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Wang Z, Zhang W, Zhou Y, Zhang Q, Kulkarni KP, Melmaiee K, Tian Y, Dong M, Gao Z, Su Y, Yu H, Xu G, Li Y, He H, Liu Q, Sun H. Genetic and epigenetic signatures for improved breeding of cultivated blueberry. HORTICULTURE RESEARCH 2024; 11:uhae138. [PMID: 38988623 PMCID: PMC11233858 DOI: 10.1093/hr/uhae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164 Vaccinium corymbosum, 15 Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB's adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the β-alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.
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Affiliation(s)
- Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Wanchen Zhang
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Yangyan Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Krishnanand P Kulkarni
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA
| | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA
| | - Youwen Tian
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Mei Dong
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Yanning Su
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Hong Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Guohui Xu
- College of Life and Health, Dalian University, Dalian 116622, China
| | - Yadong Li
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Haiyue Sun
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
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Lagarda-Clark EA, Goulet C, Duarte-Sierra A. Biochemical dynamics during postharvest: Highlighting the interplay of stress during storage and maturation of fresh produce. Biomol Concepts 2024; 15:bmc-2022-0048. [PMID: 38587059 DOI: 10.1515/bmc-2022-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
The lifecycle of fresh produce involves a sequence of biochemical events during their ontology, and these events are particularly significant for climacteric fruits. A high demand during ripening is observed in these plant products, which is reflected in a high rate of respiration and ethylene production. Increased respiratory demand triggers the activation of secondary pathways such as alternate oxidase, which do not experience critical increases in energy consumption in non-climacteric fruit. In addition, biochemical events produced by external factors lead to compensatory responses in fresh produce to counteract the oxidative stress caused by the former. The dynamics of these responses are accompanied by signaling, where reactive oxygen species play a pivotal role in fresh product cell perception. This review aims to describe the protection mechanisms of fresh produce against environmental challenges and how controlled doses of abiotic stressors can be used to improve quality and prolong their shelf-life through the interaction of stress and defense mechanisms.
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Affiliation(s)
- Ernesto Alonso Lagarda-Clark
- Food Science Department, Laval University, Quebec, QC G1V 0A6, Canada
- Center for Research in Plant Innovation (CRIV), Laval University, Quebec, QC G1V 6 0A6, Canada
- Institute on Nutrition and Functional Foods (INAF), Laval University, Quebec, QC G1V 8 0A6, Canada
| | - Charles Goulet
- Food Science Department, Laval University, Quebec, QC G1V 0A6, Canada
- Center for Research in Plant Innovation (CRIV), Laval University, Quebec, QC G1V 6 0A6, Canada
- Department of Phytology, Université Laval, Québec, QC G1V 0A6, Canada
| | - Arturo Duarte-Sierra
- Food Science Department, Laval University, Quebec, QC G1V 0A6, Canada
- Center for Research in Plant Innovation (CRIV), Laval University, Quebec, QC G1V 6 0A6, Canada
- Institute on Nutrition and Functional Foods (INAF), Laval University, Quebec, QC G1V 8 0A6, Canada
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Njuguna JN, Clark LV, Lipka AE, Anzoua KG, Bagmet L, Chebukin P, Dwiyanti MS, Dzyubenko E, Dzyubenko N, Ghimire BK, Jin X, Johnson DA, Kjeldsen JB, Nagano H, de Bem Oliveira I, Peng J, Petersen KK, Sabitov A, Seong ES, Yamada T, Yoo JH, Yu CY, Zhao H, Munoz P, Long SP, Sacks EJ. Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids. THE PLANT GENOME 2023; 16:e20401. [PMID: 37903749 DOI: 10.1002/tpg2.20401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/17/2023] [Accepted: 09/23/2023] [Indexed: 11/01/2023]
Abstract
Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.
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Affiliation(s)
- Joyce N Njuguna
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lindsay V Clark
- Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kossonou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Pavel Chebukin
- FSBSI "FSC of Agricultural Biotechnology of the Far East named after A.K. Chaiki", Ussuriysk, Russian Federation
| | - Maria S Dwiyanti
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Nicolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Bimal Kumar Ghimire
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, South Korea
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Douglas A Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, Utah, USA
| | | | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | | | - Junhua Peng
- Spring Valley Agriscience Co. Ltd., Jinan, China
| | | | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Eun Soo Seong
- Division of Bioresource Sciences, Kangwon National University, Chuncheon, South Korea
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Ji Hye Yoo
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Chang Yeon Yu
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Hua Zhao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Patricio Munoz
- Horticultural Science Department, University of Florida, Gainesville, Florida, USA
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Li Y, Li H, Wang S, Li J, Bacha SAS, Xu G, Li J. Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry ( Vaccinium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1082245. [PMID: 37152168 PMCID: PMC10157174 DOI: 10.3389/fpls.2023.1082245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.
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Affiliation(s)
- Yinping Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Haifei Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Shiyao Wang
- Department of Applied Biosciences, Toyo University, Ora-gun, Japan
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Syed Asim Shah Bacha
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Guofeng Xu
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
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5
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An Exploration of Pepino (Solanum muricatum) Flavor Compounds Using Machine Learning Combined with Metabolomics and Sensory Evaluation. Foods 2022. [PMCID: PMC9601458 DOI: 10.3390/foods11203248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Flavor is one of the most important characteristics that directly determines the popularity of a food. Moreover, the flavor of fruits is determined by the interaction of multiple metabolic components. Pepino, an emerging horticultural crop, is popular for its unique melon-like flavor. We analyzed metabolomics data from three different pepino growing regions in Haidong, Wuwei, and Jiuquan and counted the status of sweetness, acidity, flavor, and overall liking ratings of pepino fruit in these three regions by sensory panels. The metabolomics and flavor ratings were also integrated and analyzed using statistical and machine learning models, which in turn predicted the sensory panel ratings of consumers based on the chemical composition of the fruit. The results showed that pepino fruit produced in the Jiuquan region received the highest ratings in sweetness, flavor intensity, and liking, and the results with the highest contribution based on sensory evaluation showed that nucleotides and derivatives, phenolic acids, amino acids and derivatives, saccharides, and alcohols were rated in sweetness (74.40%), acidity (51.57%), flavor (56.41%), and likability (33.73%) dominated. We employed 14 machine learning strategies trained on the discovery samples to accurately predict the outcome of sweetness, sourness, flavor, and liking in the replication samples. The Radial Sigma SVM model predicted with better accuracy than the other machine learning models. Then we used the machine learning models to determine which metabolites influenced both pepino flavor and consumer preference. A total of 27 metabolites most important for pepino flavor attributes to distinguish pepino originating from three regions were screened. Substances such as N-acetylhistamine, arginine, and caffeic acid can enhance pepino‘s flavor intensity, and metabolites such as glycerol 3-phosphate, aconitic acid, and sucrose all acted as important variables in explaining the liking preference. While glycolic acid and orthophosphate inhibit sweetness and enhance sourness, sucrose has the opposite effect. Machine learning can identify the types of metabolites that influence fruit flavor by linking metabolomics of fruit with sensory evaluation among consumers, which conduces breeders to incorporate fruit flavor as a trait earlier in the breeding process, making it possible to select and release fruit with more flavor.
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Kumar S, Molloy C, Hunt M, Deng CH, Wiedow C, Andre C, Dare A, McGhie T. GWAS provides new insights into the genetic mechanisms of phytochemicals production and red skin colour in apple. HORTICULTURE RESEARCH 2022; 9:uhac218. [PMID: 36479587 PMCID: PMC9720448 DOI: 10.1093/hr/uhac218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/19/2022] [Indexed: 06/17/2023]
Abstract
Understanding the genetic architecture of apple phytochemicals, and their interplay with conventional selection traits, is critical for the development of new apple cultivars with enhanced health benefits. Apple accessions (n = 344) used for this genome-wide association study (GWAS) represented the wide diversity of metabolic profiles in the domesticated and wild Malus genepools. Fruit samples were phenotyped for 34 metabolites, including a stable vitamin C glycoside "ascorbic acid 2-β-glucoside" (AA-2βG), and the accessions were genotyped using the Apple 20 K SNP Array. Several fruit quality traits, including red skin over-colour (OCOL), were also assessed. Wild Malus accessions showed at least 2-fold higher average content of several metabolites (e.g. ascorbic acid, chlorogenic acid, phloridzin, and trilobatin) than Malus domestica accessions. Several new genomic regions and potential candidate genes underpinning the genetic diversity of apple phytochemicals were identified. The percentage of phenotypic variance explained by the best SNP ranged between 3% and 21% for the different metabolites. Novel association signals for OCOL in the syntenic regions on chromosomes 13 and 16 suggested that whole genome duplication has played a role in the evolution of apple red skin colour. Genetic correlations between phytochemicals and sensory traits were moderate. This study will assist in the selection of Malus accessions with specific phytochemical profiles to establish innovative genomics-based breeding strategies for the development of apple cultivars with enhanced nutritional value.
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Affiliation(s)
| | - Claire Molloy
- The New Zealand Institute for Plant and Food Research Limited, Hawke’s Bay Research Centre, Havelock North 4130, New Zealand
| | - Martin Hunt
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4410, New Zealand
| | - Cecilia Hong Deng
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025, New Zealand
| | - Claudia Wiedow
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4410, New Zealand
| | - Christelle Andre
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025, New Zealand
| | - Andrew Dare
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025, New Zealand
| | - Tony McGhie
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4410, New Zealand
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7
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Linear and nonlinear regression modeling of the chemical, physical and quality variations in Cardaba banana (Musa acuminata x balbisiana – ABB) during ripening. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Romero I, Escribano MI, Merodio C, Sanchez-Ballesta MT. Postharvest High-CO 2 Treatments on the Quality of Soft Fruit Berries: An Integrated Transcriptomic, Proteomic, and Metabolomic Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8593-8597. [PMID: 35792090 PMCID: PMC9305969 DOI: 10.1021/acs.jafc.2c01305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soft fruits are appreciated for their taste qualities and for being a source of health-promoting compounds. However, their postharvest is affected by their high respiratory rates and susceptibility to fungal decay. Our aim here is to provide a perspective on the application of short-term high-CO2 treatments at a low temperature to maintain the postharvest quality of soft fruits. This work also suggests using a multi-omics approach to better understand the role of the cell wall and phenolic compounds in maintaining quality. Finally, the contribution of high-throughput transcriptomic technologies to understand the mechanisms modulated by the short-term gaseous treatments is also highlighted.
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9
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Wang YW, Acharya TP, Malladi A, Tsai HJ, NeSmith DS, Doyle JW, Nambeesan SU. Atypical Climacteric and Functional Ethylene Metabolism and Signaling During Fruit Ripening in Blueberry ( Vaccinium sp.). FRONTIERS IN PLANT SCIENCE 2022; 13:932642. [PMID: 35812961 PMCID: PMC9260287 DOI: 10.3389/fpls.2022.932642] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Climacteric fruits display an increase in respiration and ethylene production during the onset of ripening, while such changes are minimal in non-climacteric fruits. Ethylene is a primary regulator of ripening in climacteric fruits. The ripening behavior and role of ethylene in blueberry (Vaccinium sp.) ripening is controversial. This work aimed to clarify the fruit ripening behavior and the associated role of ethylene in blueberry. Southern highbush (Vaccinium corymbosum hybrids) and rabbiteye (Vaccinium ashei) blueberry displayed an increase in the rate of respiration and ethylene evolution, both reaching a maxima around the Pink and Ripe stages of fruit development, consistent with climacteric fruit ripening behavior. Increase in ethylene evolution was associated with increases in transcript abundance of its biosynthesis genes, AMINOCYCLOPROPANE CARBOXYLATE (ACC) SYNTHASE1 (ACS1) and ACC OXIDASE2 (ACO2), implicating them in developmental ethylene production during ripening. Blueberry fruit did not display autocatalytic system 2 ethylene during ripening as ACS transcript abundance and ACC concentration were not enhanced upon treatment with an ethylene-releasing compound (ethephon). However, ACO transcript abundance was enhanced in response to ethephon, suggesting that ACO was not rate-limiting. Transcript abundance of multiple genes associated with ethylene signal transduction was upregulated concomitant with developmental increase in ethylene evolution, and in response to exogenous ethylene. As these changes require ethylene signal transduction, fruit ripening in blueberry appears to involve functional ethylene signaling. Together, these data indicate that blueberry fruit display atypical climacteric ripening, characterized by a respiratory climacteric, developmentally regulated but non-autocatalytic increase in ethylene evolution, and functional ethylene signaling.
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Affiliation(s)
- Yi-Wen Wang
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Tej P. Acharya
- Department of Horticulture, University of Georgia, Athens, GA, United States
| | - Anish Malladi
- Department of Horticulture, University of Georgia, Athens, GA, United States
| | - Hsuan-Ju Tsai
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Taiwan Agricultural Research Institute Council of Agriculture, Taichung, Taiwan
| | - D. Scott NeSmith
- Department of Horticulture, University of Georgia, Griffin, GA, United States
| | - John W. Doyle
- Department of Horticulture, University of Georgia, Athens, GA, United States
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10
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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: 14] [Impact Index Per Article: 7.0] [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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11
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Cárcamo de la Concepción M, Sargent DJ, Šurbanovski N, Colgan RJ, Moretto M. De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars 'Bluecrop' and 'Legacy' at harvest and following post-harvest storage. PLoS One 2021; 16:e0255139. [PMID: 34339434 PMCID: PMC8328333 DOI: 10.1371/journal.pone.0255139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, 'Bluecrop' and 'Legacy', at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for 'Bluecrop' and 'Legacy' respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in 'Legacy' only, 685 were up-regulated in 'Bluecrop', 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.
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Affiliation(s)
| | - Daniel James Sargent
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
- NIAB EMR, East Malling, Kent, United Kingdom
| | | | - Richard John Colgan
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
- * E-mail:
| | - Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
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12
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Cell Wall Calcium and Hemicellulose Have a Role in the Fruit Firmness during Storage of Blueberry ( Vaccinium spp.). PLANTS 2021; 10:plants10030553. [PMID: 33809443 PMCID: PMC7999294 DOI: 10.3390/plants10030553] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022]
Abstract
The firmness of blueberry is one of its most significant quality attributes. Modifications in the composition of the cell wall have been associated with changes in the fruit firmness. In this work, cell wall components and calcium concentration in two blueberry cultivars with contrasting firmness phenotypes were evaluated at harvest and 30 days cold storage (0 °C). High performance anion-exchange chromatography with pulse amperometric detector (HPAEC-PAD) analysis was performed using the "Emerald" (firmer) and "Jewel" (softer) blueberry cultivars, showing increased glucose in the firmer cultivar after cold storage. Moreover, the LM15 antibody, which recognizes xyloglucan domains, displayed an increased signal in the Emerald cultivar after 30 d cold storage. Additionally, the antibody 2F4, recognizing a homogalacturonan calcium-binding domain, showed a greater signal in the firmer Emerald blueberries, which correlates with a higher calcium concentration in the cell wall. These findings suggest that xyloglucan metabolism and a higher concentration of cell wall calcium influenced the firmness of the blueberry fruit. These results open new perspectives regarding the role of cell wall components as xyloglucans and calcium in blueberry firmness.
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13
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Genomic insight into the developmental history of southern highbush blueberry populations. Heredity (Edinb) 2020; 126:194-205. [PMID: 32873965 DOI: 10.1038/s41437-020-00362-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 11/08/2022] Open
Abstract
Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity to breeding populations. Southern highbush blueberry (SHB) is a blueberry cultivar group that has been intensively bred over the last 60 years. Specifically, it was developed by multiple interspecific crosses between northern highbush blueberry [NHB, Vaccinium corymbosum L. (2n = 4x = 48)] and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. In this study, we genotyped polyploid blueberries, including 105 SHB, 17 NHB, and 10 rabbiteye blueberry (RE) (Vaccinium virgatum Aiton), from the accessions planted at Poplarville, Mississippi, and accessions distributed in Japan, based on the double-digest restriction site-associated DNA sequencing. The genome-wide SNP data clearly indicated that RE cultivars were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies that breeders used for developing germplasm adapted to local climates. The genotype data implied that there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. Principal component analysis-based outlier detection analysis found a few loci associated with a variable that could partially differentiate NHB and SHB. These SNP loci were detected in Mb-scale haplotype blocks and may be close to the functional genes related to SHB development. Collectively, the data generated in this study suggest a polygenic adaptation of SHB to the southern climate, and may be relevant for future population-scale genome-wide analyses of blueberry.
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14
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Optimization of polysaccharides-based nanoemulsion using response surface methodology and application to improve postharvest storage of apple (Malus domestica). JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2020. [DOI: 10.1007/s11694-020-00514-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Cappai F, Amadeu RR, Benevenuto J, Cullen R, Garcia A, Grossman A, Ferrão LFV, Munoz P. High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry. FRONTIERS IN PLANT SCIENCE 2020; 11:562171. [PMID: 33304360 PMCID: PMC7701094 DOI: 10.3389/fpls.2020.562171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/21/2020] [Indexed: 05/21/2023]
Abstract
Blueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits related to machine harvestability through Quantitative Trait Loci (QTL) mapping is the first step toward implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses in 2-year field trials for a trait crucial to machine harvesting: fruit firmness. Preliminary insights were also sought for single evaluations of firmness retention after cold storage, and fruit detachment force traits. Significant QTL peaks were identified for all the traits and overlapping QTL intervals were detected for firmness across the years. We found low-to-moderate QTL effects explaining the phenotypic variance, which suggest a quantitative nature of these traits. The QTL intervals were further speculated for putative gene repertoire. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.
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Affiliation(s)
- Francesco Cappai
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rodrigo R. Amadeu
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Juliana Benevenuto
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Ryan Cullen
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Alexandria Garcia
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Adina Grossman
- Forage Breeding and Genetics Lab, Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Luís Felipe V. Ferrão
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Patricio Munoz
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- *Correspondence: Patricio Munoz
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