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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3
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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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4
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Mengist MF, Bostan H, De Paola D, Teresi SJ, Platts AE, Cremona G, Qi X, Mackey T, Bassil NV, Ashrafi H, Giongo L, Jibran R, Chagné D, Bianco L, Lila MA, Rowland LJ, Iovene M, Edger PP, Iorizzo M. Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum). New Phytol 2023; 237:1024-1039. [PMID: 35962608 PMCID: PMC10087351 DOI: 10.1111/nph.18428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/01/2022] [Indexed: 06/02/2023]
Abstract
Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high-density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species. Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr-6 and one of chr-10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter-crossable wild diploid species. These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.
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Affiliation(s)
- Molla F. Mengist
- Plants for Human Health InstituteNorth Carolina State UniversityKannapolisNC28081USA
| | - Hamed Bostan
- Plants for Human Health InstituteNorth Carolina State UniversityKannapolisNC28081USA
| | - Domenico De Paola
- Institute of Biosciences and BioresourcesNational Research Council of ItalyBari70126Italy
| | - Scott J. Teresi
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
| | - Adrian E. Platts
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
| | - Gaetana Cremona
- Institute of Biosciences and BioresourcesNational Research Council of ItalyPorticiNA80055Italy
| | - Xinpeng Qi
- Genetic Improvement for Fruits and Vegetables LaboratoryBeltsville Agricultural Research Center‐West, US Department of Agriculture, Agricultural Research ServiceBeltsvilleMD20705USA
| | - Ted Mackey
- Horticultural Crops Research UnitUS Department of Agriculture, Agricultural Research ServiceCorvallisOR97330USA
| | - Nahla V. Bassil
- National Clonal Germplasm RepositoryUS Department of Agriculture, Agricultural Research ServiceCorvallisOR97333USA
| | - Hamid Ashrafi
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNC27695USA
| | - Lara Giongo
- Foundation of Edmund MachSan Michele all'AdigeTN38098Italy
| | - Rubina Jibran
- Plant & Food ResearchFitzherbertPalmerston North4474New Zealand
| | - David Chagné
- Plant & Food ResearchFitzherbertPalmerston North4474New Zealand
| | - Luca Bianco
- Foundation of Edmund MachSan Michele all'AdigeTN38098Italy
| | - Mary A. Lila
- Plants for Human Health InstituteNorth Carolina State UniversityKannapolisNC28081USA
| | - Lisa J. Rowland
- Genetic Improvement for Fruits and Vegetables LaboratoryBeltsville Agricultural Research Center‐West, US Department of Agriculture, Agricultural Research ServiceBeltsvilleMD20705USA
| | - Marina Iovene
- Institute of Biosciences and BioresourcesNational Research Council of ItalyPorticiNA80055Italy
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
| | - Massimo Iorizzo
- Plants for Human Health InstituteNorth Carolina State UniversityKannapolisNC28081USA
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNC27695USA
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5
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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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6
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Yow AG, Bostan H, Castanera R, Ruggieri V, Mengist MF, Curaba J, Young R, Gillitt N, Iorizzo M. Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family. Genes (Basel) 2021; 13:genes13010052. [PMID: 35052394 PMCID: PMC8774480 DOI: 10.3390/genes13010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.
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Affiliation(s)
- Ashley G. Yow
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain;
| | | | - Molla F. Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Julien Curaba
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Roberto Young
- Research Department of Dole, Standard Fruit de Honduras, Zona Mazapan, La Ceiba 31101, Honduras;
| | - Nicholas Gillitt
- Core Genomics Lab, David H. Murdock Research Institute, Kannapolis, NC 28081, USA;
| | - Massimo Iorizzo
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
- Correspondence:
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7
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Mengist MF, Bostan H, Young E, Kay KL, Gillitt N, Ballington J, Kay CD, Ferruzzi MG, Ashrafi H, Lila MA, Iorizzo M. High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry. Hortic Res 2021; 8:169. [PMID: 34333532 PMCID: PMC8325695 DOI: 10.1038/s41438-021-00605-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 05/21/2023]
Abstract
Fruit quality traits play a significant role in consumer preferences and consumption in blueberry (Vaccinium corymbosum L). The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry. A total of 287 F1 individuals derived from a cross between two southern highbush blueberry cultivars, 'Reveille' and 'Arlen', were phenotyped over three years (2016-2018) for fruit quality-related traits, including titratable acidity, pH, total soluble solids, and fruit weight. A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers. The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM. The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits, including seven loci for fruit weight, three loci for titratable acidity, five loci for pH, and three loci for total soluble solids. Ten of these loci were detected in more than one year. These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid, and 8-13% for pH. However, the loci identified for fruit weight did not explain more than 10% of the phenotypic variance. We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits. Organic acids, citric acid, and quinic acid were significantly (P < 0.05) and positively correlated with titratable acidity. Sugar molecules showed a strong and positive correlation with total soluble solids. Overall, the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.
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Affiliation(s)
- Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Elisheba Young
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Kristine L Kay
- David H. Murdock Research Institute, Kannapolis, NC, USA
| | | | - James Ballington
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Colin D Kay
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
- Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Mario G Ferruzzi
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
- Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
- Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 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.
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Mengist MF, Burtch H, Debelo H, Pottorff M, Bostan H, Nunn C, Corbin S, Kay CD, Bassil N, Hummer K, Lila MA, Ferruzzi MG, Iorizzo M. Development of a genetic framework to improve the efficiency of bioactive delivery from blueberry. Sci Rep 2020; 10:17311. [PMID: 33057109 PMCID: PMC7560831 DOI: 10.1038/s41598-020-74280-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/23/2020] [Indexed: 01/28/2023] Open
Abstract
In the present study, we applied a novel high-throughput in vitro gastrointestinal digestion model to phenotype bioaccessibility of phenolics in a diverse germplasm collection representing cultivated highbush blueberries. Results revealed significant (P < 0.05) differences between accessions, years, and accession by year interaction for relative and absolute bioaccessibility of flavonoids and phenolic acids. Broad sense heritability estimates revealed low to moderate inheritances of relative and absolute bioaccessibility, suggesting that besides environmental variables, genetics factors could control bioaccessibility of phenolics. Acylated anthocyanins had significantly higher relative bioaccessibility than non-acylated anthocyanins. Correlation analysis indicated that relative bioaccessibility did not show significant association with fruit quality or raw concentration of metabolites. The study also identified accessions that have high relative and absolute bioaccessibility values. Overall, combining the bioaccessibility of phenolics with genetic and genomic approaches will enable the identification of genotypes and genetic factors influencing these traits in blueberry.
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Affiliation(s)
- Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Haley Burtch
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Hawi Debelo
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Marti Pottorff
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Candace Nunn
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Sydney Corbin
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Colin D Kay
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA.,Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, 27606, NC, USA
| | - Nahla Bassil
- USDA-ARS-National Clonal Germplasm Repository, Corvallis, OR, 97333, USA
| | - Kim Hummer
- USDA-ARS-National Clonal Germplasm Repository, Corvallis, OR, 97333, USA
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA.,Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, 27606, NC, USA
| | - Mario G Ferruzzi
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA. .,Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, 27606, NC, USA.
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA. .,Department of Horticultural Science, North Carolina State University, Raleigh, 27607, NC, USA.
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Mengist MF, Grace MH, Xiong J, Kay CD, Bassil N, Hummer K, Ferruzzi MG, Lila MA, Iorizzo M. Diversity in Metabolites and Fruit Quality Traits in Blueberry Enables Ploidy and Species Differentiation and Establishes a Strategy for Future Genetic Studies. Front Plant Sci 2020; 11:370. [PMID: 32318085 PMCID: PMC7147330 DOI: 10.3389/fpls.2020.00370] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/16/2020] [Indexed: 05/30/2023]
Abstract
Blueberry is well recognized as a rich source of health promoting phytochemicals such as flavonoids and phenolic acids. Multiple studies in blueberry and other crops indicated that flavonoids and phenolic acids function as bioactive compounds in the human body promoting multiple health effects. Despite their importance, information is limited about the levels of variation in bioactive compounds within and between ploidy level and species, and their association with fruit quality traits. Such information is crucial to define a strategy to study the genetic mechanisms controlling these traits and to select for these traits in blueberry breeding programs. Here we evaluated 33 health related phytochemicals belonging to four major groups of flavonoids and phenolic acids across 128 blueberry accessions over two years together with fruit quality traits, including fruit weight, titratable acidity, total soluble acids and pH. Highly significant variation between accessions, years, and accession by year interaction were identified for most of the traits. Cluster analysis grouped phytochemicals by their functional structure (e.g., anthocyanins, flavanols, flavonols, and phenolic acids). Multivariate analysis of the traits resulted in separation of diploid, tetraploid and hexaploid accessions. Broad sense heritability of the traits estimated in 100 tetraploid accessions, ranged from 20 to 90%, with most traits revealing moderate to high broad sense heritability (H2 > 40%), suggesting that strong genetic factors control these traits. Fruit size can be estimated as a proxy of fruit weight or volume and vice versa, and it was negatively correlated with content of most of phytochemicals evaluated here. However, size-independent variation for anthocyanin content and profile (e.g., acylated vs. non-acylated anthocyanin) exists in the tetraploid accessions and can be explored to identify other factors such as genes related to the biosynthetic pathway that control this trait. This result also suggests that metabolite concentrations and fruit size, to a certain degree can be improved simultaneously in breeding programs. Overall, the results of this study provide a framework to uncover the genetic basis of bioactive compounds and fruit quality traits and will be useful to advance blueberry-breeding programs focusing on integrating these traits.
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Affiliation(s)
- Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
| | - Mary H Grace
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
| | - Jia Xiong
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
| | - Colin D Kay
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
| | - Nahla Bassil
- USDA-ARS-National Clonal Germplasm Repository, Corvallis, OR, United States
| | - Kim Hummer
- USDA-ARS-National Clonal Germplasm Repository, Corvallis, OR, United States
| | - Mario G Ferruzzi
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, NCRC, Kannapolis, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
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Strauch RC, Mengist MF, Pan K, Yousef GG, Iorizzo M, Brown AF, Lila MA. Variation in anthocyanin profiles of 27 genotypes of red cabbage over two growing seasons. Food Chem 2019; 301:125289. [DOI: 10.1016/j.foodchem.2019.125289] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/25/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022]
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Mengist MF, Alves S, Griffin D, Creedon J, McLaughlin MJ, Jones PW, Milbourne D. Genetic mapping of quantitative trait loci for tuber-cadmium and zinc concentration in potato reveals associations with maturity and both overlapping and independent components of genetic control. Theor Appl Genet 2018; 131:929-945. [PMID: 29307117 DOI: 10.1007/s00122-017-3048-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
Cd is a toxic metal, whilst Zn is an essential for plant and human health. Both can accumulate in potato tubers. We examine the genetic control of this process. The aim of this study was to map quantitative trait loci (QTLs) influencing tuber concentrations of cadmium (Cd) and zinc (Zn). We developed a segregating population comprising 188 F1 progeny derived from crossing two tetraploid cultivars exhibiting divergent tuber-Cd-accumulation phenotypes. These progeny were genotyped using the SolCap 8303 SNP array, and evaluated for Cd, Zn, and maturity-related traits. Linkage and QTL mapping were performed using TetraploidSNPMap software, which incorporates all allele dosage information. The final genetic map comprised 3755 SNP markers with average marker density of 2.94 per cM. Tuber-Cd and Zn concentrations were measured in the segregating population over 2 years. QTL mapping identified four loci for tuber-Cd concentration on chromosomes 3, 5, 6, and 7, which explained genetic variance ranging from 5 to 33%, and five loci for tuber-Zn concentration on chromosome 1, 3, 5, and, 6 explaining from 5 to 38% of genetic variance. Among the QTL identified for tuber-Cd concentration, three loci coincided with tuber-Zn concentration. The largest effect QTL for both tuber-Cd and Zn concentration coincided with the maturity locus on chromosome 5 where earliness was associated with increased tuber concentration of both metals. Coincident minor-effect QTL for Cd and Zn sharing the same direction of effect was also found on chromosomes 3 and 6, and these were unrelated to maturity The results indicate partially overlapping genetic control of tuber-Cd and Zn concentration in the cross, involving both maturity-related and non-maturity-related mechanisms.
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Affiliation(s)
- Molla F Mengist
- Teagasc, Crops Research Centre, Oak Park, Carlow, R93 XE12, Ireland
- School of Biological, Earth and Environmental Sciences, University College Cork, Western Road, Cork, Ireland
| | - Sheila Alves
- Teagasc, Crops Research Centre, Oak Park, Carlow, R93 XE12, Ireland
| | - Denis Griffin
- Teagasc, Crops Research Centre, Oak Park, Carlow, R93 XE12, Ireland
| | - Joanne Creedon
- Teagasc, Environmental Research Centre, Jonhstown Castle, Wexford, Ireland
| | - Mike J McLaughlin
- Soil Science Group, School of Agriculture, Food and Wine, The University of Adelaide, PMB 1 Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter W Jones
- School of Biological, Earth and Environmental Sciences, University College Cork, Western Road, Cork, Ireland
| | - Dan Milbourne
- Teagasc, Crops Research Centre, Oak Park, Carlow, R93 XE12, Ireland.
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Mengist MF, Milbourne D, Griffin D, McLaughlin MJ, Creedon J, Jones PW, Alves S. Cadmium uptake and partitioning in potato (Solanum tuberosum L.) cultivars with different tuber-Cd concentration. Environ Sci Pollut Res Int 2017; 24:27384-27391. [PMID: 28975479 DOI: 10.1007/s11356-017-0325-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Potatoes grown in soil with high Cd concentrations can accumulate high levels of Cd in the tubers. Although there is significant environmental variation involved in the trait of crop uptake of Cd, there are also distinctive cultivar differences. In order to understand this differential Cd accumulation mechanism, two potato cultivars were chosen that accumulate high and low levels of Cd in tubers. The patterns of Cd concentration, Cd content and dry weight accumulation of the two cultivars were examined at different stages of plant growth. The data suggest that differences in total Cd uptake and in Cd partitioning among organs are the mechanisms governing differential Cd-tuber accumulation in the two cultivars. The low tuber-Cd accumulator exhibited lower root-to-shoot and shoot-to-tuber translocation driven by higher root and shoot biomass that retained more Cd in roots and shoots, respectively, reducing its movement to the tubers. Higher remobilization and more efficient tuber loading was observed in the high tuber-Cd accumulator, indicating that remobilization of Cd from leaves to tubers was a major factor, not only in tuber-Cd loading, but also in the establishment of differential tuber-Cd levels. Regardless of cultivar differences, the concentration of Cd in the tuber was very low compared to that in other organs suggesting that, despite its high phloem mobility, Cd tends to be sequestered in the shoots.
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Affiliation(s)
- Molla F Mengist
- Teagasc, Crops Research Centre, Oak Park, Co., Carlow, R93 XE12, Ireland
- School of Biological, Earth and Environmental Sciences, University College Cork, Western Road, Cork, Ireland
| | - Dan Milbourne
- Teagasc, Crops Research Centre, Oak Park, Co., Carlow, R93 XE12, Ireland
| | - Denis Griffin
- Teagasc, Crops Research Centre, Oak Park, Co., Carlow, R93 XE12, Ireland
| | - Mike J McLaughlin
- Soil Science Group, School of Agriculture, Food and Wine, University of Adelaide, PMB 1 Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Joanne Creedon
- Teagasc, Environment Research Centre, Johnstown Castle, Co., Wexford, Y35 Y521, Ireland
| | - Peter W Jones
- School of Biological, Earth and Environmental Sciences, University College Cork, Western Road, Cork, Ireland
| | - Sheila Alves
- Teagasc, Crops Research Centre, Oak Park, Co., Carlow, R93 XE12, Ireland.
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