of Engineering, University of Georgia, Athens, USA
| | - Patricio R Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Amaya Atucha
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ebrahiem M Babiker
- USDA-ARS Southern Horticultural Laboratory, Poplarville, MS 39470-0287, USA
| | - Elizabeth Canales
- Department of Agricultural Economics, Mississippi State University, Mississippi State, MS 39762, USA
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Lisa DeVetter
- Department of Horticulture, Washington State University Northwestern Washington Research and Extension Center, Mount Vernon, WA, 98221, USA
| | - Mark Ehlenfeldt
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Karina Gallardo
- School of Economic Sciences, Washington State University, Puyallup, WA 98371, USA
| | - Catrin S Günther
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Michael Hardigan
- USDA-ARS, Horticulture Crops Research Unit, Corvallis, OR 97333, USA
| | - Amanda M Hulse-Kemp
- USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh, NC 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Claire Luby
- USDA-ARS, Horticulture Crops Research Unit, Corvallis, OR 97333, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | | | | | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Marti Pottorff
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Lisa J Rowland
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705, USA
| | - Charles A Sims
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Guo-qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Jessica Spencer
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Juan Zalapa
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Matusinec D, Maule A, Wiesman E, Atucha A, Devi MJ, Zalapa J. The New Cranberry Wisconsin Research Station: Renovation Priorities of a 'Stevens' Cranberry Marsh Based on Visual Mapping, Genetic Testing, and Yield Data. Int J Fruit Sci 2022; 22:121-132. [PMID: 38107060 PMCID: PMC10725787 DOI: 10.1080/15538362.2021.2014016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cultivar contamination is a common issue in commercial cranberry production. Unknown or unwanted cranberry genotypes are found in commercial cranberry beds that are intended to be a single uniform genotype. Identification of contamination and the impacts of contamination remain crucial issues to the cranberry industry to maintain long-term high productivity. To address this issue, tissue samples were taken from the former commercial beds of the new Wisconsin Cranberry Research Station (WCRS) for genetic fingerprinting analysis. The goals of this collection were to analyze the ten beds for genetic uniformity to determine if any should be maintained or replaced, and to assess the accuracy of visual perception of genetic contamination in the field. A total of 288 DNA samples were collected in the ten cranberry beds, and the 'Stevens' cultivar represented 180 samples, or 69% of the 261 samples expected to be 'Stevens'. Therefore, genotype contamination in the 'Stevens' beds was 31% overall. Overall, visual differentiation was accurate in distinguishing between genotypes and detecting large areas of contamination. A yield analysis was conducted along with the genotypic uniformity assessments, and a significant correlation was found between the 2017 yield of the beds and their level of genetic contamination. This study demonstrates the usefulness of genetic uniformity testing and mapping for cranberry bed management and renovation decision-making.
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Affiliation(s)
- Daniel Matusinec
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Andrew Maule
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Eric Wiesman
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Amaya Atucha
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Mura Jyostna Devi
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
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Diaz-Garcia L, Garcia-Ortega LF, González-Rodríguez M, Delaye L, Iorizzo M, Zalapa J. Chromosome-Level Genome Assembly of the American Cranberry ( Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum. Front Plant Sci 2021; 12:633310. [PMID: 33643360 PMCID: PMC7902871 DOI: 10.3389/fpls.2021.633310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.
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Affiliation(s)
- Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Pabellón, Aguascalientes, Mexico
| | | | | | - Luis Delaye
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, WI, United States
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, United States
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Dharampal PS, Diaz-Garcia L, Haase MAB, Zalapa J, Currie CR, Hittinger CT, Steffan SA. Microbial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee Colonies. Insects 2020; 11:insects11040250. [PMID: 32316296 PMCID: PMC7240610 DOI: 10.3390/insects11040250] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/14/2022]
Abstract
The pollen stores of bumble bees host diverse microbiota that influence overall colony fitness. Yet, the taxonomic identity of these symbiotic microbes is relatively unknown. In this descriptive study, we characterized the microbial community of pollen provisions within captive-bred bumble bee hives obtained from two commercial suppliers located in North America. Findings from 16S rRNA and ITS gene-based analyses revealed that pollen provisions from the captive-bred hives shared several microbial taxa that have been previously detected among wild populations. While diverse microbes across phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Ascomycota were detected in all commercial hives, significant differences were detected at finer-scale taxonomic resolution based on the supplier source. The causative agent of chalkbrood disease in honey bees, Ascosphaera apis, was detected in all hives obtained from one supplier source, although none of the hives showed symptoms of infection. The shared core microbiota across both commercial supplier sources consisted of two ubiquitous bee-associated groups, Lactobacillus and Wickerhamiella/Starmerella clade yeasts that potentially contribute to the beneficial function of the microbiome of bumble bee pollen provisions.
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Affiliation(s)
- Prarthana S. Dharampal
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Correspondence:
| | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; (L.D.-G.); (J.Z.)
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Aguascalientes 20676, Mexico
| | - Max A. B. Haase
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.A.B.H.); (C.T.H.)
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; (L.D.-G.); (J.Z.)
- USDA-ARS, Vegetable Crop Research Unit, Madison, WI 53706, USA
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.A.B.H.); (C.T.H.)
| | - Shawn A. Steffan
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA;
- USDA-ARS, Vegetable Crop Research Unit, Madison, WI 53706, USA
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Diaz-Garcia L, Covarrubias-Pazaran G, Johnson-Cicalese J, Vorsa N, Zalapa J. Genotyping-by-Sequencing Identifies Historical Breeding Stages of the Recently Domesticated American Cranberry. Front Plant Sci 2020; 11:607770. [PMID: 33391320 PMCID: PMC7772218 DOI: 10.3389/fpls.2020.607770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/20/2020] [Indexed: 05/05/2023]
Abstract
The cranberry (Vaccinium macrocarpon Ait.) is a North American fruit crop domesticated less than 200 years ago. The USDA began the first cranberry breeding program in response to false-blossom disease in 1929, but after the first generation of cultivars were released in the 1950s, the program was discontinued. Decades later, renewed efforts for breeding cranberry cultivars at Rutgers University and the University of Wisconsin yielded the first modern cultivars in the 2000's. Phenotypic data suggests that current cultivars have changed significantly in terms of fruiting habits compared to original selections from endemic populations. However, due to the few breeding and selection cycles and short domestication period of the crop, it is unclear how much cultivated germplasm differs genetically from wild selections. Moreover, the extent to which selection for agricultural superior traits has shaped the genetic and phenotypic variation of cranberry remains mostly obscure. Here, a historical collection composed of 362 accessions, spanning wild germplasm, first-, second-, and third-generation selection cycles was studied to provide a window into the breeding and domestication history of cranberry. Genome-wide sequence variation of more than 20,000 loci showed directional selection across the stages of cranberry domestication and breeding. Diversity analysis and population structure revealed a partially defined progressive bottleneck when transitioning from early domestication stages to current cranberry forms. Additionally, breeding cycles correlated with phenotypic variation for yield-related traits and anthocyanin accumulation, but not for other fruit metabolites. Particularly, average fruit weight, yield, and anthocyanin content, which were common target traits during early selection attempts, increased dramatically in second- and third-generation cycle cultivars, whereas other fruit quality traits such as Brix and acids showed comparable variation among all breeding stages. Genome-wide association mapping in this diversity panel allowed us to identify marker-trait associations for average fruit weight and fruit rot, which are two traits of great agronomic relevance today and could be further exploited to accelerate cranberry genetic improvement. This study constitutes the first genome-wide analysis of cranberry genetic diversity, which explored how the recurrent use of wild germplasm and first-generation selections into cultivar development have shaped the evolutionary history of this crop species.
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Affiliation(s)
- Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Aguascalientes, Mexico
- *Correspondence: Luis Diaz-Garcia, ;
| | | | - Jennifer Johnson-Cicalese
- Marucci Center for Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, United States
| | - Nicholi Vorsa
- Marucci Center for Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, United States
- Department of Plant Science, Rutgers University, New Brunswick, NJ, United States
- Nicholi Vorsa,
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, WI, United States
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, United States
- Juan Zalapa, ;
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Diaz-Garcia L, Rodriguez-Bonilla L, Phillips M, Lopez-Hernandez A, Grygleski E, Atucha A, Zalapa J. Comprehensive analysis of the internal structure and firmness in American cranberry (Vaccinium macrocarpon Ait.) fruit. PLoS One 2019; 14:e0222451. [PMID: 31553750 PMCID: PMC6760784 DOI: 10.1371/journal.pone.0222451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 04/04/2019] [Accepted: 08/30/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cranberry (Vaccinium macrocarpon L.) fruit quality traits encompass many properties. Although visual appearance and fruit nutritional constitution have usually been the most important attributes, cranberry textural properties such as firmness have recently gained importance in the industry. Fruit firmness has become a quality standard due to the recent demand increase for sweetened and dried cranberries (SDC), which are currently the most profitable cranberry product. Traditionally, this trait has been measured by the cranberry industry using compression tests; however, it is poorly understood how fruit firmness is influenced by other characteristics. RESULTS In this study, we developed a high-throughput computer-vision method to measure the internal structure of cranberry fruit, which may in turn influence cranberry fruit firmness. We measured the internal structure of 16 cranberry cultivars measured over a 40-day period, representing more than 3000 individual fruit evaluated for 10 different traits. The internal structure data paired with fruit firmness values at each evaluation period allowed us to explore the correlations between firmness and internal morphological characteristics. CONCLUSIONS Our study highlights the potential use of internal structure and firmness data as a decision-making tool for cranberry processing, especially to determine optimal harvest times and ensure high quality fruit. In particular, this study introduces novel methods to define key parameters of cranberry fruit that have not been characterized in cranberry yet. This project will aid in the future evaluation of cranberry cultivars for in SDC production.
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Affiliation(s)
- Luis Diaz-Garcia
- University of Wisconsin-Madison, Department of Horticulture, Madison, Wisconsin, United States of America
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Aguascalientes, México
| | - Lorraine Rodriguez-Bonilla
- University of Wisconsin-Madison, Department of Horticulture, Madison, Wisconsin, United States of America
| | - Matthew Phillips
- University of Wisconsin-Madison, Department of Horticulture, Madison, Wisconsin, United States of America
| | - Arnoldo Lopez-Hernandez
- University of Wisconsin-Madison, Department of Food Science, Madison, Wisconsin, United States of America
| | | | - Amaya Atucha
- University of Wisconsin-Madison, Department of Horticulture, Madison, Wisconsin, United States of America
| | - Juan Zalapa
- University of Wisconsin-Madison, Department of Horticulture, Madison, Wisconsin, United States of America
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, United States of America
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12
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Schlautman B, Covarrubias-Pazaran G, Rodriguez-Bonilla L, Hummer K, Bassil N, Smith T, Zalapa J. Genetic diversity and cultivar variants in the NCGR cranberry ( Vaccinium macrocarpon Aiton) collection. J Genet 2018; 97:1339-1351. [PMID: 30555082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The American cranberry (Vaccinium macrocarpon) is an endemic domesticated species that has become an economically important commercial fruit crop. The USDA-ARS National Clonal Germplasm Repository (NCGR) houses the national Vaccinium collection, which includes representatives of historical cranberry cultivars and wild-selected germplasm. The objective of this study wasto examine the genotypes of 271 cranberry plants from 77 accessions representing 66 named cultivars using 12 simple-sequence repeats to assess clonal purity and cultivar relatedness. Using principal components analysis and neighbour-joining based on estimated genetic distances between individuals, we identified 64 unique genotypes and observed that intracultivar variants (i.e. subclones) existed in the germplasm collection and in the commercial bogs where some accessions originated. Finally, through a comparison of the genotypes of this study with the previous studies, pedigree analysis and the study of the geographic distribution of cranberry diversity, we identified consensus genotypes for many accessions and cultivars. We highlight the important role that the NCGR collection playsfor ex situ conservation of cranberry germplasm for future breeders and researchers. The NCGR continues to search for historically relevant cultivars absent from the collection in an effort to preserve these genotypes before they are lost and no longer commercially grown.
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Affiliation(s)
- B Schlautman
- The Land Institute, 2440 E. Water Well Road, Salina, KS, 67401, ;
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13
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Covarrubias-Pazaran G, Schlautman B, Diaz-Garcia L, Grygleski E, Polashock J, Johnson-Cicalese J, Vorsa N, Iorizzo M, Zalapa J. Multivariate GBLUP Improves Accuracy of Genomic Selection for Yield and Fruit Weight in Biparental Populations of Vaccinium macrocarpon Ait. Front Plant Sci 2018; 9:1310. [PMID: 30258453 PMCID: PMC6144488 DOI: 10.3389/fpls.2018.01310] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/20/2018] [Indexed: 05/10/2023]
Abstract
The development of high-throughput genotyping has made genome-wide association (GWAS) and genomic selection (GS) applications possible for both model and non-model species. The exploitation of genome-assisted approaches could greatly benefit breeding efforts in American cranberry (Vaccinium macrocarpon) and other minor crops. Using biparental populations with different degrees of relatedness, we evaluated multiple GS methods for total yield (TY) and mean fruit weight (MFW). Specifically, we compared predictive ability (PA) differences between univariate and multivariate genomic best linear unbiased predictors (GBLUP and MGBLUP, respectively). We found that MGBLUP provided higher predictive ability (PA) than GBLUP, in scenarios with medium genetic correlation (8-17% increase with corg~0.6) and high genetic correlations (25-156% with corg~0.9), but found no increase when genetic correlation was low. In addition, we found that only a few hundred single nucleotide polymorphism (SNP) markers are needed to reach a plateau in PA for both traits in the biparental populations studied (in full linkage disequilibrium). We observed that higher resemblance among individuals in the training (TP) and validation (VP) populations provided greater PA. Although multivariate GS methods are available, genetic correlations and other factors need to be carefully considered when applying these methods for genetic improvement.
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Affiliation(s)
| | | | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin Madison, Madison, WI, United States
- Instituto Nacional de Investigaciones, Forestales, Agrícolas y Pecuarias, Campo Experimental Pabellón, Aguascalientes, Mexico
| | | | - James Polashock
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Chatsworth, NJ, United States
| | - Jennifer Johnson-Cicalese
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, United States
| | - Nicholi Vorsa
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, United States
| | - Massimo Iorizzo
- Department of Horticulture Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Juan Zalapa
- Vegetable Crops Research Unit, USDA-ARS, University of Wisconsin, Madison, WI, United States
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14
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Diaz-Garcia L, Covarrubias-Pazaran G, Schlautman B, Grygleski E, Zalapa J. Image-based phenotyping for identification of QTL determining fruit shape and size in American cranberry ( Vaccinium macrocarpon L.). PeerJ 2018; 6:e5461. [PMID: 30128209 PMCID: PMC6098679 DOI: 10.7717/peerj.5461] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/26/2018] [Indexed: 12/12/2022] Open
Abstract
Image-based phenotyping methodologies are powerful tools to determine quality parameters for fruit breeders and processors. The fruit size and shape of American cranberry (Vaccinium macrocarpon L.) are particularly important characteristics that determine the harvests’ processing value and potential end-use products (e.g., juice vs. sweetened dried cranberries). However, cranberry fruit size and shape attributes can be difficult and time consuming for breeders and processors to measure, especially when relying on manual measurements and visual ratings. Therefore, in this study, we implemented image-based phenotyping techniques for gathering data regarding basic cranberry fruit parameters such as length, width, length-to-width ratio, and eccentricity. Additionally, we applied a persistent homology algorithm to better characterize complex shape parameters. Using this high-throughput artificial vision approach, we characterized fruit from 351 progeny from a full-sib cranberry population over three field seasons. Using a covariate analysis to maximize the identification of well-supported quantitative trait loci (QTL), we found 252 single QTL in a 3-year period for cranberry fruit size and shape descriptors from which 20% were consistently found in all years. The present study highlights the potential for the identified QTL and the image-based methods to serve as a basis for future explorations of the genetic architecture of fruit size and shape in cranberry and other fruit crops.
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Affiliation(s)
- Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Pabellon de Arteaga, Aguascalientes, Mexico.,University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Juan Zalapa
- University of Wisconsin-Madison, Madison, WI, USA.,Vegetable Crops Research Unit, USDA-ARS, Madison, WI, USA
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15
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Diaz-Garcia L, Schlautman B, Covarrubias-Pazaran G, Maule A, Johnson-Cicalese J, Grygleski E, Vorsa N, Zalapa J. Massive phenotyping of multiple cranberry populations reveals novel QTLs for fruit anthocyanin content and other important chemical traits. Mol Genet Genomics 2018; 293:1379-1392. [PMID: 29967963 DOI: 10.1007/s00438-018-1464-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/19/2018] [Indexed: 01/08/2023]
Abstract
Because of its known phytochemical activity and benefits for human health, American cranberry (Vaccinium macrocarpon L.) production and commercialization around the world has gained importance in recent years. Flavonoid compounds as well as the balance of sugars and acids are key quality characteristics of fresh and processed cranberry products. In this study, we identified novel QTL that influence total anthocyanin content (TAcy), titratable acidity (TA), proanthocyanidin content (PAC), Brix, and mean fruit weight (MFW) in cranberry fruits. Using repeated measurements over the fruit ripening period, different QTLs were identified at specific time points that coincide with known chemical changes during fruit development and maturation. Some genetic regions appear to be regulating more than one trait. In addition, we demonstrate the utility of digital imaging as a reliable, inexpensive and high-throughput strategy for the quantification of anthocyanin content in cranberry fruits. Using this imaging approach, we identified a set of QTLs across three different breeding populations which collocated with anthocyanin QTL identified using wet-lab approaches. We demonstrate the use of a high-throughput, reliable and highly accessible imaging strategy for predicting anthocyanin content based on cranberry fruit color, which could have a large impact for both industry and cranberry research.
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Affiliation(s)
- Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin, Madison, WI, USA. .,Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Aguascalientes, Mexico.
| | | | | | - Andrew Maule
- Department of Horticulture, University of Wisconsin, Madison, WI, USA
| | | | | | - Nicholi Vorsa
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, USA
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, WI, USA. .,USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, USA.
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Steffan SA, Dharampal PS, Diaz-Garcia L, Currie CR, Zalapa J, Hittinger CT. Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health. J Vis Exp 2017. [PMID: 29053686 DOI: 10.3791/54631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered "bee-safe," there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.
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Affiliation(s)
- Shawn A Steffan
- Vegetable Crop Research Unit, USDA-ARS; Department of Entomology, University of Wisconsin-Madison;
| | | | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin-Madison; Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias
| | | | - Juan Zalapa
- Vegetable Crop Research Unit, USDA-ARS; Department of Horticulture, University of Wisconsin-Madison
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin; DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
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17
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Affiliation(s)
- Luis Diaz-Garcia
- From the Department of Horticulture, University of Wisconsin, Madison, WI 53706 (Diaz-Garcia, Covarrubias-Pazaran, and Zalapa); Instituto Nacional de Investigaciones Forestales y Agrícolas y Pecuarias, Aguascalientes 20660, Mexico (Diaz-Garcia); The Land Institute, Salina, KS 67401 (Schlautman); and USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706 (Zalapa)
| | - Giovanny Covarrubias-Pazaran
- From the Department of Horticulture, University of Wisconsin, Madison, WI 53706 (Diaz-Garcia, Covarrubias-Pazaran, and Zalapa); Instituto Nacional de Investigaciones Forestales y Agrícolas y Pecuarias, Aguascalientes 20660, Mexico (Diaz-Garcia); The Land Institute, Salina, KS 67401 (Schlautman); and USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706 (Zalapa)
| | - Brandon Schlautman
- From the Department of Horticulture, University of Wisconsin, Madison, WI 53706 (Diaz-Garcia, Covarrubias-Pazaran, and Zalapa); Instituto Nacional de Investigaciones Forestales y Agrícolas y Pecuarias, Aguascalientes 20660, Mexico (Diaz-Garcia); The Land Institute, Salina, KS 67401 (Schlautman); and USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706 (Zalapa)
| | - Juan Zalapa
- From the Department of Horticulture, University of Wisconsin, Madison, WI 53706 (Diaz-Garcia, Covarrubias-Pazaran, and Zalapa); Instituto Nacional de Investigaciones Forestales y Agrícolas y Pecuarias, Aguascalientes 20660, Mexico (Diaz-Garcia); The Land Institute, Salina, KS 67401 (Schlautman); and USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706 (Zalapa)
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18
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Diaz-Garcia L, Covarrubias-Pazaran G, Schlautman B, Zalapa J. GiNA, an Efficient and High-Throughput Software for Horticultural Phenotyping. PLoS One 2016; 11:e0160439. [PMID: 27529547 PMCID: PMC4986961 DOI: 10.1371/journal.pone.0160439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 03/21/2016] [Accepted: 07/19/2016] [Indexed: 11/23/2022] Open
Abstract
Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables.
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Affiliation(s)
- Luis Diaz-Garcia
- University of Wisconsin, Department of Horticulture, Madison, Wisconsin, United States of America
- Instituto Nacional de Investigaciones Forestales y Agrícolas y Pecuarias, Aguascalientes, Mexico
- * E-mail: (JZ); (LDG)
| | | | - Brandon Schlautman
- University of Wisconsin, Department of Horticulture, Madison, Wisconsin, United States of America
| | - Juan Zalapa
- University of Wisconsin, Department of Horticulture, Madison, Wisconsin, United States of America
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail: (JZ); (LDG)
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Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Deutsch J, Salazar W, Hernandez-Ochoa M, Grygleski E, Steffan S, Iorizzo M, Polashock J, Vorsa N, Zalapa J. Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. BMC Genomics 2016; 17:451. [PMID: 27295982 PMCID: PMC4906896 DOI: 10.1186/s12864-016-2802-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 05/27/2016] [Indexed: 01/08/2023] Open
Abstract
Background The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. Results We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. Conclusions GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS). Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2802-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.,Instituto Nacional de Investigaciones Agrícolas, Forestales y Pecuarias, Campo Experimental Pabellón, Aguascalientes, Mexico
| | - Brandon Schlautman
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA
| | - Joseph Deutsch
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, USA
| | - Walter Salazar
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA
| | | | | | - Shawn Steffan
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, USA
| | - Massimo Iorizzo
- Department of Horticultural Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - James Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, New Jersey, USA
| | - Nicholi Vorsa
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, New Jersey, USA
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA. .,USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, USA.
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Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Salazar W, Zalapa J. Fragman: an R package for fragment analysis. BMC Genet 2016; 17:62. [PMID: 27098093 PMCID: PMC4839125 DOI: 10.1186/s12863-016-0365-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. RESULTS We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® (ABI) either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry (Vaccinium macrocarpon) genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. CONCLUSION Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.
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Affiliation(s)
| | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin, Madison, WI, USA.,Instituto Nacional de Investigaciones Forestales, Agricolas, y Pecuarias, Campo Experimental Pabellon, Aguascalientes, Mexico
| | | | - Walter Salazar
- Department of Horticulture, University of Wisconsin, Madison, WI, USA
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, WI, USA. .,USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, USA.
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Brunet J, Zalapa J, Guries R. Conservation of genetic diversity in slippery elm (Ulmus rubra) in Wisconsin despite the devastating impact of Dutch elm disease. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0838-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Ecker G, Zalapa J, Auer C. Switchgrass (Panicum virgatum L.) Genotypes Differ between Coastal Sites and Inland Road Corridors in the Northeastern US. PLoS One 2015; 10:e0130414. [PMID: 26125564 PMCID: PMC4488425 DOI: 10.1371/journal.pone.0130414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 01/20/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Switchgrass (Panicum virgatum L.) is a North American grass that exhibits vast genetic diversity across its geographic range. In the Northeastern US, local switchgrass populations were restricted to a narrow coastal zone before European settlement, but current populations inhabit inland road verges raising questions about their origin and genetics. These questions are important because switchgrass lines with novel traits are being cultivated as a biofuel feedstock, and gene flow could impact the genetic integrity and distribution of local populations. This study was designed to determine if: 1) switchgrass plants collected in the Long Island Sound Coastal Lowland coastal Level IV ecoregion represented local populations, and 2) switchgrass plants collected from road verges in the adjacent inland regions were most closely related to local coastal populations or switchgrass from other geographic regions. The study used 18 microsatellite markers to infer the genetic relationships between 122 collected switchgrass plants and a reference dataset consisting of 28 cultivars representing ecotypes, ploidy levels, and lineages from North America. Results showed that 84% of 88 plants collected in the coastal plants were most closely aligned with the Lowland tetraploid genetic pool. Among this group, 61 coastal plants were similar to, but distinct from, all Lowland tetraploid cultivars in the reference dataset leading to the designation of a genetic sub-population called the Southern New England Lowland Tetraploids. In contrast, 67% of 34 plants collected in road verges in the inland ecoregions were most similar to two Upland octoploid cultivars; only 24% of roadside plants were Lowland tetraploid. These results suggest that cryptic, non-local genotypes exist in road verges and that gene flow from biofuels plantations could contribute to further changes in switchgrass population genetics in the Northeast.
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Affiliation(s)
- Geoffrey Ecker
- Department of Plant Science and Landscape Architecture, 1390 Storrs Road, U-4163, University of Connecticut, Storrs, Connecticut, 06269, United States of America
- * E-mail:
| | - Juan Zalapa
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, United States of America
| | - Carol Auer
- Department of Plant Science and Landscape Architecture, 1390 Storrs Road, U-4163, University of Connecticut, Storrs, Connecticut, 06269, United States of America
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Schlautman B, Fajardo D, Bougie T, Wiesman E, Polashock J, Vorsa N, Steffan S, Zalapa J. Development and validation of 697 novel polymorphic genomic and EST-SSR markers in the American cranberry (Vaccinium macrocarpon Ait.). Molecules 2015; 20:2001-13. [PMID: 25633331 PMCID: PMC6272188 DOI: 10.3390/molecules20022001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 11/16/2022] Open
Abstract
The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.
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Affiliation(s)
- Brandon Schlautman
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Dr. Madison, WI 53706, USA.
| | - Diego Fajardo
- National Center for Genome Resources, 2935 Rodeo Park Dr. East, Sante Fe, NM 87505, USA.
| | - Tierney Bougie
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Dr. Madison, WI 53706, USA.
| | - Eric Wiesman
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA.
| | - James Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Rutgers University Chatsworth, NJ 08019, USA.
| | - Nicholi Vorsa
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ 08019, USA.
| | - Shawn Steffan
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA.
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Dr. Madison, WI 53706, USA.
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Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, Vorsa N. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC Plant Biol 2014; 14:165. [PMID: 24927653 PMCID: PMC4076063 DOI: 10.1186/1471-2229-14-165] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/03/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear. RESULTS The genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%). CONCLUSIONS Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.
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Affiliation(s)
- James Polashock
- USDA, Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Lab, 125A Lake Oswego Rd., Chatsworth, New Jersey 08019, USA
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 59 Dudley Rd., New Brunswick, New Jersey 08901, USA
| | - Diego Fajardo
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706, USA
| | - Juan Zalapa
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin 53706, USA
| | - Laura Georgi
- P.E. Marucci Center for Blueberry and Cranberry Research, 125A Lake Oswego Rd., Chatsworth, New Jersey 08019, USA
- Current address: American Chestnut Foundation, Meadowview Research Farms, 29010, Hawthorne, Dr., Meadowview, Virginia 24361, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 59 Dudley Rd., New Brunswick, New Jersey 08901, USA
| | - Nicholi Vorsa
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ 08901, USA
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Li D, Cuevas HE, Yang L, Li Y, Garcia-Mas J, Zalapa J, Staub JE, Luan F, Reddy U, He X, Gong Z, Weng Y. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics 2011; 12:396. [PMID: 21816110 PMCID: PMC3199783 DOI: 10.1186/1471-2164-12-396] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/05/2011] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes. RESULTS Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F(2)- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber. CONCLUSIONS Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of Cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.
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Affiliation(s)
- Dawei Li
- Horticulture College, Northwest A & F University, Yangling 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Hugo E Cuevas
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Tropical Agriculture Research Station, Mayaguez, P.R. 00680, Puerto Rico
| | - Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Yuhong Li
- Horticulture College, Northwest A & F University, Yangling 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Juan Zalapa
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Jack E Staub
- USDA-ARS, Forage & Range Research Laboratory, Utah State University, Logan, UT 84322 USA
| | - Feishi Luan
- Horticulture College, Northeast Agricultural University, Harbin, 150030, China
| | - Umesh Reddy
- Department of Biology, West Virginia State University Institute, WV 25112, USA
| | - Xiaoming He
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhenhui Gong
- Horticulture College, Northwest A & F University, Yangling 712100, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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Byars-Winston A, Estrada Y, Howard C, Davis D, Zalapa J. Influence of social cognitive and ethnic variables on academic goals of underrepresented students in science and engineering: a multiple-groups analysis. J Couns Psychol 2011; 57:205-18. [PMID: 20495610 DOI: 10.1037/a0018608] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study investigated the academic interests and goals of 223 African American, Latino/a, Southeast Asian, and Native American undergraduate students in two groups: biological science and engineering (S/E) majors. Using social cognitive career theory (Lent, Brown, & Hackett, 1994), we examined the relationships of social cognitive variables (math/science academic self-efficacy, math/science outcome expectations), along with the influence of ethnic variables (ethnic identity, other-group orientation) and perceptions of campus climate to their math/science interests and goal commitment to earn an S/E degree. Path analysis revealed that the hypothesized model provided good overall fit to the data, revealing significant relationships from outcome expectations to interests and to goals. Paths from academic self-efficacy to S/E goals and from interests to S/E goals varied for students in engineering and biological science. For both groups, other-group orientation was positively related to self-efficacy and support was found for an efficacy-mediated relationship between perceived campus climate and goals. Theoretical and practical implications of the study's findings are considered as well as future research directions.
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Affiliation(s)
- Angela Byars-Winston
- Center for Women's Health Research, University of Wisconsin-Madison, 53715-2634, USA.
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Lebeda A, Widrlechner M, Staub J, Ezura H, Zalapa J, Kristkova E. Cucurbits (Cucurbitaceae; Cucumis spp., Cucurbita spp., Citrullus spp.). Genetic Resources, Chromosome Engineering, and Crop Improvement 2006. [DOI: 10.1201/9781420009569.ch8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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