1
|
Chen K, Alexander LE, Mahgoub U, Okazaki Y, Higashi Y, Perera AM, Showman LJ, Loneman D, Dennison TS, Lopez M, Claussen R, Peddicord L, Saito K, Lauter N, Dorman KS, Nikolau BJ, Yandeau-Nelson MD. Dynamic relationships among pathways producing hydrocarbons and fatty acids of maize silk cuticular waxes. PLANT PHYSIOLOGY 2024; 195:2234-2255. [PMID: 38537616 PMCID: PMC11213258 DOI: 10.1093/plphys/kiae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 06/30/2024]
Abstract
The hydrophobic cuticle is the first line of defense between aerial portions of plants and the external environment. On maize (Zea mays L.) silks, the cuticular cutin matrix is infused with cuticular waxes, consisting of a homologous series of very long-chain fatty acids (VLCFAs), aldehydes, and hydrocarbons. Together with VLC fatty-acyl-CoAs (VLCFA-CoAs), these metabolites serve as precursors, intermediates, and end-products of the cuticular wax biosynthetic pathway. To deconvolute the potentially confounding impacts of the change in silk microenvironment and silk development on this pathway, we profiled cuticular waxes on the silks of the inbreds B73 and Mo17, and their reciprocal hybrids. Multivariate interrogation of these metabolite abundance data demonstrates that VLCFA-CoAs and total free VLCFAs are positively correlated with the cuticular wax metabolome, and this metabolome is primarily affected by changes in the silk microenvironment and plant genotype. Moreover, the genotype effect on the pathway explains the increased accumulation of cuticular hydrocarbons with a concomitant reduction in cuticular VLCFA accumulation on B73 silks, suggesting that the conversion of VLCFA-CoAs to hydrocarbons is more effective in B73 than Mo17. Statistical modeling of the ratios between cuticular hydrocarbons and cuticular VLCFAs reveals a significant role of precursor chain length in determining this ratio. This study establishes the complexity of the product-precursor relationships within the silk cuticular wax-producing network by dissecting both the impact of genotype and the allocation of VLCFA-CoA precursors to different biological processes and demonstrates that longer chain VLCFA-CoAs are preferentially utilized for hydrocarbon biosynthesis.
Collapse
Affiliation(s)
- Keting Chen
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Liza E Alexander
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Umnia Mahgoub
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Yozo Okazaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Yasuhiro Higashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ann M Perera
- W.M. Keck Metabolomics Research Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Lucas J Showman
- W.M. Keck Metabolomics Research Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Derek Loneman
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Tesia S Dennison
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Miriam Lopez
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Reid Claussen
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Layton Peddicord
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Nick Lauter
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Karin S Dorman
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Marna D Yandeau-Nelson
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
2
|
Lin Q, Chen J, Liu X, Wang B, Zhao Y, Liao L, Allan AC, Sun C, Duan Y, Li X, Grierson D, Verdonk JC, Chen K, Han Y, Bi J. A metabolic perspective of selection for fruit quality related to apple domestication and improvement. Genome Biol 2023; 24:95. [PMID: 37101232 PMCID: PMC10131461 DOI: 10.1186/s13059-023-02945-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits collected from 292 wild and cultivated accessions representing various consumption types. RESULTS We find decreased amounts of certain metabolites, including tannins, organic acids, phenolic acids, and flavonoids as the wild accessions transition to cultivated apples, while lysolipids increase in the "Golden Delicious" to "Ralls Janet" pedigree, suggesting better storage. We identify a total of 222,877 significant single-nucleotide polymorphisms that are associated with 2205 apple metabolites. Investigation of a region from 2.84 to 5.01 Mb on chromosome 16 containing co-mapping regions for tannins, organic acids, phenolic acids, and flavonoids indicates the importance of these metabolites for fruit quality and nutrition during breeding. The tannin and acidity-related genes Myb9-like and PH4 are mapped closely to fruit weight locus fw1 from 3.41 to 3.76 Mb on chromosome 15, a region under selection during domestication. Lysophosphatidylethanolamine (LPE) 18:1, which is suppressed by fatty acid desaturase-2 (FAD2), is positively correlated to fruit firmness. We find the fruit weight is negatively correlated with salicylic acid and abscisic acid levels. Further functional assays demonstrate regulation of these hormone levels by NAC-like activated by Apetala3/Pistillata (NAP) and ATP binding cassette G25 (ABCG25), respectively. CONCLUSIONS This study provides a metabolic perspective for selection on fruit quality during domestication and improvement, which is a valuable resource for investigating mechanisms controlling apple metabolite content and quality.
Collapse
Affiliation(s)
- Qiong Lin
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, 6708 PD The Netherlands
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Jing Chen
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xuan Liu
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, 430070 China
| | - Yaoyao Zhao
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Liao Liao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland Mail Centre, Auckland, 1142 New Zealand
| | - Chongde Sun
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Yuquan Duan
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xuan Li
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Donald Grierson
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
- Plant and Science Crop Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Julian C. Verdonk
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, 6708 PD The Netherlands
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Yuepeng Han
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Jinfeng Bi
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| |
Collapse
|
3
|
Dambros JI, Storch TT, Pegoraro C, Crizel GR, Gonçalves BX, Quecini V, Fialho FB, Rombaldi CV, Girardi CL. Physicochemical properties and transcriptional changes underlying the quality of 'Gala' apples (Malus × domestica Borkh.) under atmosphere manipulation in long-term storage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:576-589. [PMID: 36063445 DOI: 10.1002/jsfa.12169] [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: 04/16/2022] [Revised: 07/15/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The year-round availability of apples (Malus × domestica Borkh.) depends on post-harvest technologies, which are essential for the retention of fruit sensory and chemical properties by delaying senescence. The effectiveness of strategies for preserving the quality of apples depends on complex interactions between the storage environment and endogenous biological factors. In the current work, we integrated instrumental, sensory, and transcriptional data to determine the role of conservation technologies cold storage, controlled atmosphere, and 1-methylcyclopropene-mediated ethylene blockage on the long-term conservation of apples. RESULTS The results demonstrated that inhibition of the consumer's perception of the apples' ethylene content is essential for long-term cold storage, and such quality conservation can be achieved by reducing oxygen pressure. Overall appreciation of apples after storage was determined mainly by their texture, with crispness and juiciness contributing favorably, and mealiness contributing negatively. Reduced oxygen pressure and inhibition of ethylene perception exerted distinct effects on the transcription of candidate genes associated with ripening in apple. Hexose and cell-wall carbohydrate metabolism genes exhibit distinct expression patterns under storage. CONCLUSION Inhibition of ethylene perception and reduction of relative oxygen pressure under cold storage both promote similar conservation of apple sensory traits under long-term cold storage. Texture was the main contributor to global appreciation of apples subjected to long-term storage. The conditions that were investigated were able to delay, but not fully prevent, senescence, as evidenced by physicochemical and gene expression analyses. The expression of gene-encoding enzymes involved in hexose metabolism was mainly developmentally regulated, whereas storage conditions exerted a stronger effect on the expression of genes associated with cell-wall metabolism. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Juliele Ilone Dambros
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | - Camila Pegoraro
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Giseli Rodrigues Crizel
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Breno Xavier Gonçalves
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | | | - Cesar Valmor Rombaldi
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, Brazil
| | | |
Collapse
|
4
|
Jahed KR, Hirst PM. Fruit growth and development in apple: a molecular, genomics and epigenetics perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1122397. [PMID: 37123845 PMCID: PMC10130390 DOI: 10.3389/fpls.2023.1122397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Fruit growth and development are physiological processes controlled by several internal and external factors. This complex regulatory mechanism comprises a series of events occurring in a chronological order over a growing season. Understanding the underlying mechanism of fruit development events, however, requires consideration of the events occurring prior to fruit development such as flowering, pollination, fertilization, and fruit set. Such events are interrelated and occur in a sequential order. Recent advances in high-throughput sequencing technology in conjunction with improved statistical and computational methods have empowered science to identify some of the major molecular components and mechanisms involved in the regulation of fruit growth and have supplied encouraging successes in associating genotypic differentiation with phenotypic observations. As a result, multiple approaches have been developed to dissect such complex regulatory machinery and understand the genetic basis controlling these processes. These methods include transcriptomic analysis, quantitative trait loci (QTLs) mapping, whole-genome approach, and epigenetics analyses. This review offers a comprehensive overview of the molecular, genomic and epigenetics perspective of apple fruit growth and development that defines the final fruit size and provides a detailed analysis of the mechanisms by which fruit growth and development are controlled. Though the main emphasis of this article is on the molecular, genomic and epigenetics aspects of fruit growth and development, we will also deliver a brief overview on events occurring prior to fruit growth.
Collapse
|
5
|
Yang X, Wu B, Liu J, Zhang Z, Wang X, Zhang H, Ren X, Zhang X, Wang Y, Wu T, Xu X, Han Z, Zhang X. A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness. PLANT CELL REPORTS 2022; 41:2379-2391. [PMID: 36208306 DOI: 10.1007/s00299-022-02929-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Within a QTL, the genetic recombination and interactions among five and two functional variations at MdbHLH25 and MdWDR5A caused much complicated phenotype segregation in apple FFR and FCR. The storability of climacteric fruit like apple is a quantitative trait. We previously identified 62 quantitative trait loci (QTLs) associating flesh firmness retainability (FFR) and flesh crispness retainability (FCR), but only a few functional genetic variations were identified and validated. The genetic variation network controlling fruit storability is far to be understood and diagnostic markers are needed for molecular breeding. We previously identified overlapped QTLs F16.1/H16.2 for FFR and FCR using an F1 population derived from 'Zisai Pearl' × 'Red Fuji'. In this study, five and two single-nucleotide polymorphisms (SNPs) were identified on the candidate genes MdbHLH25 and MdWDR5A within the QTL region. The SNP1 A allele at MdbHLH25 promoter reduced the expression and SNP2 T allele and/or SNP4/5 GT alleles at the exons attenuated the function of MdbHLH25 by downregulating the expression of the target genes MdACS1, which in turn led to a reduction in ethylene production and maintenance of higher flesh crispness. The SNPs did not alter the protein-protein interaction between MdbHLH25 and MdWDR5A. The joint effect of SNP genotype combinations by the SNPs on MdbHLH25 (SNP1, SNP2, and SNP4) and MdWDR5A (SNPi and SNPii) led to a much broad spectrum of phenotypic segregation in FFR and FCR. Together, the dissection of these genetic variations contributes to understanding the complicated effects of a QTL and provides good potential for marker development in molecular breeding.
Collapse
Affiliation(s)
- Xianglong Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jing Liu
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Zhongyan Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuan Wang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Haie Zhang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xuejun Ren
- Testing and Analysis Center, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
6
|
Shen F, Bianco L, Wu B, Tian Z, Wang Y, Wu T, Xu X, Han Z, Velasco R, Fontana P, Zhang X. A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple. J Adv Res 2022; 42:149-162. [PMID: 36513410 PMCID: PMC9788957 DOI: 10.1016/j.jare.2022.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants. OBJECTIVES We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes. METHODS A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted. RESULTS By using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively. CONCLUSION The BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.
Collapse
Affiliation(s)
- Fei Shen
- College of Horticulture, China Agricultural University, Beijing 100193, China,Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, CREA, Conegliano, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Corresponding authors.
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| |
Collapse
|
7
|
Migicovsky Z, Yeats TH, Watts S, Song J, Forney CF, Burgher-MacLellan K, Somers DJ, Gong Y, Zhang Z, Vrebalov J, van Velzen R, Giovannoni JG, Rose JKC, Myles S. Apple Ripening Is Controlled by a NAC Transcription Factor. Front Genet 2021; 12:671300. [PMID: 34239539 PMCID: PMC8258254 DOI: 10.3389/fgene.2021.671300] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of pre-harvest ripening and associated textural changes following harvest are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ∼800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). We introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.
Collapse
Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Trevor H Yeats
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Sophie Watts
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | | | | | - Daryl J Somers
- Vineland Research and Innovation Centre, Vineland Station, ON, Canada
| | - Yihui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Zhaoqi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Julia Vrebalov
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Robin van Velzen
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - James G Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States.,United States Department of Agriculture, Robert W. Holley Center, Cornell University, Ithaca, NY, United States
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| |
Collapse
|
8
|
Catalano C, Di Guardo M, Distefano G, Caruso M, Nicolosi E, Deng Z, Gentile A, La Malfa SG. Biotechnological Approaches for Genetic Improvement of Lemon ( Citrus limon (L.) Burm. f.) against Mal Secco Disease. PLANTS 2021; 10:plants10051002. [PMID: 34067841 PMCID: PMC8157051 DOI: 10.3390/plants10051002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022]
Abstract
Among Citrus species, lemon is one of the most susceptible to mal secco disease, a tracheomycosis caused by the mitosporic fungus Plenodomus tracheiphilus, which induces chlorosis followed by leaf drop and progressive desiccation of twigs and branches. Severe infection can cause the death of the plant. Since no effective control strategies are available to efficiently control the pathogen spread, host tolerance is the most desirable goal in the struggle against mal secco disease. To date, both traditional breeding programs and biotechnological techniques were not efficient in developing novel varieties coupling tolerance to mal secco with optimal fruit quality. Furthermore, the genetic basis of host resistance has not been fully deciphered yet, hampering the set-up of marker-assisted selection (MAS) schemes. This paper provides an overview of the biotechnological approaches adopted so far for the selection of mal secco tolerant lemon varieties and emphasizes the promising contribution of marker-trait association analysis techniques for both unraveling the genetic determinism of the resistance to mal secco and detecting molecular markers that can be readily used for MAS. Such an approach has already proved its efficiency in several crops and could represent a valuable tool to select novel lemon varieties coupling superior fruit quality traits and resistance to mal secco.
Collapse
Affiliation(s)
- Chiara Catalano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Gaetano Distefano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Marco Caruso
- CREA, Research Centre for Olive, Fruit and Citrus Crops, Corso Savoia 190, 95024 Acireale, Italy;
| | - Elisabetta Nicolosi
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Ziniu Deng
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, China;
| | - Alessandra Gentile
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, China;
- Correspondence:
| | - Stefano Giovanni La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| |
Collapse
|
9
|
Wu B, Shen F, Wang X, Zheng WY, Xiao C, Deng Y, Wang T, Yu Huang Z, Zhou Q, Wang Y, Wu T, Feng Xu X, Hai Han Z, Zhong Zhang X. Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL-based genomics-assisted prediction. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1022-1037. [PMID: 33319456 PMCID: PMC8131039 DOI: 10.1111/pbi.13527] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/29/2020] [Accepted: 12/06/2020] [Indexed: 05/24/2023]
Abstract
Retention of flesh texture attributes during cold storage is critical for the long-term maintenance of fruit quality. The genetic variations determining flesh firmness and crispness retainability are not well understood. The objectives of this study are to identify gene markers based on quantitative trait loci (QTLs) and to develop genomics-assisted prediction (GAP) models for apple flesh firmness and crispness retainability. Phenotype data of 2664 hybrids derived from three Malus domestica cultivars and a M. asiatica cultivar were collected in 2016 and 2017. The phenotype segregated considerably with high broad-sense heritability of 83.85% and 83.64% for flesh firmness and crispness retainability, respectively. Fifty-six candidate genes were predicted from the 62 QTLs identified using bulked segregant analysis and RNA-seq. The genotype effects of the markers designed on each candidate gene were estimated. The genomics-predicted values were obtained using pyramiding marker genotype effects and overall mean phenotype values. Fivefold cross-validation revealed that the prediction accuracy was 0.5541 and 0.6018 for retainability of flesh firmness and crispness, respectively. An 8-bp deletion in the MdERF3 promoter disrupted MdDOF5.3 binding, reduced MdERF3 expression, relieved the inhibition on MdPGLR3, MdPME2, and MdACO4 expression, and ultimately decreased flesh firmness and crispness retainability. A 3-bp deletion in the MdERF118 promoter decreased its expression by disrupting the binding of MdRAVL1, which increased MdPGLR3 and MdACO4 expression and reduced flesh firmness and crispness retainability. These results provide insights regarding the genetic variation network regulating flesh firmness and crispness retainability, and the GAP models can assist in apple breeding.
Collapse
Affiliation(s)
- Bei Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Fei Shen
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xuan Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Wen Yan Zheng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Chen Xiao
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yang Deng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Yu Huang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Qian Zhou
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yi Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xue Feng Xu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Hai Han
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xin Zhong Zhang
- College of HorticultureChina Agricultural UniversityBeijingChina
| |
Collapse
|
10
|
Howard NP, Troggio M, Durel CE, Muranty H, Denancé C, Bianco L, Tillman J, van de Weg E. Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls. BMC Genomics 2021; 22:246. [PMID: 33827434 PMCID: PMC8028180 DOI: 10.1186/s12864-021-07565-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07565-7.
Collapse
Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Univ., Oldenburg, Germany.,Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | | | - Charles-Eric Durel
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Hélène Muranty
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - John Tillman
- Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | - Eric van de Weg
- Department of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
11
|
Wu B, Shen F, Chen CJ, Liu L, Wang X, Zheng WY, Deng Y, Wang T, Huang ZY, Xiao C, Zhou Q, Wang Y, Wu T, Xu XF, Han ZH, Zhang XZ. Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life. THE PLANT GENOME 2021; 14:e20084. [PMID: 33605090 DOI: 10.1002/tpg2.20084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/13/2020] [Indexed: 05/18/2023]
Abstract
Room-temperature shelf life is a key factor in fresh market apple (Malus domestica Borkh.) quality and commercial value. To investigate the genetic and molecular mechanism underlying apple shelf life, quantitative trait loci (QTL) were identified using bulked segregant analysis via sequencing (BSA-seq). Ethylene emission, flesh firmness, or crispness of apple fruit from 1,273 F1 plants of M. asiatica Nakai 'Zisai Pearl' × M. domestica 'Golden Delicious' were phenotyped prior to and during 6 wk of room-temperature storage. Segregation of ethylene emission and the flesh firmness or crispness traits was detected in the population. Thirteen QTL, including three major ones, were identified on chromosome 03, 08, and 16. A candidate gene encoding pectin acetylesterase, MdPAE10, from the QTL Z16.1 negatively affected fruit shelf life. A 379-bp deletion in the coding sequence of MdPAE10 disrupted its function. A single nucleotide polymorphism (SNP) in the MdPAE10 promoter region reduced its transcription activity. These findings provided insight into the genetic control of fruit shelf life and can be potentially used in apple marker-assisted selection.
Collapse
Affiliation(s)
- Bei Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chi Jie Chen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Li Liu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xuan Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Wen Yan Zheng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yang Deng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Ting Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhen Yu Huang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chen Xiao
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Qian Zhou
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xue Feng Xu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhen Hai Han
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xin Zhong Zhang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| |
Collapse
|
12
|
Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
Collapse
|
13
|
Kostick SA, Teh SL, Norelli JL, Vanderzande S, Peace C, Evans KM. Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in 'Honeycrisp'. HORTICULTURE RESEARCH 2021; 8:28. [PMID: 33518709 PMCID: PMC7847996 DOI: 10.1038/s41438-021-00466-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 05/17/2023]
Abstract
Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with 'Honeycrisp' being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. 'Honeycrisp' inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent 'Frostbite'. The highly resistant IBP 'Enterprise' had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.
Collapse
Affiliation(s)
- Sarah A Kostick
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, Wenatchee, WA, 98801, USA
| | - Soon Li Teh
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, Wenatchee, WA, 98801, USA
| | - John L Norelli
- United States Department of Agriculture, Agricultural Research Service, Appalachian Fruit Research Laboratory, Kearneysville, WV, 25430, USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Kate M Evans
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, Wenatchee, WA, 98801, USA.
| |
Collapse
|
14
|
Zheng W, Shen F, Wang W, Wu B, Wang X, Xiao C, Tian Z, Yang X, Yang J, Wang Y, Wu T, Xu X, Han Z, Zhang X. Quantitative trait loci-based genomics-assisted prediction for the degree of apple fruit cover color. THE PLANT GENOME 2020; 13:e20047. [PMID: 33217219 DOI: 10.1002/tpg2.20047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Apple fruit cover color is an important appearance trait determining fruit quality, high degree of fruit cover color or completely red fruit skin is also the ultimate breeding goal. MdMYB1 has repeatedly been reported as a major gene controlling apple fruit cover color. There are also multiple minor-effect genes affecting degree of fruit cover color (DFC). This study was to identify genome-wide quantitative trait loci (QTLs) and to develop genomics-assisted prediction for apple DFC. The DFC phenotype data of 9,422 hybrids from five full-sib families of Malus asiatica 'Zisai Pearl', M. domestica 'Red Fuji', 'Golden Delicious', and 'Jonathan' were collected in 2014-2017. The phenotype varied considerably among hybrids with the same MdMYB1 genotype. Ten QTLs for DFC were identified using MapQTL and bulked segregant analysis via sequencing. From these QTLs, ten candidate genes were predicted, including MdMYB1 from a year-stable QTL on chromosome 9 of 'Zisai Pearl' and 'Red Fuji'. Then, kompetitive allele-specific polymerase chain reaction (KASP) markers were designed on these candidate genes and 821 randomly selected hybrids were genotyped. The genotype effects of the markers were estimated. MdMYB1-1 (represented by marker H162) exhibited a partial dominant allelic effect on MdMYB1-2 and showed non-allelic epistasis on markers H1245 and G6. Finally, a non-additive QTL-based genomics assisted prediction model was established for DFC. The Pearson's correlation coefficient between the genomic predicted value and the observed phenotype value was 0.5690. These results can be beneficial for apple genomics-assisted breeding and may provide insights for understanding the mechanism of fruit coloration.
Collapse
Affiliation(s)
- Wenyan Zheng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Fei Shen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Wuqian Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Bei Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xuan Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Chen Xiao
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xianglong Yang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Jing Yang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Yi Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Ting Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| |
Collapse
|
15
|
Roth M, Muranty H, Di Guardo M, Guerra W, Patocchi A, Costa F. Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple. HORTICULTURE RESEARCH 2020; 7:148. [PMID: 32922820 PMCID: PMC7459338 DOI: 10.1038/s41438-020-00370-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 05/11/2023]
Abstract
Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a gene controlling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorly understood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is therefore necessary. In this study, we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture. Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance (0.64). Predictions for biparental families using the entire training set varied from low to high accuracy, depending on the family considered. While adding siblings or half-siblings into the training set did not clearly improve predictions, we performed an optimization of the training set size and composition for each validation set. This allowed us to increase prediction accuracies by 0.17 on average, with a maximal accuracy of 0.81 when predicting firmness in the 'Gala' × 'Pink Lady' family. Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple. In particular, we advise to rely on a large training population, with high phenotypic variability from which a 'tailored training population' can be extracted using a priori information on genetic relatedness, in order to predict a specific target population.
Collapse
Affiliation(s)
- Morgane Roth
- Plant Breeding Research Division, Agroscope, Wädenswil, Zurich, Switzerland
- Present Address: GAFL, INRAE, 84140 Montfavet, France
| | - Hélène Muranty
- IRHS, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Mario Di Guardo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Walter Guerra
- Research Centre Laimburg, Laimburg 6, 39040 Auer, Italy
| | - Andrea Patocchi
- Plant Breeding Research Division, Agroscope, Wädenswil, Zurich, Switzerland
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, Via Mach 1, 38010 San Michele all’Adige, Italy
| |
Collapse
|
16
|
Nybom H, Ahmadi-Afzadi M, Rumpunen K, Tahir I. Review of the Impact of Apple Fruit Ripening, Texture and Chemical Contents on Genetically Determined Susceptibility to Storage Rots. PLANTS 2020; 9:plants9070831. [PMID: 32630736 PMCID: PMC7411992 DOI: 10.3390/plants9070831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
Abstract
Fungal storage rots like blue mould, grey mould, bull's eye rot, bitter rot and brown rot destroy large amounts of the harvested apple crop around the world. Application of fungicides is nowadays severely restricted in many countries and production systems, and these problems are therefore likely to increase. Considerable variation among apple cultivars in resistance/susceptibility has been reported, suggesting that efficient defence mechanisms can be selected for and used in plant breeding. These are, however, likely to vary between pathogens, since some fungi are mainly wound-mediated while others attack through lenticels or by infecting blossoms. Since mature fruits are considerably more susceptible than immature fruits, mechanisms involving fruit-ripening processes are likely to play an important role. Significant associations have been detected between the susceptibility to rots in harvested fruit and various fruit maturation-related traits like ripening time, fruit firmness at harvest and rate of fruit softening during storage, as well as fruit biochemical contents like acidity, sugars and polyphenols. Some sources of resistance to blue mould have been described, but more research is needed on the development of spore inoculation methods that produce reproducible data and can be used for large screenings, especially for lenticel-infecting fungi.
Collapse
Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
- Correspondence:
| | - Masoud Ahmadi-Afzadi
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631818356, Iran;
| | - Kimmo Rumpunen
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Ibrahim Tahir
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 23053 Alnarp, Sweden;
| |
Collapse
|
17
|
Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes ( Vitis vinifera L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2020; 21:ijms21030797. [PMID: 31991832 PMCID: PMC7037167 DOI: 10.3390/ijms21030797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.
Collapse
|
18
|
Paauw M, Koes R, Quattrocchio FM. Alteration of flavonoid pigmentation patterns during domestication of food crops. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3719-3735. [PMID: 30949670 DOI: 10.1093/jxb/erz141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/15/2019] [Indexed: 05/20/2023]
Abstract
Flavonoids are plant pigments that provide health benefits for human and animal consumers. Understanding why domesticated crops have altered pigmentation patterns and unraveling the molecular/genetic mechanisms that underlie this will facilitate the breeding of new (healthier) varieties. We present an overview of changes in flavonoid pigmentation patterns that have occurred during crop domestication and, where possible, link them to the molecular changes that brought about the new phenotypes. We consider species that lost flavonoid pigmentation in the edible part of the plant at some point during domestication (like cereals). We also consider the converse situation, for example eggplant (aubergine), which instead gained strong anthocyanin accumulation in the skin of the fruit during domestication, and some varieties of citrus and apple that acquired anthocyanins in the fruit flesh. Interestingly, the genes responsible for such changes are sometimes closely linked to, or have pleiotropic effects on, important domestication genes, suggesting accidental and perhaps inevitable changes of anthocyanin patterning during domestication. In other cases, flavonoid pigmentation patterns in domesticated crops are the result of cultural preferences, with examples being found in varieties of citrus, barley, wheat, and maize. Finally, and more recently, in some species, anthocyanins seem to have been the direct target of selection in a second wave of domestication that followed the introduction of industrial food processing.
Collapse
Affiliation(s)
- Misha Paauw
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, XH, Amsterdam, Netherlands
| | - Ronald Koes
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, XH, Amsterdam, Netherlands
| | | |
Collapse
|
19
|
High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow. PLoS One 2019; 14:e0210928. [PMID: 31246947 PMCID: PMC6597046 DOI: 10.1371/journal.pone.0210928] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/19/2019] [Indexed: 12/14/2022] Open
Abstract
High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae.
Collapse
|
20
|
Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. HORTICULTURE RESEARCH 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
Collapse
Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| |
Collapse
|
21
|
Salinas N, Verma S, Peres N, Whitaker VM. FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1109-1120. [PMID: 30564908 PMCID: PMC6449309 DOI: 10.1007/s00122-018-3263-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/07/2018] [Indexed: 05/18/2023]
Abstract
Optimal strategies for genetic improvement in crops depend on accurate assessments of the genetic architecture of traits. The overall objective of the present study was to determine the genetic architecture of anthracnose fruit rot (AFR) resistance caused by the fungus Colletotrichum acutatum in the University of Florida strawberry (Fragaria × ananassa) breeding germplasm. In 2016-2017, 33 full-sib families resulting from crosses between parents with varying levels of AFR resistance were tested. In 2017-2018, six full-sib families resulting from putative heterozygous resistant parents and homozygous susceptible parents were tested. Additionally, a validation population consisting of 77 advanced selections and ten cultivars was tested in the second season. Inoculation was performed using a mixture of three local isolates of the C. acutatum species complex. Phenotypes were scored weekly, and genotyping was performed using the IStraw35 Affymetrix Axiom® SNP array. A pedigree-based QTL analysis was performed using FlexQTL™ software. A major resistance locus, which we name FaRCa1, was detected in both seasons with a peak located at 55-56 cM on LG 6B and explaining at least 50% of the phenotypic variation across trials and seasons. The resistant allele exhibited partial dominance in all trials. The FaRCa1 locus is distinct from the previously discovered Rca2 locus, which mapped to LG 7B. While Rca2 is effective against European isolates from pathogenicity group 2, FaRCa1 appears to confer resistance to isolates of pathogenicity group 1.
Collapse
Affiliation(s)
- Natalia Salinas
- Department of Horticultural Sciences, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA
| | - Sujeet Verma
- Department of Horticultural Sciences, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA
| | - Natalia Peres
- Department of Plant Pathology, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA.
| |
Collapse
|
22
|
Calle A, Cai L, Iezzoni A, Wünsch A. Genetic Dissection of Bloom Time in Low Chilling Sweet Cherry ( Prunus avium L.) Using a Multi-Family QTL Approach. FRONTIERS IN PLANT SCIENCE 2019; 10:1647. [PMID: 31998337 PMCID: PMC6962179 DOI: 10.3389/fpls.2019.01647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Bloom time in sweet cherry (Prunus avium L.) is a highly heritable trait that varies between genotypes and depends on the environmental conditions. Bud-break occurs after chill and heat requirements of each genotype are fulfilled, and dormancy is released. Bloom time is a critical trait for fruit production as matching cultivar adaptation to the growing area is essential for adequate fruit set. Additionally, low chilling cultivars are of interest to extend sweet cherry production to warmer regions, and for the crop adaptation to increasing winter and spring temperatures. The aim of this work is to investigate the genetic control of this trait by analyzing multiple families derived from the low chilling and extra-early flowering local Spanish cultivar 'Cristobalina' and other cultivars with higher chilling requirements and medium to late bloom times. Bloom time evaluation in six related sweet cherry populations confirmed a high heritability of this trait, and skewed distribution toward late flowering, revealing possible dominance of the late bloom alleles. SNP genotyping of the six populations (n = 406) resulted in a consensus map of 1269 SNPs. Quantitative trait loci (QTL) analysis using the Bayesian approach implemented by FlexQTL™ software revealed two major QTLs on linkage groups 1 and 2 (qP-BT1.1m and qP-BT2.1m) that explained 47.6% of the phenotypic variation. The QTL on linkage group 1 was mapped to a 0.26 Mbp region that overlaps with the DORMANCY ASSOCIATED MADS-BOX (DAM) genes. This finding is consistent with peach results that indicate that these genes are major determinants of chilling requirement in Prunus. Haplotype analysis of the linkage group 1 and 2 QTL regions showed that 'Cristobalina' was the only cultivar tested that contributed early bloom time alleles for these two QTLs. This work contributes to knowledge of the genetic control of chilling requirement and bloom date and will enable marker-assisted selection for low chilling in sweet cherry breeding programs.
Collapse
Affiliation(s)
- Alejandro Calle
- Unidad de Hotofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Ana Wünsch
- Unidad de Hotofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, (CITA-Universidad de Zaragoza), Zaragoza, Spain
- *Correspondence: Ana Wünsch,
| |
Collapse
|
23
|
Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grappadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Pascal T, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, van de Weg E. An integrated approach for increasing breeding efficiency in apple and peach in Europe. HORTICULTURE RESEARCH 2018; 5:11. [PMID: 29507735 PMCID: PMC5830435 DOI: 10.1038/s41438-018-0016-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/23/2017] [Indexed: 05/02/2023]
Abstract
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.
Collapse
Affiliation(s)
- Francois Laurens
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Pere Arus
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
| | - Marco Bink
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708PB The Netherlands
- Present Address: Hendrix Genetics Research, Technology & Services, Boxmeer, 5830 AC The Netherlands
| | - Joan Bonany
- IRTA-Mas Badia, Mas Badia, La Tallada, 17134 Spain
| | - Andrea Caprera
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | | | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | | | - Hélène Muranty
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Nelson Nazzicari
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | - Andrea Patocchi
- Agroscope, Research Division Plant Breeding, Schloss 1, Wädenswil, 8820 Switzerland
| | - Andreas Peil
- Julius Kühn-Institute (JKI); Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, Dresden, 01326 Germany
| | | | - Laura Rossini
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Alessandra Stella
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Riccardo Velasco
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- CREA-VE, Center of Viticulture and Enology, via XXVIII Aprile 26, Conegliano (TV), 31015 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O.Box 386, Wageningen, 6700AJ The Netherlands
| |
Collapse
|
24
|
Farneti B, Di Guardo M, Khomenko I, Cappellin L, Biasioli F, Velasco R, Costa F. Genome-wide association study unravels the genetic control of the apple volatilome and its interplay with fruit texture. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1467-1478. [PMID: 28338794 PMCID: PMC5441895 DOI: 10.1093/jxb/erx018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fruit quality represents a fundamental factor guiding consumers' preferences. Among apple quality traits, volatile organic compounds and texture features play a major role. Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-ToF-MS), coupled with an artificial chewing device, was used to profile the entire apple volatilome of 162 apple accessions, while the fruit texture was dissected with a TAXT-AED texture analyzer. The array of volatile compounds was classed into seven major groups and used in a genome-wide association analysis carried out with 9142 single nucleotide polymorphisms (SNPs). Marker-trait associations were identified on seven chromosomes co-locating with important candidate genes for aroma, such as MdAAT1 and MdIGS. The integration of volatilome and fruit texture data conducted with a multiple factor analysis unraveled contrasting behavior, underlying opposite regulation of the two fruit quality aspects. The association analysis using the first two principal components identified two QTLs located on chromosomes 10 and 2, respectively. The distinction of the apple accessions on the basis of the allelic configuration of two functional markers, MdPG1 and MdACO1, shed light on the type of interplay existing between fruit texture and the production of volatile organic compounds.
Collapse
Affiliation(s)
- Brian Farneti
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Mario Di Guardo
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento, Italy
- Graduate School Experimental Plant Sciences, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Iuliia Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento, Italy
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Technikerstr. 25/3, 6020 Innsbruck, Austria
| | - Luca Cappellin
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Fabrizio Costa
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| |
Collapse
|
25
|
Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. FRONTIERS IN PLANT SCIENCE 2017; 8:1923. [PMID: 29176988 PMCID: PMC5686452 DOI: 10.3389/fpls.2017.01923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 05/17/2023]
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
Collapse
Affiliation(s)
- Jorge Urrestarazu
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- Department of Agricultural Sciences, Public University of Navarre, Pamplona, Spain
- *Correspondence: Jorge Urrestarazu
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Diane Leforestier
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Elisa Ravon
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Arnaud Guyader
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Rémi Guisnel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Laurence Feugey
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Patrick Houben
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czechia
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Charles Poncet
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Anthony Théron
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Shigeki Moriya
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Marco C. A. M. Bink
- Wageningen UR, Biometris, Wageningen, Netherlands
- Hendrix Genetics, Boxmeer, Netherlands
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Charles-Eric Durel
| |
Collapse
|