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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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2
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Song J, Campbell L, Vinqvist-Tymchuk M. Application of quantitative proteomics to investigate fruit ripening and eating quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153766. [PMID: 35921768 DOI: 10.1016/j.jplph.2022.153766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.
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Affiliation(s)
- Jun Song
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada.
| | - Leslie Campbell
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
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Bilbrey EA, Williamson K, Hatzakis E, Miller DD, Fresnedo-Ramírez J, Cooperstone JL. Integrating genomics and multiplatform metabolomics enables metabolite quantitative trait loci detection in breeding-relevant apple germplasm. THE NEW PHYTOLOGIST 2021; 232:1944-1958. [PMID: 34472097 DOI: 10.1111/nph.17693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/10/2021] [Indexed: 05/12/2023]
Abstract
Apple (Malus × domestica) has commercial and nutritional value, but breeding constraints of tree crops limit varietal improvement. Marker-assisted selection minimises these drawbacks, but breeders lack applications for targeting fruit phytochemicals. To understand genotype-phytochemical associations in apples, we have developed a high-throughput integration strategy for genomic and multiplatform metabolomics data. Here, 124 apple genotypes, including members of three pedigree-connected breeding families alongside diverse cultivars and wild selections, were genotyped and phenotyped. Metabolite genome-wide association studies (mGWAS) were conducted with c. 10 000 single nucleotide polymorphisms and phenotypic data acquired via LC-MS and 1 H NMR untargeted metabolomics. Putative metabolite quantitative trait loci (mQTL) were then validated via pedigree-based analyses (PBA). Using our developed method, 519, 726 and 177 putative mQTL were detected in LC-MS positive and negative ionisation modes, and NMR, respectively. mQTL were indicated on each chromosome, with hotspots on linkage groups 16 and 17. A chlorogenic acid mQTL was discovered on chromosome 17 via mGWAS and validated with a two-step PBA, enabling discovery of novel candidate gene-metabolite relationships. Complementary data from three metabolomics approaches and dual genomics analyses increased confidence in validity of compound annotation and mQTL detection. Our platform demonstrates the utility of multiomic integration to advance data-driven, phytochemical-based plant breeding.
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Affiliation(s)
- Emma A Bilbrey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Kathryn Williamson
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Emmanuel Hatzakis
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Diane Doud Miller
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | | | - Jessica L Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
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Si W, Zhang Y, Li X, Du Y, Xu Q. Understanding the Functional Activity of Polyphenols Using Omics-Based Approaches. Nutrients 2021; 13:nu13113953. [PMID: 34836207 PMCID: PMC8625961 DOI: 10.3390/nu13113953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023] Open
Abstract
Plant polyphenols are the main category of natural active substances, and are distributed widely in vegetables, fruits, and plant-based processed foods. Polyphenols have a beneficial performance in preventing diseases and maintaining body health. However, its action mechanism has not been well understood. Foodomics is a novel method to sequence and widely used in nutrition, combining genomics, proteomics, transcriptomics, microbiome, and metabolomics. Based on multi-omics technologies, foodomics provides abundant data to study functional activities of polyphenols. In this paper, physiological functions of various polyphenols based on foodomics and microbiome was discussed, especially the anti-inflammatory and anti-tumor activities and gut microbe regulation. In conclusion, omics (including microbiomics) is a useful approach to explore the bioactive activities of polyphenols in the nutrition and health of human and animals.
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Affiliation(s)
- Wenjin Si
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (X.L.); (Y.D.)
- Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Xiang Li
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (X.L.); (Y.D.)
- Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yufeng Du
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (X.L.); (Y.D.)
- Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingbiao Xu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (X.L.); (Y.D.)
- Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence:
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Valderrama-Soto D, Salazar J, Sepúlveda-González A, Silva-Andrade C, Gardana C, Morales H, Battistoni B, Jiménez-Muñoz P, González M, Peña-Neira Á, Infante R, Pacheco I. Detection of Quantitative Trait Loci Controlling the Content of Phenolic Compounds in an Asian Plum ( Prunus salicina L.) F1 Population. FRONTIERS IN PLANT SCIENCE 2021; 12:679059. [PMID: 34305977 PMCID: PMC8299277 DOI: 10.3389/fpls.2021.679059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Consumption of fresh fruit is known to protect against non-communicable diseases due to the fruit's content in compounds with an antioxidant capacity, among them is polyphenols. Asian plums (Prunus salicina L.) accumulate more than 40 phenolic compounds, with a remarkable diversity in their profiles, depending on the variety and environmental conditions. Although candidate genes have been indicated to control this trait, the loci controlling its phenotypic variation have not yet been defined in this species. The aim of this work was to identify the quantitative trait Loci (QTL) controlling the phenolic compounds content in the Asian plum skin and flesh. Using UHPLC-DAD-Orbitrap-MS, we determined that cyanidin-3-glucoside and cyanidin-3-rutinoside are the main anthocyanins in Asian plums. Other anthocyanins found to a lesser extent were tentatively identified as cyanidin bound to different sugar and procyanidin moieties. Then we phenotyped fruits of 92 and 80 F1 seedlings from the cross < "98.99" × "Angeleno"> (98 Ang) for two harvest seasons. We used HPLC-DAD to quantify single anthocyanin and spectrophotometric techniques to determine the total content of phenols, flavonoids, procyanidins, and antioxidant activity (DPPH and FRAP). To determine the phenotype-genotype association of phenolic compounds content, phenotypic values (adjusted by linear mixed-effects models), genotypic data and linkage maps were analyzed with the multiple QTL model (MQM) approach. We found a total of 21 significant trait-marker associations: 13 QTLs segregating from "98.99" and 8 QTLs from "Angeleno." From these associations, 8 corresponded to phenolic compound content in the flesh and 13 in the skin. Phenotype variance was explained by the detected loci, ranging from 12.4 to 27.1%. The identified loci are related to the content of cyanidin-3-glucoside (LG4), cyanidin-3-rutinoside (LG4), total flavonoids and procyanidins (LG5 and LG8), and minor anthocyanin compounds (LG3 and LG4). These results will help improve the efficiency of breeding programs for the generation of Asian plum varieties with high phenolic compound content.
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Affiliation(s)
- Diego Valderrama-Soto
- Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Juan Salazar
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Murcia, Spain
| | | | - Claudia Silva-Andrade
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Claudio Gardana
- Dipartimento di Scienze per gli Alimenti, la Nutrizione, l'Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Héctor Morales
- Departamento de Agroindustria y Enología, Universidad de Chile, Santiago, Chile
| | - Benjamin Battistoni
- Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santiago, Chile
| | - Pablo Jiménez-Muñoz
- Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Departamento de Producción Agrícola, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Center for Genome Regulation (CGR), Santiago, Chile
| | - Álvaro Peña-Neira
- Departamento de Agroindustria y Enología, Universidad de Chile, Santiago, Chile
| | - Rodrigo Infante
- Departamento de Producción Agrícola, Universidad de Chile, Santiago, Chile
| | - Igor Pacheco
- Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, Santiago, Chile
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Chen Z, Yu L, Liu W, Zhang J, Wang N, Chen X. Research progress of fruit color development in apple (Malus domestica Borkh.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:267-279. [PMID: 33711720 DOI: 10.1016/j.plaphy.2021.02.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Apple (Malus domestica Borkh.) is one of the most widely produced and economically important fruits in temperate regions. Fruit color development in apple is a major focus for both breeders and researchers as consumers associate brightly colored red apples with ripeness and a good flavor. In recent years, great progress has been made in the research of apple fruit color development, but its development mechanism has not been systematic dissected from the aspects of genetics, transcription or environmental factors. Here, we summarize research on the coloration of apple fruit, including the development of important genomic databases to identify important genomic regions and genes, genetic and transcriptional factors that regulate pigment accumulation, environmental factors that affect anthocyanin synthesis, and the current breeding progress of red-skinned and red-fleshed apples. We describe key transcription factors, such as MYB, bHLH, and WD40, which are involved in the regulation of anthocyanin synthesis and fruit color development in apple. We also discuss the regulation of apple color by external environmental factors such as light, temperature, and water. The aim of this review is to provide insights into the molecular mechanisms underlying anthocyanin biosynthesis in apple. This information will provide significant guidance for the breeding of high-quality red-skinned and red-fleshed apple varieties.
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Affiliation(s)
- Zijing Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Lei Yu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China.
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China.
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Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis MC, Laroche J, Boyle B, Hammerbacher A, Isabel N, Bousquet J. Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. FRONTIERS IN PLANT SCIENCE 2021; 12:675108. [PMID: 34079574 PMCID: PMC8166253 DOI: 10.3389/fpls.2021.675108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.
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Affiliation(s)
- Justine Laoué
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- *Correspondence: Justine Laoué
| | - Claire Depardieu
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Claude Bomal
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Aïda Azaiez
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Almuth Hammerbacher
- Department of Zoology, Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Jean Bousquet
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Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet 2020; 52:1423-1432. [PMID: 33139952 PMCID: PMC7728601 DOI: 10.1038/s41588-020-00723-9] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality. Phased diploid genomes of the cultivated apple Malus domestica cv. Gala and its two major wild progenitors M. sieversii and M. sylvestris, as well as pan-genome analyses, provide insights into the genetic history of apple domestication.
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9
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Busatto N, Matsumoto D, Tadiello A, Vrhovsek U, Costa F. Multifaceted analyses disclose the role of fruit size and skin-russeting in the accumulation pattern of phenolic compounds in apple. PLoS One 2019; 14:e0219354. [PMID: 31306452 PMCID: PMC6629076 DOI: 10.1371/journal.pone.0219354] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/23/2019] [Indexed: 12/14/2022] Open
Abstract
Fruits are nowadays considered important suppliers of anti-oxidant molecules. Apples are particularly rich in phenolic compounds, non-nutritional phytochemicals that play active roles in controlling severe chronic diseases. In this work, 19 phenolic compounds were investigated in both skin and pulp tissues of seven apple accessions across the Malus genus collected at two stages: during fruit development and at harvest. The primary difference in phenolic concentration between wild and domesticated accessions, especially in the pulp, could be explained by the larger growth rate of the domesticated varieties. The proposed dilution effect was also confirmed through the observation of the increased content of procyanidin B2+B4 and phloridzin in russet-skinned apples, known to have higher concentrations of these compounds. The metabolite screening was also accompanied by the expression analysis of 16 polyphenolic genes showing, for nine elements, a higher expression at harvest than during fruit development. Finally, a polyphenolic comparison with red-fleshed apples was also carried out, underlying a larger amount of procyanidins and quercetin-3rhamnoside in the white-fleshed accessions. The results presented and discussed in this work suggest that specific white-fleshed apples, especially with russeted-skin, may play an important role in ameliorating the nutraceutical potential of apple fruit.
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Affiliation(s)
- Nicola Busatto
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Daiki Matsumoto
- Faculty of Agriculture, Department of Food, Life, and Environmental Sciences, Yamagata University, Tsuruoka, Japan
| | - Alice Tadiello
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Urska Vrhovsek
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- * E-mail:
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10
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Whitehead SR, Poveda K. Resource allocation trade-offs and the loss of chemical defences during apple domestication. ANNALS OF BOTANY 2019; 123:1029-1041. [PMID: 30770925 PMCID: PMC6589505 DOI: 10.1093/aob/mcz010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/17/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Most crops have been dramatically altered from their wild ancestors with the primary goal of increasing harvestable yield. A long-held hypothesis is that increased allocation to yield has reduced plant investment in defence and resulted in crops that are highly susceptible to pests. However, clear demonstrations of these trade-offs have been elusive due to the many selective pressures that occur concurrently during crop domestication. METHODS To provide a robust test of whether increased allocation to yield can alter plant investment in defence, this study examined fruit chemical defence traits and herbivore resistance across 52 wild and 56 domesticated genotypes of apples that vary >26-fold in fruit size. Ninety-six phenolic metabolites were quantified in apple skin, pulp and seeds, and resistance to the codling moth was assessed with a series of bioassays. KEY RESULTS The results show that wild apples have higher total phenolic concentrations and a higher diversity of metabolites than domesticated apples in skin, pulp and seeds. A negative phenotypic relationship between fruit size and phenolics indicates that this pattern is driven in part by allocation-based trade-offs between yield and defence. There were no clear differences in codling moth performance between wild and domesticated apples and no overall effects of total phenolic concentration on codling moth performance, but the results did show that codling moth resistance was increased in apples with higher phenolic diversity. The concentrations of a few individual compounds (primarily flavan-3-ols) also correlated with increased resistance, primarily driven by a reduction in pupal mass of female moths. CONCLUSIONS The negative phenotypic relationship between fruit size and phenolic content, observed across a large number of wild and domesticated genotypes, supports the hypothesis of yield-defence trade-offs in crops. However, the limited effects of phenolics on codling moth highlight the complexity of consequences that domestication has for plant-herbivore interactions. Continued studies of crop domestication can further our understanding of the multiple trade-offs involved in plant defence, while simultaneously leading to novel discoveries that can improve the sustainability of crop production.
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Affiliation(s)
- Susan R Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA
- Department of Entomology, Cornell University, Ithaca, USA
| | - Katja Poveda
- Department of Entomology, Cornell University, Ithaca, USA
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McClure KA, Gong Y, Song J, Vinqvist-Tymchuk M, Campbell Palmer L, Fan L, Burgher-MacLellan K, Zhang Z, Celton JM, Forney CF, Migicovsky Z, Myles S. Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols. HORTICULTURE RESEARCH 2019; 6:107. [PMID: 31645962 PMCID: PMC6804656 DOI: 10.1038/s41438-019-0190-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 05/03/2023]
Abstract
Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
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Affiliation(s)
- Kendra A. McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - YuiHui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Leslie Campbell Palmer
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Lihua Fan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Karen Burgher-MacLellan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - ZhaoQi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jean-Marc Celton
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Charles F. Forney
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
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12
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Bars-Cortina D, Macià A, Iglesias I, Garanto X, Badiella L, Motilva MJ. Seasonal Variability of the Phytochemical Composition of New Red-Fleshed Apple Varieties Compared with Traditional and New White-Fleshed Varieties. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10011-10025. [PMID: 30176730 DOI: 10.1021/acs.jafc.8b03950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The main objective of this study was to evaluate the impact of the season on the apple phytochemical composition (phenolic compounds, triterpenes, and organic and ascorbic acids). For this proposal, four red-fleshed and five white-fleshed apple varieties from two consecutive seasons (2015 and 2016) were studied. A significant interaction with the season in some compounds was observed. The total phenolic content in the apple flesh from 2015 was higher than that from 2016 probably related with the lower rainfall during the harvest period in 2015 that could have favored hydric stress in the apple trees. The impact of the season on the apple skin was different. The 2016 season was characterized by higher maximum and minimum temperatures resulting in a higher content of flavonols, triterpenes, and organic acids. Anthocyanin concentration in both the flesh and skin of the red-fleshed apples showed no clear relationship to the season, and each variety showed an individual pattern.
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Affiliation(s)
- David Bars-Cortina
- Food Technology Department, XaRTA-TPV, Agrotecnio Center, Escola Tècnica Superior d'Enginyeria Agrària , Universitat de Lleida , Avinguda Alcalde Rovira Roure 191 , 25198 Lleida , Catalonia, Spain
| | - Alba Macià
- Food Technology Department, XaRTA-TPV, Agrotecnio Center, Escola Tècnica Superior d'Enginyeria Agrària , Universitat de Lleida , Avinguda Alcalde Rovira Roure 191 , 25198 Lleida , Catalonia, Spain
| | - Ignasi Iglesias
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre , PCiTAL , Parc de Gardeny , 25003 Lleida , Catalonia, Spain
| | - Xavier Garanto
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre , PCiTAL , Parc de Gardeny , 25003 Lleida , Catalonia, Spain
| | - Llorenç Badiella
- Statistical Consulting Service , Universitat Autònoma de Barcelona , 08193 Bellaterra , Catalonia, Spain
| | - Maria-Jose Motilva
- Food Technology Department, XaRTA-TPV, Agrotecnio Center, Escola Tècnica Superior d'Enginyeria Agrària , Universitat de Lleida , Avinguda Alcalde Rovira Roure 191 , 25198 Lleida , Catalonia, Spain
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13
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Thiyagarajan K, Vitali F, Tolaini V, Galeffi P, Cantale C, Vikram P, Singh S, De Rossi P, Nobili C, Procacci S, Del Fiore A, Antonini A, Presenti O, Brunori A. Genomic Characterization of Phenylalanine Ammonia Lyase Gene in Buckwheat. PLoS One 2016; 11:e0151187. [PMID: 26990297 PMCID: PMC4798664 DOI: 10.1371/journal.pone.0151187] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/24/2016] [Indexed: 01/05/2023] Open
Abstract
Phenylalanine Ammonia Lyase (PAL) gene which plays a key role in bio-synthesis of medicinally important compounds, Rutin/quercetin was sequence characterized for its efficient genomics application. These compounds possessing anti-diabetic and anti-cancer properties and are predominantly produced by Fagopyrum spp. In the present study, PAL gene was sequenced from three Fagopyrum spp. (F. tataricum, F. esculentum and F. dibotrys) and showed the presence of three SNPs and four insertion/deletions at intra and inter specific level. Among them, the potential SNP (position 949th bp G>C) with Parsimony Informative Site was selected and successfully utilised to individuate the zygosity/allelic variation of 16 F. tataricum varieties. Insertion mutations were identified in coding region, which resulted the change of a stretch of 39 amino acids on the putative protein. Our Study revealed that autogamous species (F. tataricum) has lower frequency of observed SNPs as compared to allogamous species (F. dibotrys and F. esculentum). The identified SNPs in F. tataricum didn't result to amino acid change, while in other two species it caused both conservative and non-conservative variations. Consistent pattern of SNPs across the species revealed their phylogenetic importance. We found two groups of F. tataricum and one of them was closely related with F. dibotrys. Sequence characterization information of PAL gene reported in present investigation can be utilized in genetic improvement of buckwheat in reference to its medicinal value.
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Affiliation(s)
- Karthikeyan Thiyagarajan
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
- Bioversity International, 00054, Maccarese (Fiumicino), Italy
| | - Fabio Vitali
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Valentina Tolaini
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Patrizia Galeffi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Cristina Cantale
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Prashant Vikram
- Genetic Resource Program, International Center for Maize and Wheat Improvement, El Batan, Texcoco, Mexico
| | - Sukhwinder Singh
- Genetic Resource Program, International Center for Maize and Wheat Improvement, El Batan, Texcoco, Mexico
| | - Patrizia De Rossi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Chiara Nobili
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Silvia Procacci
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Antonella Del Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Alessandro Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Ombretta Presenti
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Andrea Brunori
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
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14
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Le Gall S, Even S, Lahaye M. Fast Estimation of Dietary Fiber Content in Apple. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:1401-1405. [PMID: 26813795 DOI: 10.1021/acs.jafc.5b05301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dietary fibers (DF) are one of the nutritional benefits of fleshy fruit consumption that is becoming a quality criterion for genetic selection by breeders. However, the AOAC total DF content determination is not readily amenable for screening large fruit collections. A new screening method of DF content in an apple collection based on the automated preparation of cell wall material as an alcohol-insoluble residue (AIR) is proposed. The yield of AIR from 27 apple genotypes was compared with DF measured according to AOAC method 985.29. Although residual protein content in AIRs did not affect DF measurement, subtraction of starch content above 3% dry weight in AIRs was needed to agree with AOAC measured DF. A fast colorimetric screening of starch in AIR was developed to detect samples needing correction. The proposed method may prove useful for the rapid determination of DF in collections of other fleshy fruit besides apple.
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Affiliation(s)
- Sophie Le Gall
- INRA , UR1268 Biopolymères Interactions Assemblages, rue de la Géraudière, F-44316 Nantes, France
| | - Sonia Even
- INRA , UR1268 Biopolymères Interactions Assemblages, rue de la Géraudière, F-44316 Nantes, France
| | - Marc Lahaye
- INRA , UR1268 Biopolymères Interactions Assemblages, rue de la Géraudière, F-44316 Nantes, France
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15
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Cai S, Han Z, Huang Y, Hu H, Dai F, Zhang G. Identification of Quantitative Trait Loci for the Phenolic Acid Contents and Their Association with Agronomic Traits in Tibetan Wild Barley. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:980-987. [PMID: 26757245 DOI: 10.1021/acs.jafc.5b05441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phenolic acids have been of considerable interest in human nutrition because of their strong antioxidative properties. However, even in a widely grown crop, such as barley, their genetic architecture is still unclear. In this study, genetic control of two main phenolic acids, ferulic acid (FA) and p-coumaric acid (p-CA), and their associations with agronomic traits were investigated among 134 Tibetan wild barley accessions. A genome-wide association study (GWAS) identified three DArT markers (bpb-2723, bpb-7199, and bpb-7273) associated with p-CA content and one marker (bpb-3653) associated with FA content in 2 consecutive years. The contents of the two phenolic acids were positively correlated with some agronomic traits, such as the first internode length, plant height, and some grain color parameters, and negatively correlated with the thousand-grain weight (TGW). This study provides DNA markers for barley breeding programs to improve the contents of phenolic acids.
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Affiliation(s)
- Shengguan Cai
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhigang Han
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yuqing Huang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Hongliang Hu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Fei Dai
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Guoping Zhang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
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16
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Igarashi M, Hatsuyama Y, Harada T, Fukasawa-Akada T. Biotechnology and apple breeding in Japan. BREEDING SCIENCE 2016; 66:18-33. [PMID: 27069388 PMCID: PMC4780799 DOI: 10.1270/jsbbs.66.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/23/2015] [Indexed: 05/11/2023]
Abstract
Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.
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Affiliation(s)
- Megumi Igarashi
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
| | - Yoshimichi Hatsuyama
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center,
Fukutami 24, Botandaira, Kuroishi, Aomori 036-0332,
Japan
| | - Takeo Harada
- Department of Agriculture and Life Science, Hirosaki University,
Bunkyouchou 3, Hirosaki, Aomori 036-8563,
Japan
| | - Tomoko Fukasawa-Akada
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
- Corresponding author (e-mail: )
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17
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Cai S, Han Z, Huang Y, Chen ZH, Zhang G, Dai F. Genetic Diversity of Individual Phenolic Acids in Barley and Their Correlation with Barley Malt Quality. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7051-7. [PMID: 26173650 DOI: 10.1021/acs.jafc.5b02960] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phenolic acids have been quite extensively studied in food science research because of their antioxidative effect. In this study, the genotypic difference and genetic control of phenolic acids, and their correlation with malt quality, were investigated in barley. Ferulic acid (FA) and p-coumaric acid (p-CA) were identified as two main phenolic acids, showing wide variations among 68 barley genotypes. The mean content of FA and p-CA were 2.15 μg g(-1) and 1.10 μg g(-1) in grains and 4.07 μg g(-1) and 1.44 μg g(-1) in malt, respectively. After malting, FA and p-CA were increased significantly in 55 and 37 genotypes and were reduced in 2 and 14 genotypes, respectively. Both malt FA and p-CA were positively correlated with soluble N content and Kolbach index and negatively correlated with malt extract and viscosity. The results indicated that the effect of malting on the change of an individual phenolic acid is genotype independent. Association mapping identified that 8 markers on Chromosomes 1H, 2H, 4H, and 7H are associated with grain p-CA and 4 markers on Chromosomes 3H and 7H are linked with grain FA. However, only a single marker on Chromosome 3H was found to be associated with malt FA. Moreover, a lack of overlapping markers between grain and malt indicated the genetic diversity of phenolic acids in barley grain and malt. Our results strengthen the understanding of phenolic acids in barley and their responses to the malting process.
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Affiliation(s)
- Shengguan Cai
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Zhigang Han
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Yuqing Huang
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Zhong-Hua Chen
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Fei Dai
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
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18
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Falginella L, Cipriani G, Monte C, Gregori R, Testolin R, Velasco R, Troggio M, Tartarini S. A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'. BMC PLANT BIOLOGY 2015; 15:150. [PMID: 26084469 PMCID: PMC4472412 DOI: 10.1186/s12870-015-0507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/27/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Russeting is a disorder developed by apple fruits that consists of cuticle cracking followed by the replacement of the epidermis by a corky layer that protects the fruit surface from water loss and pathogens. Although influenced by many environmental conditions and orchard management practices, russeting is under genetic control. The difficulty in classifying offspring and consequent variable segregation ratios have led several authors to conclude that more than one genetic determinant could be involved, although some evidence favours a major gene (Ru). RESULTS In this study we report the mapping of a major genetic russeting determinant on linkage group 12 of apple as inferred from the phenotypic observation in a segregating progeny derived from 'Renetta Grigia di Torriana', the construction of a 20 K Illumina SNP chip based genetic map, and QTL analysis. Recombination analysis in two mapping populations restricted the region of interest to approximately 400 Kb. Of the 58 genes predicted from the Golden Delicious sequence, a putative ABCG family transporter has been identified. Within a small set of russeted cultivars tested with markers of the region, only six showed the same haplotype of 'Renetta Grigia di Torriana'. CONCLUSIONS A major determinant (Ru_RGT) for russeting development putatively involved in cuticle organization is proposed as a candidate for controlling the trait. SNP and SSR markers tightly co-segregating with the Ru_RGT locus may assist the breeder selection. The observed segregations and the analysis of the 'Renetta Grigia di Torriana' haplotypic region in a panel of russeted and non-russeted cultivars may suggest the presence of other determinants for russeting in apple.
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Affiliation(s)
- Luigi Falginella
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Guido Cipriani
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Corinne Monte
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Via Fanin 44, 40127, Bologna, Italy.
| | - Raffaele Testolin
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Riccardo Velasco
- Research and Innovation Centre - Fondazione Edmund Mach - Department of Genomics and Biology of Fruit Crop, Via E. Mach 1, 38010 S, Michele all'Adige TN, Italy.
| | - Michela Troggio
- Research and Innovation Centre - Fondazione Edmund Mach - Department of Genomics and Biology of Fruit Crop, Via E. Mach 1, 38010 S, Michele all'Adige TN, Italy.
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Via Fanin 44, 40127, Bologna, Italy.
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19
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Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel CE, Branca A. Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 2015; 8:650-61. [PMID: 26240603 PMCID: PMC4516418 DOI: 10.1111/eva.12270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/15/2015] [Indexed: 12/26/2022] Open
Abstract
Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier FST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.
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Affiliation(s)
- Diane Leforestier
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Elisa Ravon
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Hélène Muranty
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Christophe Lemaire
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Charles-Eric Durel
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
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20
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Liao L, Vimolmangkang S, Wei G, Zhou H, Korban SS, Han Y. Molecular characterization of genes encoding leucoanthocyanidin reductase involved in proanthocyanidin biosynthesis in apple. FRONTIERS IN PLANT SCIENCE 2015; 6:243. [PMID: 25914714 PMCID: PMC4392590 DOI: 10.3389/fpls.2015.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/26/2015] [Indexed: 05/03/2023]
Abstract
Proanthocyanidins (PAs) are the major component of phenolics in apple, but mechanisms involved in PA biosynthesis remain unclear. Here, the relationship between the PA biosynthesis and the expression of genes encoding leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) was investigated in fruit skin of one apple cultivar and three crabapples. Transcript levels of LAR1 and ANR2 genes were significantly correlated with the contents of catechin and epicatechin, respectively, which suggests their active roles in PA synthesis. Surprisingly, transcript levels for both LAR1 and LAR2 genes were almost undetectable in two crabapples that accumulated both flavan-3-ols and PAs. This contradicts the previous finding that LAR1 gene is a strong candidate regulating the accumulation of metabolites such as epicatechin and PAs in apple. Ectopic expression of apple MdLAR1 gene in tobacco suppresses expression of the late genes in anthocyanin biosynthetic pathway, resulting in loss of anthocyanin in flowers. Interestingly, a decrease in PA biosynthesis was also observed in flowers of transgenic tobacco plants overexpressing the MdLAR1 gene, which could be attributed to decreased expression of both the NtANR1 and NtANR2 genes. Our study not only confirms the in vivo function of apple LAR1 gene, but it is also helpful for understanding the mechanism of PA biosynthesis.
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Affiliation(s)
- Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
| | - Sornkanok Vimolmangkang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn UniversityBangkok, Thailand
| | - Guochao Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Schuyler S. Korban
- Department of Biology, University of Massachusetts BostonBoston, MA, USA
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- *Correspondence: Yuepeng Han, Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Lumo Road No. 1, 430074 Wuhan, China
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