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Maule AF, Loarca J, Diaz-Garcia L, Lopez-Moreno H, Johnson-Cicalese J, Vorsa N, Iorizzo M, Neyhart JL, Zalapa JE. Of buds and bits: a meta-QTL study identifies stable QTL for berry quality and yield traits in cranberry mapping populations ( Vaccinium macrocarpon Ait.). FRONTIERS IN PLANT SCIENCE 2024; 15:1294570. [PMID: 39354940 PMCID: PMC11442229 DOI: 10.3389/fpls.2024.1294570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 07/31/2024] [Indexed: 10/03/2024]
Abstract
Introduction For nearly two centuries, cranberry (Vaccinium macrocarpon Ait.) breeders have improved fruit quality and yield by selecting traits on fruiting stems, termed "reproductive uprights." Crop improvement is accelerating rapidly in contemporary breeding programs due to modern genetic tools and high-throughput phenotyping methods, improving selection efficiency and accuracy. Methods We conducted genotypic evaluation on 29 primary traits encompassing fruit quality, yield, and chemical composition in two full-sib cranberry breeding populations-CNJ02 (n = 168) and CNJ04 (n = 67)-over 3 years. Genetic characterization was further performed on 11 secondary traits derived from these primary traits. Results For CNJ02, 170 major quantitative trait loci (QTL; R 2 ≥ 0.10) were found with interval mapping, 150 major QTL were found with model mapping, and 9 QTL were found to be stable across multiple years. In CNJ04, 69 major QTL were found with interval mapping, 81 major QTL were found with model mapping, and 4 QTL were found to be stable across multiple years. Meta-QTL represent stable genomic regions consistent across multiple years, populations, studies, or traits. Seven multi-trait meta-QTL were found in CNJ02, one in CNJ04, and one in the combined analysis of both populations. A total of 22 meta-QTL were identified in cross-study, cross-population analysis using digital traits for berry shape and size (8 meta-QTL), digital images for berry color (2 meta-QTL), and three-study cross-analysis (12 meta-QTL). Discussion Together, these meta-QTL anchor high-throughput fruit quality phenotyping techniques to traditional phenotyping methods, validating state-of-the-art methods in cranberry phenotyping that will improve breeding accuracy, efficiency, and genetic gain in this globally significant fruit crop.
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Affiliation(s)
- Andrew F. Maule
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture - Agricultural Research Service, Madison, WI, United States
| | - Jenyne Loarca
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture - Agricultural Research Service, Madison, WI, United States
| | - Luis Diaz-Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Hector Lopez-Moreno
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture - Agricultural Research Service, Madison, WI, United States
| | - Jennifer Johnson-Cicalese
- P.E. Marucci Center for Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, United States
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Nicholi Vorsa
- P.E. Marucci Center for Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, United States
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Massimo Iorizzo
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Raleigh, NC, United States
| | - Jeffrey L. Neyhart
- Genetic Improvement for Fruits & Vegetables Laboratory, United States Department of Agriculture-Agricultural Research Service, Chatsworth, NJ, United States
| | - Juan E. Zalapa
- Vegetable Crops Research Unit, United States Department of Agriculture - Agricultural Research Service, Madison, WI, United States
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Kawash J, Erndwein L, Johnson-Cicalese J, Knowles S, Vorsa N, Polashock J. Quantitative Trait Loci Analysis and Marker Development for Fruit Rot Resistance in Cranberry Shows Potential Genetic Association with Epicuticular Wax. PHYTOPATHOLOGY 2024; 114:1366-1372. [PMID: 38281162 DOI: 10.1094/phyto-12-23-0477-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Fruit rot is a fungal disease complex that threatens cranberry yields in North American growing operations. Management of fruit rot is especially difficult because of the diversity of the infecting fungal species, and although infections take place early in the season, the pathogens usually remain latent in the ovary until the fruit ripen. Control methods heavily rely on fungicide applications, a practice that may be limited in viability long term. Breeding for fruit rot resistance (FRR) is essential for sustainable production. It is likely that field resistance is multifaceted and involves a myriad of traits that fortify cranberry plants against the biotic and abiotic stresses contributing to fruit rot. In this study, we identified quantitative trait loci (QTL) for FRR in a segregating population. Interestingly, a QTL associated with resistance was found to overlap with one associated with fruit epicuticular wax (ECW). A single-nucleotide polymorphism genotyping assay successfully identified accessions that exhibit the desired phenotypes (i.e., less rot and more ECW), thus making it a useful tool for marker-assisted selection. Candidate genes that may contribute to FRR and ECW were also identified. This work will expedite breeding for improved cranberry fruit quality.
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Affiliation(s)
- Joseph Kawash
- U.S. Department of Agriculture-Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ 08019
| | - Lindsay Erndwein
- U.S. Department of Agriculture-Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ 08019
| | - Jennifer Johnson-Cicalese
- Rutgers University, P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019
| | - Sara Knowles
- Rutgers University, P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019
| | - Nicholi Vorsa
- Professor Emeritus, Rutgers University, P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019
| | - James Polashock
- U.S. Department of Agriculture-Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ 08019
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Hirabayashi K, Debnath SC, Owens GL. Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies. G3 (BETHESDA, MD.) 2024; 14:jkad294. [PMID: 38142435 PMCID: PMC10917501 DOI: 10.1093/g3journal/jkad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 10/23/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Lingonberry (Vaccinium vitis-idaea L.) produces tiny red berries that are tart and nutty in flavor. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for 2 subspecies of lingonberry (V. vitis-idaea ssp. minus and ssp. vitis-idaea var. 'Red Candy') were sequenced and de novo assembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (Vaccinium myrtillus) to generate a chromosome-anchored reference genome consisting of 12 chromosomes each with a total length of 548.07 Mb [contig N50 = 1.17 Mb, BUSCO (C%) = 96.5%] for ssp. vitis-idaea and 518.70 Mb [contig N50 = 1.40 Mb, BUSCO (C%) = 96.9%] for ssp. minus. RNA-seq-based gene annotation identified 27,243 and 25,718 genes on the respective assembly, and transposable element detection methods found that 45.82 and 44.58% of the genome were repeats. Phylogenetic analysis confirmed that lingonberry was most closely related to bilberry and was more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1-3 MYA, possibly due to the impacts of repeated glacial cycles during the Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry-relevant genes (e.g. anthocyanin production), infer phylogeny, and call sequence-level variants (e.g. SNPs) in future research.
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Affiliation(s)
- Kaede Hirabayashi
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Samir C Debnath
- Agriculture and Agri-Food Canada, St.John's Research and Development Centre, 204 Brookfield Road, St. John’s, Newfoundland and Labrador L A1E 0B2, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
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Younuskunju S, Mohamoud YA, Mathew LS, Mayer KFX, Suhre K, Malek JA. Genome-wide association of dry (Tamar) date palm fruit color. THE PLANT GENOME 2023; 16:e20373. [PMID: 37621134 DOI: 10.1002/tpg2.20373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 08/26/2023]
Abstract
Date palm (Phoenix dactylifera) fruit (dates) are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some date palm traits have been performed, including sex determination, sugar content, and fresh fruit color. In this study, we used genome sequences and image data of 199 dry dates (Tamar) collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover both the previously identified VIRESCENS (VIR) genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of date color phenotype, especially at the most commercially important Tamar stage.
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Affiliation(s)
- Shameem Younuskunju
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Doha, Qatar
- School of Life Sciences, Technical University of Munich, Munich, Germany
| | | | - Lisa S Mathew
- Clinical Genomics Laboratory, Sidra Medicine, Doha, Qatar
| | - Klaus F X Mayer
- School of Life Sciences, Technical University of Munich, Munich, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, Munich, Germany
| | - Karsten Suhre
- Department of Physiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Joel A Malek
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
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Erndwein L, Kawash J, Knowles S, Vorsa N, Polashock J. Cranberry fruit epicuticular wax benefits and identification of a wax-associated molecular marker. BMC PLANT BIOLOGY 2023; 23:181. [PMID: 37020185 PMCID: PMC10074888 DOI: 10.1186/s12870-023-04207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND As the global climate changes, periods of abiotic stress throughout the North American cranberry growing regions will become more common. One consequence of high temperature extremes and drought conditions is sunscald. Scalding damages the developing berry and reduces yields through fruit tissue damage and/or secondary pathogen infection. Irrigation runs to cool the fruit is the primary approach to controlling sunscald. However, it is water intensive and can increase fungal-incited fruit rot. Epicuticular wax functions as a barrier to various environmental stresses in other fruit crops and may be a promising feature to mitigate sunscald in cranberry. In this study we assessed the function of epicuticular wax in cranberries to attenuate stresses associated with sunscald by subjecting high and low epicuticular wax cranberries to controlled desiccation and light/heat exposure. A cranberry population that segregates for epicuticular wax was phenotyped for epicuticular fruit wax levels and genotyped using GBS. Quantitative trait loci (QTL) analyses of these data identified a locus associated with epicuticular wax phenotype. A SNP marker was developed in the QTL region to be used for marker assisted selection. RESULTS Cranberries with high epicuticular wax lost less mass percent and maintained a lower surface temperature following heat/light and desiccation experiments as compared to fruit with low wax. QTL analysis identified a marker on chromosome 1 at position 38,782,094 bp associated with the epicuticular wax phenotype. Genotyping assays revealed that cranberry selections homozygous for a selected SNP have consistently high epicuticular wax scores. A candidate gene (GL1-9), associated with epicuticular wax synthesis, was also identified near this QTL region. CONCLUSIONS Our results suggest that high cranberry epicuticular wax load may help reduce the effects of heat/light and water stress: two primary contributors to sunscald. Further, the molecular marker identified in this study can be used in marker assisted selection to screen cranberry seedlings for the potential to have high fruit epicuticular wax. This work serves to advance the genetic improvement of cranberry crops in the face of global climate change.
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Affiliation(s)
- Lindsay Erndwein
- ORISE Postdoctoral Research Associate, Chatsworth, NJ, 08019, USA
| | - Joseph Kawash
- Genetic Improvement of Fruit and Vegetables Laboratory, Agricultural Research Service, USDA-ARS, Chatsworth, NJ, 08019, USA
| | - Sara Knowles
- P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ, 08019, USA
| | - Nicholi Vorsa
- P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ, 08019, USA
| | - James Polashock
- Genetic Improvement of Fruit and Vegetables Laboratory, Agricultural Research Service, USDA-ARS, Chatsworth, NJ, 08019, USA.
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Vaccinium Species (Ericaceae): Phytochemistry and Biological Properties of Medicinal Plants. Molecules 2023; 28:molecules28041533. [PMID: 36838522 PMCID: PMC9966428 DOI: 10.3390/molecules28041533] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The Vaccinium L. (Ericaceae) genus consists of a globally widespread and diverse genus of around 4250 species, of which the most valuable is the Vaccinioidae subfamily. The current review focuses on the distribution, history, bioactive compounds, and health-related effects of three species: cranberry, blueberry, and huckleberry. Several studies highlight that the consumption of Vaccinium spp. presents numerous beneficial health-related outcomes, including antioxidant, antimicrobial, anti-inflammatory, and protective effects against diabetes, obesity, cancer, neurodegenerative diseases and cardiovascular disorders. These plants' prevalence and commercial value have enhanced in the past several years; thus, the generated by-products have also increased. Consequently, the identified phenolic compounds found in the discarded leaves of these plants are also presented, and their impact on health and economic value is discussed. The main bioactive compounds identified in this genus belong to anthocyanins (cyanidin, malvidin, and delphinidin), flavonoids (quercetin, isoquercetin, and astragalin), phenolic acids (gallic, p-Coumaric, cinnamic, syringic, ferulic, and caffeic acids), and iridoids.
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Montanari S, Thomson S, Cordiner S, Günther CS, Miller P, Deng CH, McGhie T, Knäbel M, Foster T, Turner J, Chagné D, Espley R. High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content. FRONTIERS IN PLANT SCIENCE 2022; 13:965397. [PMID: 36247546 PMCID: PMC9555082 DOI: 10.3389/fpls.2022.965397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Highbush blueberry (Vaccinium corymbosum, 2n = 4x = 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value is conferred by phytonutrients, particularly anthocyanins. Identifying the genetic mechanisms that control the biosynthesis of these metabolites would enable faster development of cultivars with improved fruit qualities. Here, we used recently released tools for genetic mapping in autotetraploids to build a high-density linkage map in highbush blueberry and to detect quantitative trait loci (QTLs) for fruit anthocyanin content. Genotyping was performed by target sequencing, with ∼18,000 single nucleotide polymorphism (SNP) markers being mapped into 12 phased linkage groups (LGs). Fruits were harvested when ripe for two seasons and analyzed with high-performance liquid chromatography-mass spectrometry (HPLC-MS): 25 different anthocyanin compounds were identified and quantified. Two major QTLs that were stable across years were discovered, one on LG2 and one on LG4, and the underlying candidate genes were identified. Interestingly, the presence of anthocyanins containing acylated sugars appeared to be under strong genetic control. Information gained in this study will enable the design of molecular markers for marker-assisted selection and will help build a better understanding of the genetic control of anthocyanin biosynthesis in this crop.
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Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Sarah Cordiner
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Catrin S. Günther
- The New Zealand Institute for Plant and Food Research Limited, Ruakura, New Zealand
| | - Poppy Miller
- The New Zealand Institute for Plant and Food Research Limited, Te Puke, New Zealand
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Tony McGhie
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Mareike Knäbel
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Toshi Foster
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Janice Turner
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Richard Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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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. HORTICULTURE RESEARCH 2022; 9:uhac083. [PMID: 35611183 PMCID: PMC9123236 DOI: 10.1093/hr/uhac083] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [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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Zhang R, Koh SS, Teo MJT, Bi R, Zhang S, Dev K, Urano D, Dinish US, Olivo M. Handheld Multifunctional Fluorescence Imager for Non-invasive Plant Phenotyping. FRONTIERS IN PLANT SCIENCE 2022; 13:822634. [PMID: 35463443 PMCID: PMC9024405 DOI: 10.3389/fpls.2022.822634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Fluorescence imaging has shown great potential in non-invasive plant monitoring and analysis. However, current systems have several limitations, such as bulky size, high cost, contact measurement, and lack of multifunctionality, which may hinder its applications in a wide range of settings including indoor vertical farming. Herein, we developed a compact handheld fluorescence imager enabling multipurpose plant phenotyping, such as continuous photosynthetic activity monitoring and non-destructive anthocyanin quantification. The compact imager comprises of pulse-amplitude-modulated multi-color light emitting diodes (LEDs), optimized light illumination and collection, dedicated driver circuit board, miniaturized charge-coupled device camera, and associated image analytics. Experiments conducted in drought stressed lettuce proved that the novel imager could quantitatively evaluate the plant stress by the non-invasive measurement of photosynthetic activity efficiency. Moreover, a non-invasive and fast quantification of anthocyanins in green and red Batavia lettuce leaves had excellent correlation (>84%) with conventional destructive biochemical analysis. Preliminary experimental results emphasize the high throughput monitoring capability and multifunctionality of our novel handheld fluorescence imager, indicating its tremendous potential in modern agriculture.
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Affiliation(s)
- Ruochong Zhang
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
| | - Sally Shuxian Koh
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Mark Ju Teng Teo
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
| | - Renzhe Bi
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
| | - Shuyan Zhang
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
| | - Kapil Dev
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - U. S. Dinish
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
| | - Malini Olivo
- Translational Biophotonic Laboratory, Institute of Bioengineering and Bioimaging, A*STAR, Singapore, Singapore
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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. HORTICULTURE RESEARCH 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] [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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11
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Chang F, Lv W, Lv P, Xiao Y, Yan W, Chen S, Zheng L, Xie P, Wang L, Karikari B, Abou-Elwafa SF, Jiang H, Zhao T. Exploring genetic architecture for pod-related traits in soybean using image-based phenotyping. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:28. [PMID: 37309355 PMCID: PMC10236113 DOI: 10.1007/s11032-021-01223-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/18/2021] [Indexed: 06/14/2023]
Abstract
Mature pod color (PC) and pod size (PS) served as important characteristics are used in the soybean breeding programs. However, manual phenotyping of such complex traits is time-consuming, laborious, and expensive for breeders. Here, we collected pod images from two different populations, namely, a soybean association panel (SAP) consisting of 187 accessions and an inter-specific recombinant inbred line (RIL) population containing 284 RILs. An image-based phenotyping method was developed and used to extract the pod color- and size-related parameters from images. Genome-wide association study (GWAS) and linkage mapping were performed to decipher the genetic control of pod color- and size-related traits across 2 successive years. Both populations exhibited wide phenotypic variations and continuous distribution in pod color- and size-related traits, indicating quantitative polygenic inheritance of these traits. GWAS and linkage mapping approaches identified the two major quantitative trait loci (QTL) underlying the pod color parameters, i.e., qPC3 and qPC19, located to chromosomes 3 and 19, respectively, and 12 stable QTLs for pod size-related traits across nine chromosomes. Several genes residing within the genomic region of stable QTL were identified as potential candidates underlying these pod-related traits based on the gene annotation and expression profiling data. Our results provide the useful information for fine-mapping/map-based cloning of QTL and marker-assisted selection of elite varieties with desirable pod traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01223-2.
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Affiliation(s)
- Fangguo Chang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenhuan Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Peiyun Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuntao Xiao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenliang Yan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shu Chen
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Lingyi Zheng
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ping Xie
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ling Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P. O. Box TL, 1882 Tamale, Ghana
| | | | - Haiyan Jiang
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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12
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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. FRONTIERS IN PLANT SCIENCE 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] [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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13
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Qi X, Ogden EL, Bostan H, Sargent DJ, Ward J, Gilbert J, Iorizzo M, Rowland LJ. High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population. FRONTIERS IN PLANT SCIENCE 2021; 12:692628. [PMID: 34234801 PMCID: PMC8256855 DOI: 10.3389/fpls.2021.692628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/24/2021] [Indexed: 05/11/2023]
Abstract
Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85-20) with the parent W85-23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.
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Affiliation(s)
- Xinpeng Qi
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Elizabeth L. Ogden
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Hamed Bostan
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | | | - Judson Ward
- Driscoll’s Inc., Watsonville, CA, United States
| | | | - Massimo Iorizzo
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Lisa J. Rowland
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- *Correspondence: Lisa J. Rowland, ;
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14
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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. FRONTIERS IN PLANT SCIENCE 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] [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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15
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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] [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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Pacbio Sequencing Reveals Identical Organelle Genomes between American Cranberry ( Vaccinium macrocarpon Ait.) and a Wild Relative. Genes (Basel) 2019; 10:genes10040291. [PMID: 30974783 PMCID: PMC6523495 DOI: 10.3390/genes10040291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 11/23/2022] Open
Abstract
Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry, and could be useful to improve fruit quality such as phytochemical content. Furthermore, given their northern distribution, they could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, the Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V. microcarpum. Finally, we provided important data regarding the polyploid origin of V. oxycoccos.
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17
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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. FRONTIERS IN PLANT SCIENCE 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] [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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