1
|
Anders C, Hoengenaert L, Boerjan W. Accelerating wood domestication in forest trees through genome editing: Advances and prospects. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102329. [PMID: 36586396 PMCID: PMC7614060 DOI: 10.1016/j.pbi.2022.102329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The high economic value of wood requires intensive breeding towards multipurpose biomass. However, long breeding cycles hamper the fast development of novel tree varieties that have improved biomass properties, are tolerant to biotic and abiotic stresses, and resilient to climate change. To speed up domestication, the integration of conventional breeding and new breeding techniques is needed. In this review, we discuss recent advances in genome editing and Cas-DNA-free genome engineering of forest trees, and briefly discuss how multiplex editing combined with multi-omics approaches can accelerate the genetic improvement of forest trees, with a focus on wood.
Collapse
Affiliation(s)
- Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| |
Collapse
|
2
|
Jia S, Liu X, Wen X, Waheed A, Ding Y, Kahar G, Li X, Zhang D. Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:620. [PMID: 36771705 PMCID: PMC9919239 DOI: 10.3390/plants12030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/15/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.
Collapse
Affiliation(s)
- Shanshan Jia
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaojie Liu
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Xuejing Wen
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Abdul Waheed
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Yu Ding
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Gulnaz Kahar
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaoshuang Li
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Daoyuan Zhang
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| |
Collapse
|
3
|
Li X, Zeng S, Wisniewski M, Droby S, Yu L, An F, Leng Y, Wang C, Li X, He M, Liao Q, Liu J, Wang Y, Sui Y. Current and future trends in the biocontrol of postharvest diseases. Crit Rev Food Sci Nutr 2022:1-13. [PMID: 36530065 DOI: 10.1080/10408398.2022.2156977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Postharvest diseases of fruits and vegetables cause significant economic losses to producers and marketing firms. Many of these diseases are caused by necrotrophic fungal pathogens that require wounded or injured tissues to establish an infection. Biocontrol of postharvest diseases is an evolving science that has moved from the traditional paradigm of one organism controlling another organism to viewing biocontrol as a system involving the biocontrol agent, the pathogen, the host, the physical environment, and most recently the resident microflora. Thus, the paradigm has shifted from one of simplicity to complexity. The present review provides an overview of how the field of postharvest biocontrol has evolved over the past 40 years, a brief review of the biology of necrotrophic pathogens, the discovery of BCAs, their commercialization, and mechanisms of action. Most importantly, current research on the use of marker-assisted-selection, the fruit microbiome and its relationship to the pathobiome, and the use of double-stranded RNA as a biocontrol strategy is discussed. These latter subjects represent evolving trends in postharvest biocontrol research and suggestions for future research are presented.
Collapse
Affiliation(s)
- Xiaojiao Li
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Shixian Zeng
- College of Agriculture, Key Laboratory of Agricultural Microbiology of Guizhou Province, Guizhou University, Guiyang, Guizhou, China
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Samir Droby
- Department of Postharvest Science, ARO, the Volcani Center, Rishon LeZion, Israel
| | - Longfeng Yu
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Fuquan An
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Yan Leng
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Chaowen Wang
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Xiaojun Li
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Min He
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, China
| | - Qinhong Liao
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yong Wang
- College of Agriculture, Key Laboratory of Agricultural Microbiology of Guizhou Province, Guizhou University, Guiyang, Guizhou, China
| | - Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| |
Collapse
|
4
|
De Meester B, Vanholme R, Mota T, Boerjan W. Lignin engineering in forest trees: From gene discovery to field trials. PLANT COMMUNICATIONS 2022; 3:100465. [PMID: 36307984 PMCID: PMC9700206 DOI: 10.1016/j.xplc.2022.100465] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Wood is an abundant and renewable feedstock for the production of pulp, fuels, and biobased materials. However, wood is recalcitrant toward deconstruction into cellulose and simple sugars, mainly because of the presence of lignin, an aromatic polymer that shields cell-wall polysaccharides. Hence, numerous research efforts have focused on engineering lignin amount and composition to improve wood processability. Here, we focus on results that have been obtained by engineering the lignin biosynthesis and branching pathways in forest trees to reduce cell-wall recalcitrance, including the introduction of exotic lignin monomers. In addition, we draw general conclusions from over 20 years of field trial research with trees engineered to produce less or altered lignin. We discuss possible causes and solutions for the yield penalty that is often associated with lignin engineering in trees. Finally, we discuss how conventional and new breeding strategies can be combined to develop elite clones with desired lignin properties. We conclude this review with priorities for the development of commercially relevant lignin-engineered trees.
Collapse
Affiliation(s)
- Barbara De Meester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Thatiane Mota
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
| |
Collapse
|
5
|
Volk GM, Peace CP, Henk AD, Howard NP. DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions. FRONTIERS IN PLANT SCIENCE 2022; 13:1015658. [PMID: 36311081 PMCID: PMC9606829 DOI: 10.3389/fpls.2022.1015658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species' centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were compared with a dataset of more than 5000 unique M. domestica apple cultivars. Only 212 accessions (151 M. sieversii, 26 M. orientalis, and 35 M. sylvestris) were identified as "pure" species representatives because their DNA profiles did not exhibit genotypic signatures of recent hybridization with M. domestica. Twenty-one accessions (17 M. sieversii, 1 M. orientalis, and 3 M. sylvestris) previously labeled as wild species were instead fully M. domestica. Previously unrealized hybridization and admixture between wild species and M. domestica was identified in 230 accessions (215 M. sieversii, 9 M. orientalis, and 6 M. sylvestris). Among these species-mislabeled accessions, 'Alexander', 'Gold Reinette', 'Charlamoff', 'Rosmarina Bianca', and 'King of the Pippins' were the most frequently detected M. domestica parents or grandparents. These results have implications for collection management, including germplasm distribution, and might affect conclusions of previous research focused on these three progenitor species in the NPGS apple collection. Specifically, accessions received from the NPGS for breeding and genomics, genetics, and evolutionary biology research might not be truly representative of their previously assigned species.
Collapse
Affiliation(s)
- Gayle M. Volk
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
| | - Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Adam D. Henk
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
| | | |
Collapse
|
6
|
Pathirana R, Carimi F. Management and Utilization of Plant Genetic Resources for a Sustainable Agriculture. PLANTS 2022; 11:plants11152038. [PMID: 35956515 PMCID: PMC9370719 DOI: 10.3390/plants11152038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/02/2022]
Abstract
Despite the dramatic increase in food production thanks to the Green Revolution, hunger is increasing among human populations around the world, affecting one in nine people. The negative environmental and social consequences of industrial monocrop agriculture is becoming evident, particularly in the contexts of greenhouse gas emissions and the increased frequency and impact of zoonotic disease emergence, including the ongoing COVID-19 pandemic. Human activity has altered 70–75% of the ice-free Earth’s surface, squeezing nature and wildlife into a corner. To prevent, halt, and reverse the degradation of ecosystems worldwide, the UN has launched a Decade of Ecosystem Restoration. In this context, this review describes the origin and diversity of cultivated species, the impact of modern agriculture and other human activities on plant genetic resources, and approaches to conserve and use them to increase food diversity and production with specific examples of the use of crop wild relatives for breeding climate-resilient cultivars that require less chemical and mechanical input. The need to better coordinate in situ conservation efforts with increased funding has been highlighted. We emphasise the need to strengthen the genebank infrastructure, enabling the use of modern biotechnological tools to help in genotyping and characterising accessions plus advanced ex situ conservation methods, identifying gaps in collections, developing core collections, and linking data with international databases. Crop and variety diversification and minimising tillage and other field practices through the development and introduction of herbaceous perennial crops is proposed as an alternative regenerative food system for higher carbon sequestration, sustaining economic benefits for growers, whilst also providing social and environmental benefits.
Collapse
Affiliation(s)
- Ranjith Pathirana
- Plant & Food Research Australia Pty Ltd., Waite Campus Research Precinct—Plant Breeding WT46, University of Adelaide, Waite Rd, Urrbrae, SA 5064, Australia
- School of Agriculture, Food and Wine, Waite Campus Research Precinct—Plant Breeding WT46, University of Adelaide, Waite Rd, Urrbrae, SA 5064, Australia
- Correspondence:
| | - Francesco Carimi
- Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy
| |
Collapse
|
7
|
Leng J, Yu L, Dai Y, Leng Y, Wang C, Chen Z, Wisniewski M, Wu X, Liu J, Sui Y. Recent advances in research on biocontrol of postharvest fungal decay in apples. Crit Rev Food Sci Nutr 2022; 63:10607-10620. [PMID: 35608023 DOI: 10.1080/10408398.2022.2080638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Apple is the largest fruit crop produced in temperate regions and is a popular fruit worldwide. It is, however, susceptible to a variety of postharvest fungal pathogens, including Penicillium expansum, Botrytis cinerea, Botryosphaeria dothidea, Monilia spp., and Alternaria spp. Decays resulting from fungal infections severely reduce apple quality and marketable yield. Biological control utilizing bacterial and fungal antagonists is an eco-friendly and effective method of managing postharvest decay in horticultural crops. In the current review, research on the pathogenesis of major decay fungi and isolation of antagonists used to manage postharvest decay in apple is presented. The mode of action of postharvest biocontrol agents (BCAs), including recent molecular and genomic studies, is also discussed. Recent research on the apple microbiome and its relationship to disease management is highlighted, and the use of additives and physical treatments to enhance biocontrol efficacy of BCAs is reviewed. Biological control is a critical component of an integrated management system for the sustainable approaches to apple production. Additional research will be required to explore the feasibility of developing beneficial microbial consortia and novel antimicrobial compounds derived from BCAs for postharvest disease management, as well as genetic approaches, such as the use of CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Jinsong Leng
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Longfeng Yu
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Yuan Dai
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yan Leng
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Chaowen Wang
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Zhuo Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, China
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jia Liu
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yuan Sui
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| |
Collapse
|
8
|
Penicillium expansum Impact and Patulin Accumulation on Conventional and Traditional Apple Cultivars. Toxins (Basel) 2021; 13:toxins13100703. [PMID: 34678996 PMCID: PMC8541162 DOI: 10.3390/toxins13100703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/26/2021] [Accepted: 09/30/2021] [Indexed: 11/26/2022] Open
Abstract
Penicillium expansum is a necrotrophic plant pathogen among the most ubiquitous fungi disseminated worldwide. It causes blue mould rot in apples during storage, transport and sale, threatening human health by secreting patulin, a toxic secondary metabolite that contaminates apples and apple-derived products. Nevertheless, there is still a lack of sufficient data regarding the resistance of different apple cultivars to P. expansum, especially ancient ones, which showed to possess certain resistance to plant diseases. In this work, we investigated the polyphenol profile of 12 traditional and 8 conventional apple cultivar and their resistance to P. expansum CBS 325.48. Eight polyphenolic compounds were detected; the most prominent were catechin, epicatechin and gallic acid. The highest content of catechin was detected in ‘Apistar’—91.26 mg/100 g of fresh weight (FW), epicatechin in ‘Bobovac’—67.00 mg/100 g of FW, and gallic acid in ‘Bobovac’ and ‘Kraljevčica’—8.35 and 7.40 mg/100 g of FW, respectively. The highest content of patulin was detected in ‘Kraljevčica’ followed by ‘Apistar’—1687 and 1435 µg/kg, respectively. In apple cultivars ‘Brčko’, ‘Adamčica’ and ‘Idared’, patulin was not detected. Furthermore, the patulin content was positively correlated with gallic acid (r = 0.4226; p = 0.002), catechin (r = 0.3717; p = 0.008) and epicatechin (r = 0.3305; p = 0.019). This fact indicates that higher contents of gallic acid, catechin and epicatechin negatively affected and boost patulin concentration in examined apple cultivars. This can be related to the prooxidant activity of polyphenolic compounds and sensitivity of P. expansum to the disturbance of oxidative status.
Collapse
|
9
|
Fox Hunting in Wild Apples: Searching for Novel Genes in Malus Sieversii. Int J Mol Sci 2020; 21:ijms21249516. [PMID: 33327659 PMCID: PMC7765095 DOI: 10.3390/ijms21249516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/04/2022] Open
Abstract
Malus sieversii is considered the progenitor of modern apple (Malus pumila) cultivars and to represent a valuable source of genetic diversity. Despite the importance of M. sieversii as a source of disease resistance, stress tolerance, and novel fruit traits, little is known about gene function and diversity in M. sieversii. Notably, a publicly annotated genome sequence for this species is not available. In the current study, the FOX (Full-length cDNA OvereXpressing) gene hunting system was used to construct a library of transgenic lines of Arabidopsis in which each transgenic line overexpresses a full-length gene obtained from a cDNA library of the PI619283 accession of M. sieversii. The cDNA library was constructed from mRNA obtained from bark tissues collected in late fall–early winter, a time at which many abiotic stress-adaptative genes are expressed. Over 4000 apple FOX Arabidopsis lines have been established from the pool of transgenic seeds and cDNA inserts corresponding to various Gene Ontology (GO) categories have been identified. A total of 160 inserts appear to be novel, with no or limited homology to M. pumila, Arabidopsis, or poplar. Over 1300 lines have also been screened for freezing resistance. The constructed library of transgenic lines provides a valuable genetic resource for exploring gene function and diversity in Malus sieversii. Notably, no such library of t-DNA lines currently exists for any Malus species.
Collapse
|
10
|
Tsanova T, Stefanova L, Topalova L, Atanasov A, Pantchev I. DNA-free gene editing in plants: a brief overview. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1858159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Tsveta Tsanova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Lidia Stefanova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Lora Topalova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | | | - Ivelin Pantchev
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
- Joint Genomic Center Ltd, Sofia, Bulgaria
| |
Collapse
|
11
|
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet 2020; 52:1423-1432. [PMID: 33139952 PMCID: PMC7728601 DOI: 10.1038/s41588-020-00723-9] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality. Phased diploid genomes of the cultivated apple Malus domestica cv. Gala and its two major wild progenitors M. sieversii and M. sylvestris, as well as pan-genome analyses, provide insights into the genetic history of apple domestication.
Collapse
|
12
|
Iezzoni AF, McFerson J, Luby J, Gasic K, Whitaker V, Bassil N, Yue C, Gallardo K, McCracken V, Coe M, Hardner C, Zurn JD, Hokanson S, van de Weg E, Jung S, Main D, da Silva Linge C, Vanderzande S, Davis TM, Mahoney LL, Finn C, Peace C. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. HORTICULTURE RESEARCH 2020; 7:177. [PMID: 33328430 PMCID: PMC7603521 DOI: 10.1038/s41438-020-00398-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 08/30/2020] [Indexed: 05/05/2023]
Abstract
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
Collapse
Affiliation(s)
- Amy F Iezzoni
- Michigan State University, East Lansing, MI, 48824, USA.
| | - Jim McFerson
- Washington State University, Wenatchee, WA, 98801, USA
| | - James Luby
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | - Chengyan Yue
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | - Michael Coe
- Cedar Lake Research Group, Portland, OR, 97215, USA
| | | | | | | | - Eric van de Weg
- Wageningen University and Research, 6700 AA, Wageningen, The Netherlands
| | - Sook Jung
- Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Washington State University, Pullman, WA, 99164, USA
| | | | | | | | | | | | - Cameron Peace
- Washington State University, Pullman, WA, 99164, USA
| |
Collapse
|
13
|
Luciano‐Rosario D, Keller NP, Jurick WM. Penicillium expansum: biology, omics, and management tools for a global postharvest pathogen causing blue mould of pome fruit. MOLECULAR PLANT PATHOLOGY 2020; 21:1391-1404. [PMID: 32969130 PMCID: PMC7548999 DOI: 10.1111/mpp.12990] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/17/2020] [Indexed: 05/02/2023]
Abstract
UNLABELLED Blue mould, caused primarily by Penicillium expansum, is a major threat to the global pome fruit industry, causing multimillion-dollar losses annually. The blue mould fungus negatively affects fruit quality, thereby reducing fresh fruit consumption, and significantly contributes to food loss. P. expansum also produces an array of mycotoxins that are detrimental to human health. Management options are limited and the emergence of fungicide-resistant Penicillium spp. makes disease management difficult, therefore new approaches and tools are needed to combat blue mould in storage. This species profile comprises a comprehensive literature review of this aggressive pathogen associated with pomes (apple, pear, quince), focusing on biology, mechanisms of disease, control, genomics, and the newest developments in disease management. TAXONOMY Penicillium expansum Link 1809. Domain Eukaryota, Kingdom Fungi, Phylum Ascomycota, Subphylum Pezizomycotina, Class Eurotiomycetes, Subclass: Eurotiomycetidae, Order Eurotiales; Family Trichocomaceae, Genus Penicillium, Species expansum. BIOLOGY A wide host range necrotrophic postharvest pathogen that requires a wound (e.g., stem pull, punctures, bruises, shoulder cracks) or natural openings (e.g., lenticel, stem end, calyx sinus) to gain ingress and infect. TOXINS Patulin, citrinin, chaetoglobosins, communesins, roquefortine C, expansolides A and B, ochratoxin A, penitrem A, rubratoxin B, and penicillic acid. HOST RANGE Primarily apples, European pear, Asian pear, medlar, and quince. Blue mould has also been reported on stone fruits (cherry, plum, peach), small fruits (grape, strawberry, kiwi), and hazel nut. DISEASE SYMPTOMS Blue mould initially appears as light tan to dark brown circular lesions with a defined margin between the decayed and healthy tissues. The decayed tissue is soft and watery, and blue-green spore masses appear on the decayed area, starting at the infection site and radiating outward as the decayed area ages. DISEASE CONTROL Preharvest fungicides with postharvest activity and postharvest fungicides are primarily used to control decay. Orchard and packinghouse sanitation methods are also critical components of an integrated pest management strategy. USEFUL WEBSITES Penn State Tree Fruit Production Guide (https://extension.psu.edu/forage-and-food-crops/fruit), Washington State Comprehensive Tree Fruit (http://treefruit.wsu.edu/crop-protection/disease-management/blue-mold/), The Apple Rot Doctor (https://waynejurick.wixsite.com/applerotdr), penicillium expansum genome sequences and resources (https://www.ncbi.nlm.nih.gov/genome/browse/#!/eukaryotes/11336/).
Collapse
Affiliation(s)
| | - Nancy P. Keller
- Department of Medical Microbiology and ImmunologyDepartment of BacteriologyFood Research InstituteUniversity of Wisconsin at MadisonMadisonWisconsinUSA
| | | |
Collapse
|
14
|
Emeriewen OF, Richter K, Berner T, Keilwagen J, Schnable PS, Malnoy M, Peil A. Construction of a dense genetic map of the Malus fusca fire blight resistant accession MAL0045 using tunable genotyping-by-sequencing SNPs and microsatellites. Sci Rep 2020; 10:16358. [PMID: 33005026 PMCID: PMC7529804 DOI: 10.1038/s41598-020-73393-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Although, the Pacific crabapple, Malus fusca, is a hardy and disease resistant species, studies relating to the genetics of its unique traits are very limited partly due to the lack of a genetic map of this interesting wild apple. An accession of M. fusca (MAL0045) of Julius Kühn-Institut collection in Germany is highly resistant to fire blight disease, incited by different strains of the causative pathogen—Erwinia amylovora. This is the most destructive bacterial disease of Malus of which most of the domesticated apples (Malus domestica) are susceptible. Using a scarcely dense genetic map derived from a population of 134 individuals of MAL0045 × ‘Idared’, the locus (Mfu10) controlling fire blight resistance mapped on linkage group 10 (LG10) and explained up to 66% of the phenotypic variance with different strains. Although the development of robust and tightly linked molecular markers on LG10 through chromosome walking approach led to the identification of a major candidate gene, any minor effect locus remained elusive possibly due to the lack of marker density of the entire genetic map. Therefore, we have developed a dense genetic map of M. fusca using tunable genotyping-by-sequencing (tGBS) approach. Of thousands of de novo SNPs identified, 2677 were informative in M. fusca and 90.5% of these successfully mapped. In addition, integration of SNP data and microsatellite (SSR) data resulted in a final map comprising 17 LGs with 613 loci spanning 1081.35 centi Morgan (cM). This map will serve as a template for mapping using different strains of the pathogen.
Collapse
Affiliation(s)
- Ofere Francis Emeriewen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany.
| | - Klaus Richter
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Thomas Berner
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA.,Plant Sciences Institute, Iowa State University, 2035B Carver, Ames, IA, 50011-3650, USA
| | - Mickael Malnoy
- Research and Innovation Centre, Genomics and Biology of Fruit Crops Department, Fondazione Edmund Mach, Via E. Mach, 1, 38010, San Michele all 'Adige (Trentino), Italy
| | - Andreas Peil
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany.
| |
Collapse
|
15
|
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
|
16
|
Kaiser N, Douches D, Dhingra A, Glenn KC, Herzig PR, Stowe EC, Swarup S. The role of conventional plant breeding in ensuring safe levels of naturally occurring toxins in food crops. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.03.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
17
|
Magoye E, Pfister M, Hilber-Bodmer M, Freimoser FM. Competition Assays to Quantify the Effect of Biocontrol Yeasts against Plant Pathogenic Fungi on Fruits. Bio Protoc 2020; 10:e3518. [PMID: 33654743 DOI: 10.21769/bioprotoc.3518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 11/02/2022] Open
Abstract
Yeasts such as Aureobasidium pullulans are unicellular fungi that occur in all environments and play important roles in biotechnology, medicine, food and beverage production, research, and agriculture. In the latter, yeasts are explored as biocontrol agents for the control of plant pathogenic fungi (e.g., Botrytis cinerea, Fusarium sp.); mainly on flowers and fruits. Eventually, such yeasts must be evaluated under field conditions, but such trials require a lot of time and resources and are often difficult to control. Experimental systems of intermediate complexity, between in vitro Petri dish assays and field trials, are thus required. For pre- and post-harvest applications, competition assays on fruits are reproducible, economical and thus widely used. Here, we present a general protocol for competition assays with fruits that can be adapted depending on the biocontrol yeast, plant pathogen, type of assay or fruit to be studied.
Collapse
Affiliation(s)
- Electine Magoye
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| | - Melanie Pfister
- Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Maja Hilber-Bodmer
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| | - Florian M Freimoser
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| |
Collapse
|
18
|
Souleyre EJF, Bowen JK, Matich AJ, Tomes S, Chen X, Hunt MB, Wang MY, Ileperuma NR, Richards K, Rowan DD, Chagné D, Atkinson RG. Genetic control of α-farnesene production in apple fruit and its role in fungal pathogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1148-1162. [PMID: 31436867 DOI: 10.1111/tpj.14504] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/28/2019] [Accepted: 08/05/2019] [Indexed: 05/05/2023]
Abstract
Terpenes are important compounds in plant trophic interactions. A meta-analysis of GC-MS data from a diverse range of apple (Malus × domestica) genotypes revealed that apple fruit produces a range of terpene volatiles, with the predominant terpene being the acyclic branched sesquiterpene (E,E)-α-farnesene. Four quantitative trait loci (QTLs) for α-farnesene production in ripe fruit were identified in a segregating 'Royal Gala' (RG) × 'Granny Smith' (GS) population with one major QTL on linkage group 10 co-locating with the MdAFS1 (α-farnesene synthase-1) gene. Three of the four QTLs were derived from the GS parent, which was consistent with GC-MS analysis of headspace and solvent-extracted terpenes showing that cold-treated GS apples produced higher levels of (E,E)-α-farnesene than RG. Transgenic RG fruit downregulated for MdAFS1 expression produced significantly lower levels of (E,E)-α-farnesene. To evaluate the role of (E,E)-α-farnesene in fungal pathogenesis, MdAFS1 RNA interference transgenic fruit and RG controls were inoculated with three important apple post-harvest pathogens [Colletotrichum acutatum, Penicillium expansum and Neofabraea alba (synonym Phlyctema vagabunda)]. From results obtained over four seasons, we demonstrate that reduced (E,E)-α-farnesene is associated with decreased disease initiation rates of all three pathogens. In each case, the infection rate was significantly reduced 7 days post-inoculation, although the size of successful lesions was comparable with infections on control fruit. These results indicate that (E,E)-α-farnesene production is likely to be an important factor involved in fungal pathogenesis in apple fruit.
Collapse
Affiliation(s)
- Edwige J F Souleyre
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Adam J Matich
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Sumathi Tomes
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Xiuyin Chen
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Martin B Hunt
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Mindy Y Wang
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nadeesha R Ileperuma
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kate Richards
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Daryl D Rowan
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| |
Collapse
|
19
|
Zhebentyayeva TN, Sisco PH, Georgi LL, Jeffers SN, Perkins MT, James JB, Hebard FV, Saski C, Nelson CD, Abbott AG. Dissecting Resistance to Phytophthora cinnamomi in Interspecific Hybrid Chestnut Crosses Using Sequence-Based Genotyping and QTL Mapping. PHYTOPATHOLOGY 2019; 109:1594-1604. [PMID: 31287366 DOI: 10.1094/phyto-11-18-0425-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The soilborne oomycete Phytophthora cinnamomi-which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development. Introduction of resistant genotypes is the most practical solution for disease management in forests because treatment with fungicides and eradication of the pathogen are neither practical nor economically feasible in natural ecosystems. Using backcross families derived from crosses of American chestnuts with two resistant Chinese chestnut cultivars Mahogany and Nanking, we constructed linkage maps and identified quantitative trait loci (QTLs) for resistance to P. cinnamomi that had been introgressed from these Chinese chestnut cultivars. In total, 957 plants representing five cohorts of three hybrid crosses were genotyped by sequencing and phenotyped by standardized inoculation and visual examination over a 6-year period from 2011 to 2016. Eight parental linkage maps comprising 7,715 markers were constructed, and 17 QTLs were identified on four linkage groups (LGs): LG_A, LG_C, LG_E, and LG_K. The most consistent QTLs were detected on LG_E in seedlings from crosses with both 'Mahogany' and 'Nanking' and LG_K in seedlings from 'Mahogany' crosses. Two consistent large and medium effect QTLs located ∼10 cM apart were present in the middle and at the lower end of LG_E; other QTLs were considered to have small effects. These results imply that the genetic architecture of resistance to P. cinnamomi in Chinese chestnut × American chestnut hybrid progeny may resemble the P. sojae-soybean pathosystem, with a few dominant QTLs along with quantitatively inherited partial resistance conferred by multiple small-effect QTLs.
Collapse
Affiliation(s)
- Tetyana N Zhebentyayeva
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802
- Clemson University Genomics and Computational Biology Laboratory, Clemson, SC 29634
| | - Paul H Sisco
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Laura L Georgi
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - M Taylor Perkins
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | | | - Frederick V Hebard
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - C Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, U.S. Department of Agriculture Forest Service, Saucier, MS 39574
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
| |
Collapse
|
20
|
Cornille A, Antolín F, Garcia E, Vernesi C, Fietta A, Brinkkemper O, Kirleis W, Schlumbaum A, Roldán-Ruiz I. A Multifaceted Overview of Apple Tree Domestication. TRENDS IN PLANT SCIENCE 2019; 24:770-782. [PMID: 31296442 DOI: 10.1016/j.tplants.2019.05.007] [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: 01/03/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.
Collapse
Affiliation(s)
- Amandine Cornille
- Génétique Quantitative et Evolution- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Ferran Antolín
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Elena Garcia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, USA
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Alice Fietta
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Otto Brinkkemper
- Cultural Heritage Agency, PO Box 1600, 3800 BP Amersfoort, The Netherlands
| | - Wiebke Kirleis
- Institute for Prehistoric and Protohistoric Archeology/Graduate School Human Development in Landscapes, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Angela Schlumbaum
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
| |
Collapse
|
21
|
Baró-Montel N, Eduardo I, Usall J, Casals C, Arús P, Teixidó N, Torres R. Exploring sources of resistance to brown rot in an interspecific almond × peach population. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:4105-4113. [PMID: 30784078 DOI: 10.1002/jsfa.9640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Monilinia spp. are responsible for brown rot, one of the most significant stone fruit diseases. Planting resistant cultivars seems a promising alternative, although most commercial cultivars are susceptible to brown rot. The aim of this study was to explore resistance to Monilinia fructicola over two seasons in a backcross one interspecific population between almond 'Texas' and peach 'Earlygold' (named T1E). RESULTS 'Texas' almond was resistant to brown rot inoculation, whereas peach was highly susceptible. Phenotypic data from the T1E population indicated wide differences in response to M. fructicola. Additionally, several non-wounded individuals exhibited resistance to brown rot. Quantitative trait loci (QTLs) were identified in several linkage groups, but only two proximal QTLs in G4 were detected over both seasons and accounted for 11.3-16.2% of the phenotypic variation. CONCLUSION Analysis of the progeny allowed the identification of resistant genotypes that could serve as a source of resistance in peach breeding programs. The finding of loci associated with brown rot resistance would shed light on implementing a strategy based on marker-assisted selection (MAS) for introgression of this trait into elite peach materials. New peach cultivars resistant to brown rot may contribute to the implementation of more sustainable crop protection strategies. © 2019 Society of Chemical Industry.
Collapse
Affiliation(s)
- Núria Baró-Montel
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Josep Usall
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Carla Casals
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Neus Teixidó
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Rosario Torres
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| |
Collapse
|
22
|
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
|
23
|
Zhong L, Carere J, Lu Z, Lu F, Zhou T. Patulin in Apples and Apple-Based Food Products: The Burdens and the Mitigation Strategies. Toxins (Basel) 2018; 10:E475. [PMID: 30445713 PMCID: PMC6267208 DOI: 10.3390/toxins10110475] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023] Open
Abstract
Apples and apple-based products are among the most popular foods around the world for their delightful flavors and health benefits. However, the commonly found mold, Penicillium expansum invades wounded apples, causing the blue mold decay and ensuing the production of patulin, a mycotoxin that negatively affects human health. Patulin contamination in apple products has been a worldwide problem without a satisfactory solution yet. A comprehensive understanding of the factors and challenges associated with patulin accumulation in apples is essential for finding such a solution. This review will discuss the effects of the pathogenicity of Penicillium species, quality traits of apple cultivars, and environmental conditions on the severity of apple blue mold and patulin contamination. Moreover, beyond the complicated interactions of the three aforementioned factors, patulin control is also challenged by the lack of reliable detection methods in food matrices, as well as unclear degradation mechanisms and limited knowledge about the toxicities of the metabolites resulting from the degradations. As apple-based products are mainly produced with stored apples, pre- and post-harvest strategies are equally important for patulin mitigation. Before storage, disease-resistance breeding, orchard-management, and elicitor(s) application help control the patulin level by improving the storage qualities of apples and lowering fruit rot severity. From storage to processing, patulin mitigation strategies could benefit from the optimization of apple storage conditions, the elimination of rotten apples, and the safe and effective detoxification or biodegradation of patulin.
Collapse
Affiliation(s)
- Lei Zhong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu District, Nanjing 210095, China.
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada.
| | - Jason Carere
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada.
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu District, Nanjing 210095, China.
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu District, Nanjing 210095, China.
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada.
| |
Collapse
|
24
|
García-Arias FL, Osorio-Guarín JA, Núñez Zarantes VM. Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry ( Physalis peruviana L.). FRONTIERS IN PLANT SCIENCE 2018; 9:362. [PMID: 29616069 PMCID: PMC5869928 DOI: 10.3389/fpls.2018.00362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/05/2018] [Indexed: 05/27/2023]
Abstract
Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana.
Collapse
|
25
|
Chen L, Li W, Katin-Grazzini L, Ding J, Gu X, Li Y, Gu T, Wang R, Lin X, Deng Z, McAvoy RJ, Gmitter FG, Deng Z, Zhao Y, Li Y. A method for the production and expedient screening of CRISPR/Cas9-mediated non-transgenic mutant plants. HORTICULTURE RESEARCH 2018; 5:13. [PMID: 29531752 PMCID: PMC5834642 DOI: 10.1038/s41438-018-0023-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 05/20/2023]
Abstract
Developing CRISPR/Cas9-mediated non-transgenic mutants in asexually propagated perennial crop plants is challenging but highly desirable. Here, we report a highly useful method using an Agrobacterium-mediated transient CRISPR/Cas9 gene expression system to create non-transgenic mutant plants without the need for sexual segregation. We have also developed a rapid, cost-effective, and high-throughput mutant screening protocol based on Illumina sequencing followed by high-resolution melting (HRM) analysis. Using tetraploid tobacco as a model species and the phytoene desaturase (PDS) gene as a target, we successfully created and expediently identified mutant plants, which were verified as tetra-allelic mutants. We produced pds mutant shoots at a rate of 47.5% from tobacco leaf explants, without the use of antibiotic selection. Among these pds plants, 17.2% were confirmed to be non-transgenic, for an overall non-transgenic mutation rate of 8.2%. Our method is reliable and effective in creating non-transgenic mutant plants without the need to segregate out transgenes through sexual reproduction. This method should be applicable to many economically important, heterozygous, perennial crop species that are more difficult to regenerate.
Collapse
Affiliation(s)
- Longzheng Chen
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
| | - Lorenzo Katin-Grazzini
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
| | - Jing Ding
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xianbin Gu
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
| | - Yanjun Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
| | - Tingting Gu
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Ren Wang
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
| | - Xinchun Lin
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Zhejiang Hangzhou, China
| | - Ziniu Deng
- College of Horticulture, Hunan Agricultural University, Hunan Changsha, China
| | - Richard J. McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
| | - Frederick G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL USA
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093 USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT USA
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
26
|
Ballester AR, Norelli J, Burchard E, Abdelfattah A, Levin E, González-Candelas L, Droby S, Wisniewski M. Transcriptomic Response of Resistant (PI613981- Malus sieversii) and Susceptible ("Royal Gala") Genotypes of Apple to Blue Mold ( Penicillium expansum) Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:1981. [PMID: 29201037 PMCID: PMC5696741 DOI: 10.3389/fpls.2017.01981] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/02/2017] [Indexed: 05/18/2023]
Abstract
Malus sieversii from Central Asia is a progenitor of the modern domesticated apple (Malus × domestica). Several accessions of M. sieversii are highly resistant to the postharvest pathogen Penicillium expansum. A previous study identified the qM-Pe3.1 QTL on LG3 for resistance to P. expansum in the mapping population GMAL4593, developed using the resistant accession, M. sieversii -PI613981, and the susceptible cultivar "Royal Gala" (RG) (M. domestica), as parents. The goal of the present study was to characterize the transcriptomic response of susceptible RG and resistant PI613981 apple fruit to wounding and inoculation with P. expansum using RNA-Seq. Transcriptomic analyses 0-48 h post inoculation suggest a higher basal level of resistance and a more rapid and intense defense response to wounding and wounding plus inoculation with P. expansum in M. sieversii -PI613981 than in RG. Functional analysis showed that ethylene-related genes and genes involved in "jasmonate" and "MYB-domain transcription factor family" were over-represented in the resistant genotype. It is suggested that the more rapid response in the resistant genotype (Malus sieversii-PI613981) plays a major role in the resistance response. At least twenty DEGs were mapped to the qM-Pe3.1 QTL (M × d v.1: 26,848,396-28,424,055) on LG3, and represent potential candidate genes responsible for the observed resistance QTL in M. sieversii-PI613981. RT-qPCR of several of these genes was used to validate the RNA-Seq data and to confirm their higher expression in MS0.
Collapse
Affiliation(s)
- Ana-Rosa Ballester
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Valencia, Spain
- *Correspondence: Ana-Rosa Ballester
| | - John Norelli
- United States Department of Agriculture–Agricultural Research Service, Kearneysville, WV, United States
| | - Erik Burchard
- United States Department of Agriculture–Agricultural Research Service, Kearneysville, WV, United States
| | - Ahmed Abdelfattah
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Elena Levin
- Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | | | - Samir Droby
- Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | - Michael Wisniewski
- United States Department of Agriculture–Agricultural Research Service, Kearneysville, WV, United States
- Michael Wisniewski
| |
Collapse
|