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Feldmann MJ, Pincot DDA, Vachev MV, Famula RA, Cole GS, Knapp SJ. Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry. THE PLANT GENOME 2024; 17:e20405. [PMID: 37961831 DOI: 10.1002/tpg2.20405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × $\times$ ananassa), has caused economic losses for nearly a century. This disease is caused by the soil-borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW-resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids (n = 564 $n = 564$ ) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids (n = 386 $n = 386$ ), genomic prediction accuracies of 0.47-0.48 were achieved and were predicted to explain 70%-75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations.
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Affiliation(s)
- Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Mishi V Vachev
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, Davis, California, USA
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2
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Yang Y, Zhang J, Li M, Ning Y, Tao Y, Shi S, Dark A, Song Z. Heterologous Expression of a Ferritin Homologue Gene PpFer1 from Prunus persica Enhances Plant Tolerance to Iron Toxicity and H 2O 2 Stress in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:4093. [PMID: 38140420 PMCID: PMC10747543 DOI: 10.3390/plants12244093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/24/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
In plants, ferritin proteins play an important role in iron (Fe) storage which contributes to plant growth and development. However, the biological functions of ferritins in fruit trees are essentially unknown. In this study, three Ferritin genes were isolated from 'Zhentong No. 3' peach, which were named PpFer1-PpFer3. The expression levels of these genes were different in distinct tissues/organs. Notably, PpFer1 was the most abundantly expressed Ferritin family gene in all tested tissues of 'Zhentong No. 3' peach; its expression levels were significantly enhanced throughout the entire peach seedling under Fe toxicity and H2O2 stress, particularly in the leaves. In addition, over-expression of PpFer1 was effective in rescuing the retarded growth of Arabidopsis fer1-2 knockout mutant, embodied in enhanced fresh weight, primary root length, lateral root numbers, total root length, total leaf chlorophyll, stomatal conductance (Gs), net photosynthetic rate (Pn), transpiration rate, and tissue Fe concentration. This study provides insights into understanding the molecular mechanisms of Fe storage and sequestration in perennial fruit trees.
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Affiliation(s)
- Yong Yang
- Zhenjiang Academy of Agricultural Sciences, Zhenjiang Institute of Agricultural Sciences in Hilly Areas of Jiangsu Province, Zhenjiang 212400, China;
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, No. 186 Hongqizhong Road, Yantai 264025, China; (M.L.); (Y.T.)
| | - Jinjin Zhang
- Faculty of Modern Agriculture, Linyi Vocational University of Science and Technology, No. 1 Macau Road, Linyi 276000, China;
| | - Mengyuan Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, No. 186 Hongqizhong Road, Yantai 264025, China; (M.L.); (Y.T.)
| | - Youzheng Ning
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, UK; (Y.N.); (S.S.); (A.D.)
| | - Yifei Tao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, No. 186 Hongqizhong Road, Yantai 264025, China; (M.L.); (Y.T.)
| | - Shengpeng Shi
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, UK; (Y.N.); (S.S.); (A.D.)
- Wolfson College, University of Cambridge, Cambridge CB3 9BB, UK
| | - Adeeba Dark
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, UK; (Y.N.); (S.S.); (A.D.)
| | - Zhizhong Song
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, No. 186 Hongqizhong Road, Yantai 264025, China; (M.L.); (Y.T.)
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, UK; (Y.N.); (S.S.); (A.D.)
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Abdullah-Zawawi MR, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein ZA. Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom. PLANTS (BASEL, SWITZERLAND) 2022; 11:2614. [PMID: 36235479 PMCID: PMC9573505 DOI: 10.3390/plants11192614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
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Affiliation(s)
- Muhammad-Redha Abdullah-Zawawi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Nisha Govender
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Sarahani Harun
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Zamri Zainal
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
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4
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Shafi KM, Sowdhamini R. Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. BMC Genomics 2022; 23:516. [PMID: 35842574 PMCID: PMC9288012 DOI: 10.1186/s12864-022-08751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members. Results Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species. Conclusions Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08751-x.
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Affiliation(s)
- K Mohamed Shafi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,The University of Trans-Disciplinary Health Sciences & Technology (TDU), Yelahanka, Bangalore, Karnataka, 560064, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India. .,Molecular BIophysics Unit, Indian Institute of Science, 560012, Bangalore, India.
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Vignati E, Lipska M, Dunwell JM, Caccamo M, Simkin AJ. Fruit Development in Sweet Cherry. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11121531. [PMID: 35736682 PMCID: PMC9227597 DOI: 10.3390/plants11121531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 05/19/2023]
Abstract
Fruits are an important source of vitamins, minerals and nutrients in the human diet. They also contain several compounds of nutraceutical importance that have significant antioxidant and anti-inflammatory roles, which can protect the consumer from diseases, such as cancer, and cardiovascular disease as well as having roles in reducing the build-up of LDL-cholesterol in blood plasma and generally reduce the risks of disease and age-related decline in health. Cherries contain high concentrations of bioactive compounds and minerals, including calcium, phosphorous, potassium and magnesium, and it is, therefore, unsurprising that cherry consumption has a positive impact on health. This review highlights the development of sweet cherry fruit, the health benefits of cherry consumption, and the options for increasing consumer acceptance and consumption.
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Affiliation(s)
- Edoardo Vignati
- NIAB, New Road, East Malling ME19 6BJ, UK; (E.V.); (M.L.)
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, UK;
| | - Marzena Lipska
- NIAB, New Road, East Malling ME19 6BJ, UK; (E.V.); (M.L.)
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, UK;
| | - Mario Caccamo
- NIAB, Cambridge Crop Research, Lawrence Weaver Road, Cambridge CB3 0LE, UK;
| | - Andrew J. Simkin
- NIAB, New Road, East Malling ME19 6BJ, UK; (E.V.); (M.L.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence:
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Pavan S, Delvento C, Mazzeo R, Ricciardi F, Losciale P, Gaeta L, D'Agostino N, Taranto F, Sánchez-Pérez R, Ricciardi L, Lotti C. Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight. HORTICULTURE RESEARCH 2021; 8:15. [PMID: 33423037 PMCID: PMC7797004 DOI: 10.1038/s41438-020-00447-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 05/04/2023]
Abstract
Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy.
- Institute of Biomedical Technologies, National Research Council (CNR), Via Amendola 122/D, Bari, 70126, Italy.
| | - Chiara Delvento
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Rosa Mazzeo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy
| | - Francesca Ricciardi
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy
| | - Pasquale Losciale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Liliana Gaeta
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment (CREA-AA), Bari, 70125, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, 80055, Italy
| | | | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy.
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7
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Cloning and Functional Determination of Ammonium Transporter PpeAMT3;4 in Peach. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2147367. [PMID: 33344631 PMCID: PMC7732375 DOI: 10.1155/2020/2147367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 01/29/2023]
Abstract
Ammonium (NH4+) plays key roles in plant growth, development, fruit quality, and yield. In plants, NH4+ uptake and transport are facilitated by NH4+ transporters (AMT). However, molecular mechanisms and physiological functions of type-II AMT (AMT2) transporters in fruit trees are still unclear, especially in peach. In this study, we cloned and characterized an AMT2 family gene from peach, PpeAMT3;4, and determined its function in yeast mutant. Expression analysis showed that PpeAMT3;4 was majorly expressed in peach roots and significantly decreased by NH4+ excess but had no response to NH4+ deficiency. Functional determination and 15nitrogen-labeled NH4+ uptake assay in yeast cells implied that PpeAMT3;4 was a typical high-affinity transporter, with a Km value of 86.3 μM, that can uptake external NH4+ in yeast cells. This study provides gene resources to uncover the biological function of AMT2 transporters and reveals molecular basis for NH4+ uptake and nitrogen (N) nutrition mechanisms in fruit trees.
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Gong Y, Kang NK, Kim YU, Wang Z, Wei L, Xin Y, Shen C, Wang Q, You W, Lim JM, Jeong SW, Park YI, Oh HM, Pan K, Poliner E, Yang G, Li-Beisson Y, Li Y, Hu Q, Poetsch A, Farre EM, Chang YK, Jeong WJ, Jeong BR, Xu J. The NanDeSyn database for Nannochloropsis systems and synthetic biology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1736-1745. [PMID: 33103271 DOI: 10.1111/tpj.15025] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.
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Affiliation(s)
- Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Nam K Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Young U Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Chen Shen
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wuxin You
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Suk-Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Kehou Pan
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Laboratory of Applied Microalgae, College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Eric Poliner
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Guanpin Yang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China
- Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Yonghua Li-Beisson
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, University of Maryland, Baltimore County, Baltimore, MD, 21202, USA
| | - Qiang Hu
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ansgar Poetsch
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Eva M Farre
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Yong K Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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9
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Rawandoozi ZJ, Hartmann TP, Carpenedo S, Gasic K, da Silva Linge C, Cai L, Van de Weg E, Byrne DH. Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach. BMC Genomics 2020; 21:522. [PMID: 32727362 PMCID: PMC7392839 DOI: 10.1186/s12864-020-06927-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/20/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time. RESULTS Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles. CONCLUSIONS A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.
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Affiliation(s)
- Zena J. Rawandoozi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Timothy P. Hartmann
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Silvia Carpenedo
- Embrapa Clima Temperado, BR-392, km 78, Cx. Postal 403, Pelotas, Rio Grande do Sul 96010-971 Brazil
| | - Ksenija Gasic
- Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634 USA
| | - Cassia da Silva Linge
- Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634 USA
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Eric Van de Weg
- Department of Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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10
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Characterization and Expression of KT/HAK/KUP Transporter Family Genes in Willow under Potassium Deficiency, Drought, and Salt Stresses. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2690760. [PMID: 32596286 PMCID: PMC7303730 DOI: 10.1155/2020/2690760] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) transporters dominate K+ uptake, transport, and allocation that play a pivotal role in mineral homeostasis and plant adaptation to adverse abiotic stresses. However, molecular mechanisms towards K+ nutrition in forest trees are extremely rare, especially in willow. In this study, we identified 22 KT/HAK/KUP transporter genes in purple osier willow (designated as SpuHAK1 to SpuHAK22) and examined their expression under K+ deficiency, drought, and salt stress conditions. Both transcriptomic and quantitative real-time PCR (qRT-PCR) analyses demonstrated that SpuHAKs were predominantly expressed in stems, and the expression levels of SpuHAK1, SpuHAK2, SpuHAK3, SpuHAK7, and SpuHAK8 were higher at the whole plant level, whereas SpuHAK9, SpuHAK11, SpuHAK20, and SpuHAK22 were hardly detected in tested tissues. In addition, both K+ deficiency and salt stress decreased the tissue K+ content, while drought increased the tissue K+ content in purple osier plant. Moreover, SpuHAK genes were differentially responsive to K+ deficiency, drought, and salt stresses in roots. K+ deficiency and salt stress mainly enhanced the expression level of responsive SpuHAK genes. Fifteen putative cis-acting regulatory elements, including the stress response, hormone response, circadian regulation, and nutrition and development, were identified in the promoter region of SpuHAK genes. Our findings provide a foundation for further functional characterization of KT/HAK/KUP transporters in forest trees and may be useful for breeding willow rootstocks that utilize potassium more efficiently.
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11
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Foliar Spraying with Compound Amino Acid-Iron Fertilizer Increases Leaf Fresh Weight, Photosynthesis, and Fe-S Cluster Gene Expression in Peach ( Prunus persica (L.) Batsch). BIOMED RESEARCH INTERNATIONAL 2020; 2020:2854795. [PMID: 32596289 PMCID: PMC7273464 DOI: 10.1155/2020/2854795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/27/2020] [Accepted: 05/04/2020] [Indexed: 01/12/2023]
Abstract
As one of the most important micronutrients, iron (Fe) plays a critical role in various metabolic processes during plant growth and development. However, the molecular mechanisms towards Fe metabolism and nutrition in fruit trees are largely unknown. In this study, we examined the effects of amino acid-Fe compound fertilizer spraying on leaf development in peach (Prunus persica (L.) Batsch) at different developmental stages. Foliar spraying with amino acid-Fe compound fertilizer did not cause any significant changes in leaf morphology but remarkably increased leaf fresh weights. Fe concentration, photosynthetic parameter, and Fe-S protein analyses revealed that Fe accumulation, total chlorophyll content, net photosynthetic rate (P N), and stomatal conductance (g s), as well as nitrite reductase (NIR) and succinate dehydrogenase (SDH) activities, were significantly higher in the leaves sprayed with amino acid-Fe compound fertilizer than in the control leaves sprayed with distilled water. Further quantitative real-time PCR (qRT-PCR) analyses demonstrated that Fe-S cluster biosynthesis genes were differentially expressed in the leaves at different developmental stages. Foliar spraying with amino acid-Fe compound fertilizer significantly increased the expression of the most tested Fe-S cluster biosynthesis genes. Our findings provide new insights into the understanding of effects of Fe fertilization application on leaf development in perennial woody fruit trees.
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12
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Xie SQ, Xing JF, Zhang XM, Liu ZY, Luan MW, Zhu J, Ling P, Xiao CL, Song XQ, Zheng J, Chen Y. N 6-Methyladenine DNA Modification in the Woodland Strawberry ( Fragaria vesca) Genome Reveals a Positive Relationship With Gene Transcription. Front Genet 2020; 10:1288. [PMID: 31998359 PMCID: PMC6967393 DOI: 10.3389/fgene.2019.01288] [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: 04/28/2019] [Accepted: 11/22/2019] [Indexed: 01/24/2023] Open
Abstract
N 6-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, where it plays important roles in gene regulation and epigenetic memory maintenance. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in woodland strawberry (Fragaria vesca) remain largely unknown. Here, we examined the 6mA landscape in the F. vesca genome by adopting single-molecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the woodland strawberry genome. The pattern of 6mA distribution in the long non-coding RNA was significantly different from that in protein-coding genes. The 6mA modification influenced the gene transcription and was positively associated with gene expression, which was validated by computational and experimental analyses. Our study provides new insights into the DNA methylation in F. vesca.
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Affiliation(s)
- Shang-Qian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Jian-Feng Xing
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Ming Zhang
- Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen, China
| | - Zhao-Yu Liu
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Mei-Wei Luan
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Jie Zhu
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Peng Ling
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xi-Qiang Song
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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13
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Zhang S, Ma M, Zhang H, Zhang S, Qian M, Zhang Z, Luo W, Fan J, Liu Z, Wang L. Genome-wide analysis of polygalacturonase gene family from pear genome and identification of the member involved in pear softening. BMC PLANT BIOLOGY 2019; 19:587. [PMID: 31881836 PMCID: PMC6935220 DOI: 10.1186/s12870-019-2168-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/27/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Polygalacturonase (PG), as an important hydrolase participating in the degradation of pectin, plays an important role in softening process of fruit. However, information on PG gene family in pear genome and the specific member involved in fruit softening is still rudimentary. RESULTS In this study, a total of 61 PG genes, which could be divided into six subclasses, were identified from the pear genome with diverse chromosome locations, gene structures, motifs and cis-acting elements. Most PbrPGs were derived from WGD/segmental duplication blocks, and purifying selection was the main driving force for their expansion. The expression profiles of PbrPGs in pear were tissue/development-stage/cultivar-dependent. During 'Housui' pear storage, associated with the reduction of firmness was the accumulation of PG activity. Totally, 28 PbrPGs were expressed during fruit storage, which could be classified into five categories based on different expression patterns; most demonstrated an increased trend. Of these, PbrPG6 were proposed to account for pear softening in combination of the phylogenetic and correlation analysis among firmness, PG activity and PbrPGs. By constructing the silencing vector, a higher firmness was observed in PbrPG6-silenced fruit when compared with that of the control (empty vector). In a further study, we found that the expression of PbrPG6 was regulated by postharvest 1-MCP/ethrel treatment, and several PbrERFs might function in this process. CONCLUSIONS We identified 61 PbrPG genes from pear genome; of these, PbrPG6 was involved in fruit softening process; furthermore, the expression of PbrPG6 might be under the control of PbrERF. This study provides a foundation for future work aimed at elucidating the molecular mechanism underlying pear softening.
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Affiliation(s)
- Suling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Min Ma
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Huping Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ming Qian
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhen Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Weiqi Luo
- USDA, ARS, U.S. Horticultural Research Laboratory, 2001 S. Rock Road, Fort Pierce, FL, 34945, USA
| | - Jinbu Fan
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhiqiang Liu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Libin Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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14
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Wang M, Ogé L, Voisine L, Perez-Garcia MD, Jeauffre J, Hibrand Saint-Oyant L, Grappin P, Hamama L, Sakr S. Posttranscriptional Regulation of RhBRC1 ( Rosa hybrida BRANCHED1) in Response to Sugars is Mediated via its Own 3' Untranslated Region, with a Potential Role of RhPUF4 (Pumilio RNA-Binding Protein Family). Int J Mol Sci 2019; 20:ijms20153808. [PMID: 31382685 PMCID: PMC6695800 DOI: 10.3390/ijms20153808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/07/2023] Open
Abstract
The shoot branching pattern is a determining phenotypic trait throughout plant development. During shoot branching, BRANCHED1 (BRC1) plays a master regulator role in bud outgrowth, and its transcript levels are regulated by various exogenous and endogenous factors. RhBRC1 (the homologous gene of BRC1 in Rosa hybrida) is a main branching regulator whose posttranscriptional regulation in response to sugar was investigated through its 3'UTR. Transformed Rosa calluses containing a construction composed of the CaMV35S promoter, the green fluorescent protein (GFP) reporter gene, and the 3'UTR of RhBRC1 (P35S:GFP::3'UTRRhBRC1) were obtained and treated with various combinations of sugars and with sugar metabolism effectors. The results showed a major role of the 3'UTR of RhBRC1 in response to sugars, involving glycolysis/the tricarboxylic acid cycle (TCA) and the oxidative pentose phosphate pathway (OPPP). In Rosa vegetative buds, sequence analysis of the RhBRC1 3'UTR identified six binding motifs specific to the Pumilio/FBF RNA-binding protein family (PUF) and probably involved in posttranscriptional regulation. RhPUF4 was highly expressed in the buds of decapitated plants and in response to sugar availability in in-vitro-cultured buds. RhPUF4 was found to be close to AtPUM2, which encodes an Arabidopsis PUF protein. In addition, sugar-dependent upregulation of RhPUF4 was also found in Rosa calluses. RhPUF4 expression was especially dependent on the OPPP, supporting its role in OPPP-dependent posttranscriptional regulation of RhBRC1. These findings indicate that the 3'UTR sequence could be an important target in the molecular regulatory network of RhBRC1 and pave the way for investigating new aspects of RhBRC1 regulation.
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Affiliation(s)
- Ming Wang
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Laurent Ogé
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Linda Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | | | - Julien Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | | | - Philippe Grappin
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Latifa Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Soulaiman Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France.
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15
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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16
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Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, Humann J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Peace C, Olmstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res 2019; 47:D1137-D1145. [PMID: 30357347 PMCID: PMC6324069 DOI: 10.1093/nar/gky1000] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
Abstract
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634-0310, USA
| | - Kristin Scott
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Morgan Frank
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Sushan Ru
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, USA
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Kate Evans
- Department of Horticulture, Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA 98801, USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Mercy Olmstead
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Lisa W DeVetter
- Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273, USA
| | - James McFerson
- Department of Horticulture, Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA 98801, USA
| | - Michael Coe
- Cedar Lake Research Group, LLC, Portland, OR 97293, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Albert G Abbott
- Forest Health Research and Extension Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
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17
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Buti M, Moretto M, Barghini E, Mascagni F, Natali L, Brilli M, Lomsadze A, Sonego P, Giongo L, Alonge M, Velasco R, Varotto C, Šurbanovski N, Borodovsky M, Ward JA, Engelen K, Cavallini A, Cestaro A, Sargent DJ. The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). Gigascience 2018; 7:1-14. [PMID: 29659812 PMCID: PMC5893959 DOI: 10.1093/gigascience/giy010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 02/07/2018] [Indexed: 11/20/2022] Open
Abstract
Background The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca. Findings In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced. Conclusions Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca.The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.
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Affiliation(s)
- Matteo Buti
- 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 for the Development and Improvement of Agri-Food Resources (BIOGEST-SITEIA) University of Modena and Reggio Emilia, P.le Europa 1, 42124 Reggio nell'Emilia (RE), Italy
| | - Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Elena Barghini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Matteo Brilli
- 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 Agronomy, Food, Natural Resources, Animals and Environment, University of Padova Agripolis, V.le dell'Università 16, 35020 Legnaro (PD), Italy.,Dipartimento di Bioscienze e Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, Georgia
| | - Paolo Sonego
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Lara Giongo
- 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
| | - Michael Alonge
- Driscoll's Strawberry Associates, Cassin Ranch, 121 Silliman Drive, Watsonville, California
| | - Riccardo Velasco
- 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
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Nada Šurbanovski
- 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
| | - Mark Borodovsky
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova Agripolis, V.le dell'Università 16, 35020 Legnaro (PD), Italy
| | - Judson A Ward
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, Georgia
| | - Kristof Engelen
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Alessandro Cestaro
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Daniel James Sargent
- 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.,Driscoll's Genetics Limited, East Malling Enterprise Centre, New Road, East Malling, Kent ME19 6BJ, UK
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18
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da Silva Linge C, Antanaviciute L, Abdelghafar A, Arús P, Bassi D, Rossini L, Ficklin S, Gasic K. High-density multi-population consensus genetic linkage map for peach. PLoS One 2018; 13:e0207724. [PMID: 30462743 PMCID: PMC6248993 DOI: 10.1371/journal.pone.0207724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/04/2018] [Indexed: 11/19/2022] Open
Abstract
Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.
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Affiliation(s)
- Cassia da Silva Linge
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Laima Antanaviciute
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Asma Abdelghafar
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas (CSIC)-IRTA–Universitat Autònoma de Barcelona (UAB)–University of Barcelona (UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Daniele Bassi
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Stephen Ficklin
- Washington State University, Department of Horticulture, Pullman, WA, United States of America
| | - Ksenija Gasic
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
- * E-mail:
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19
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Shu LJ, Liao JY, Lin NC, Chung CL. Identification of a strawberry NPR-like gene involved in negative regulation of the salicylic acid-mediated defense pathway. PLoS One 2018; 13:e0205790. [PMID: 30312354 PMCID: PMC6185849 DOI: 10.1371/journal.pone.0205790] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022] Open
Abstract
Hormonal modulation plays a central role in triggering various resistant responses to biotic and abiotic stresses in plants. In cultivated strawberry (Fragaria x ananassa), the salicylic acid (SA)-dependent defense pathway has been associated with resistance to Colletotrichum spp. and the other pathogens. To better understand the SA-mediated defense mechanisms in strawberry, we analyzed two strawberry cultivars treated with SA for their resistance to anthracnose and gene expression profiles at 6, 12, 24, and 48 hr post-treatment. Strawberry genes related to SA biosynthesis, perception, and signaling were identified from SA-responsive transcriptomes of the two cultivars, and the induction of 17 candidate genes upon SA treatment was confirmed by qRT-PCR. Given the pivotal role of the non-expressor of pathogenesis-related (NPR) family in controlling the SA-mediated defense signaling pathway, we then analyzed NPR orthologous genes in strawberry. From the expression profile, FaNPRL-1 [ortholog of FvNPRL-1 (gene20070 in F. vesca)] was identified as an NPR-like gene significantly induced after SA treatment in both cultivars. With a conserved BTB/POZ domain, ankyrin repeat domain, and nuclear localization signal, FvNPRL-1 was found phylogenetically closer to NPR3/NPR4 than NPR1 in Arabidopsis. Ectopic expression of FvNPRL-1 in the Arabidopsis thaliana wild type suppressed the SA-mediated PR1 expression and the resistance to Pseudomonas syringae pv. tomato DC3000. Transient expression of FvNPRL-1 fused with green fluorescent protein in Arabidopsis protoplasts showed that SA affected nuclear translocation of FvNPRL-1. FvNPRL-1 likely functions similar to Arabidopsis NPR3/NPR4 as a negative regulator of the SA-mediated defense.
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Affiliation(s)
- Lin-Jie Shu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Jui-Yu Liao
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Nai-Chun Lin
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
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20
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Yagi M. Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants. BREEDING SCIENCE 2018; 68:62-70. [PMID: 29681748 PMCID: PMC5903975 DOI: 10.1270/jsbbs.17080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/19/2017] [Indexed: 05/21/2023]
Abstract
Genome information is useful for functional analysis of genes, comparative genomic analysis, breeding of new varieties by marker-assisted selection, and map-based gene isolation. Genome-related research in ornamentals plants has been relatively slow to develop because of their heterozygosity or polyploidy. Advances in analytical instruments, such as next-generation sequencers and information processing technologies have revolutionized biology, and have been applied in a large number and variety of species, including ornamental plants. Recently, high-quality whole genome sequences have been reported in plant genetics and physiology studies of model ornamentals, such as those in genus Petunia and Japanese morning glory (Ipomoea nil). In this review, whole genome sequencing and construction of high-density genetic linkage maps based on SNP markers of ornamentals will be discussed. The databases that store this information for ornamentals are also described.
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21
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Shirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Res 2017; 24:499-508. [PMID: 28541388 PMCID: PMC5737369 DOI: 10.1093/dnares/dsx020] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site–associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kanji Isuzugawa
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Mitsunobu Ikenaga
- Central Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan
| | - Yutaro Saito
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8605, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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22
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Sun J, Li L, Wang P, Zhang S, Wu J. Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes. BMC Genomics 2017; 18:763. [PMID: 29017442 PMCID: PMC5635495 DOI: 10.1186/s12864-017-4155-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively. RESULTS All LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%. CONCLUSIONS Our results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.
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Affiliation(s)
- Jiangmei Sun
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juyou Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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23
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Phylogenetic analysis of IDD gene family and characterization of its expression in response to flower induction in Malus. Mol Genet Genomics 2017; 292:755-771. [DOI: 10.1007/s00438-017-1306-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 03/02/2017] [Indexed: 11/27/2022]
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24
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Lee J. Rosaceae products: Anthocyanin quality and comparisons between dietary supplements and foods. NFS JOURNAL 2016. [DOI: 10.1016/j.nfs.2016.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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25
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Genomics and expression analysis of DHHC-cysteine-rich domain S-acyl transferase protein family in apple. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Ong Q, Nguyen P, Thao NP, Le L. Bioinformatics Approach in Plant Genomic Research. Curr Genomics 2016; 17:368-78. [PMID: 27499685 PMCID: PMC4955030 DOI: 10.2174/1389202917666160331202956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/11/2015] [Accepted: 09/18/2015] [Indexed: 11/22/2022] Open
Abstract
The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity.
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Affiliation(s)
- Quang Ong
- Plant Abiotic Stress Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuc Nguyen
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
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Identification of Known and Novel microRNAs and Their Targets in Peach (Prunus persica) Fruit by High-Throughput Sequencing. PLoS One 2016; 11:e0159253. [PMID: 27466805 PMCID: PMC4965121 DOI: 10.1371/journal.pone.0159253] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 06/29/2016] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of non-coding RNAs that have functions in post-transcriptional gene regulation in plants. Although the most important economic component of peach trees (Prunus persica) is the fruit, not much is known about miRNAs in this organ. In this study, miRNAs and their targets were identified and characterized from libraries of small RNAs of peach fruit through Solexa based-sequencing and bioinformatics approaches. A total of 557 known peach miRNAs belonging to 34 miRNA families were identified, and some of these miRNAs were found to be highly conserved in at least four other plant species. Using the most current criteria for miRNA annotation, 275 putative novel miRNAs were predicted, and the sequencing frequencies of these novel miRNAs were less than those of the conserved miRNAs. In total, 3959 and 1614 target genes for 349 known and 193 novel miRNAs, respectively, were predicted with the criteria that a single target gene can be targeted by different miRNAs and that a single miRNA can also have a large number of target genes. Three targets were even found to be targeted by 13 novel miRNAs that contained the same complete miRNA sequence at different locations and had different scaffolds. The proteins predicted to be targeted by the miRNAs identified in this study encompass a wide range of transcription factors and are involved in many biological processes and pathways, including development, metabolism, stress responses and signal transduction. A total of 115 and 101 target genes were identified to be cleaved by 60 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequences from the 5’ to the 3’ end. Thirty conserved miRNAs and 19 novel miRNAs exhibited differential expression profiles in the peach, and the expression patterns of some miRNAs appeared to be tissue- or developmental stage-specific. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.
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28
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Genero M, Gismondi M, Monti LL, Gabilondo J, Budde CO, Andreo CS, Lara MV, Drincovich MF, Bustamante CA. Cell wall-related genes studies on peach cultivars with differential susceptibility to woolliness: looking for candidates as indicators of chilling tolerance. PLANT CELL REPORTS 2016; 35:1235-46. [PMID: 26905727 DOI: 10.1007/s00299-016-1956-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/15/2016] [Indexed: 05/07/2023]
Abstract
The results obtained indicate that a β-xylosidase gene may act as good indicator of chilling tolerance and provide new insights into the complex issue of peach fruit woolliness. The storage of peaches at low temperatures for prolonged periods can induce a form of chilling injury (CI) called woolliness, characterized by a lack of juiciness and a mealy texture. As this disorder has been associated with abnormal cell wall dismantling, the levels of 12 transcripts encoding proteins involved in cell wall metabolism were analysed in cultivars with contrasting susceptibility to this disorder selected from five melting flesh peach cultivars. The resistant ('Springlady') and susceptible ('Flordaking') cultivars displayed differences in the level of expression of some of the selected genes during fruit softening and in woolly versus non-woolly fruits. From these genes, the level of expression of PpXyl, which encodes for a putative β-xylosidase, was the one that presented the highest correlation (negative) with the susceptibility to woolliness. PpXyl expression was also analysed in a cultivar ('Rojo 2') with intermediate susceptibility to woolliness, reinforcing the conclusion about the correlation of PpXyl expression to the presence of woolliness symptom. Moreover, the level of expression of PpXyl correlated to protein level detected by Western blot. Analyses of the promoter region of the PpXyl gene (1637 bp) isolated from the three cultivars showed no differences suggesting that cis-elements from other regions of the genome and/or trans elements could be responsible of the differential PpXyl expression patterns. Overall, the results obtained indicate that PpXyl may act as a good indicator of woolliness tolerance and that the regulation of expression of this gene in different cultivars does not depend on sequences upstream the coding sequence.
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Affiliation(s)
- Melisa Genero
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Mauro Gismondi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Laura L Monti
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Julieta Gabilondo
- Estación Experimental Agropecuaria San Pedro, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta Nacional nº 9 km 170, San Pedro, Argentina
| | - Claudio O Budde
- Estación Experimental Agropecuaria San Pedro, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta Nacional nº 9 km 170, San Pedro, Argentina
| | - Carlos S Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María V Lara
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia A Bustamante
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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Barad S, Sela N, Kumar D, Kumar-Dubey A, Glam-Matana N, Sherman A, Prusky D. Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by Penicillium expansum. BMC Genomics 2016; 17:330. [PMID: 27146851 PMCID: PMC4855365 DOI: 10.1186/s12864-016-2665-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/26/2016] [Indexed: 11/26/2022] Open
Abstract
Background Penicillium expansum is a destructive phytopathogen that causes decay in deciduous fruits during postharvest handling and storage. During colonization the fungus secretes D-gluconic acid (GLA), which modulates environmental pH and regulates mycotoxin accumulation in colonized tissue. Till now no transcriptomic analysis has addressed the specific contribution of the pathogen's pH regulation to the P. expansum colonization process. For this purpose total RNA from the leading edge of P. expansum-colonized apple tissue of cv. 'Golden Delicious' and from fungal cultures grown under pH 4 or 7 were sequenced and their gene expression patterns were compared. Results We present a large-scale analysis of the transcriptome data of P. expansum and apple response to fungal colonization. The fungal analysis revealed nine different clusters of gene expression patterns that were divided among three major groups in which the colonized tissue showed, respectively: (i) differing transcript expression patterns between mycelial growth at pH 4 and pH 7; (ii) similar transcript expression patterns of mycelial growth at pH 4; and (iii) similar transcript expression patterns of mycelial growth at pH 7. Each group was functionally characterized in order to decipher genes that are important for pH regulation and also for colonization of apple fruits by Penicillium. Furthermore, comparison of gene expression of healthy apple tissue with that of colonized tissue showed that differentially expressed genes revealed up-regulation of the jasmonic acid and mevalonate pathways, and also down-regulation of the glycogen and starch biosynthesis pathways. Conclusions Overall, we identified important genes and functionalities of P. expansum that were controlled by the environmental pH. Differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions (pH, in vitro or in vivo) to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Comparison between the activation of the colonized host's gene responses by alkalizing Colletotrichum gloeosporioides and acidifying P. expansum pathogens indicated similar gene response patterns, but stronger responses to P. expansum, suggesting the importance of acidification by P. expansum as a factor in its increased aggressiveness. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2665-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiri Barad
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.,Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan, 50250, Israel
| | - Dilip Kumar
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel
| | - Amit Kumar-Dubey
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel
| | - Nofar Glam-Matana
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.,Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Amir Sherman
- Genomics Unit, ARO, the Volcani Center, Bet Dagan, 50250, Israel
| | - Dov Prusky
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.
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30
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Harrison N, Harrison RJ, Barber-Perez N, Cascant-Lopez E, Cobo-Medina M, Lipska M, Conde-Ruíz R, Brain P, Gregory PJ, Fernández-Fernández F. A new three-locus model for rootstock-induced dwarfing in apple revealed by genetic mapping of root bark percentage. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1871-81. [PMID: 26826217 PMCID: PMC4783367 DOI: 10.1093/jxb/erw001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Rootstock-induced dwarfing of apple scions revolutionized global apple production during the twentieth century, leading to the development of modern intensive orchards. A high root bark percentage (the percentage of the whole root area constituted by root cortex) has previously been associated with rootstock-induced dwarfing in apple. In this study, the root bark percentage was measured in a full-sib family of ungrafted apple rootstocks and found to be under the control of three loci. Two quantitative trait loci (QTLs) for root bark percentage were found to co-localize to the same genomic regions on chromosome 5 and chromosome 11 previously identified as controlling dwarfing, Dw1 and Dw2, respectively. A third QTL was identified on chromosome 13 in a region that has not been previously associated with dwarfing. The development of closely linked sequence-tagged site markers improved the resolution of allelic classes, thereby allowing the detection of dominance and epistatic interactions between loci, with high root bark percentage only occurring in specific allelic combinations. In addition, we report a significant negative correlation between root bark percentage and stem diameter (an indicator of tree vigour), measured on a clonally propagated grafted subset of the mapping population. The demonstrated link between root bark percentage and rootstock-induced dwarfing of the scion leads us to propose a three-locus model that is able to explain levels of dwarfing from the dwarf 'M.27' to the semi-invigorating rootstock 'M.116'. Moreover, we suggest that the QTL on chromosome 13 (Rb3) might be analogous to a third dwarfing QTL, Dw3, which has not previously been identified.
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Affiliation(s)
- Nicola Harrison
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK Centre for Food Security, School of Agriculture, Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading RG6 6AR, UK
| | - Richard J Harrison
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK Centre for Food Security, School of Agriculture, Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading RG6 6AR, UK
| | | | - Emma Cascant-Lopez
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK Centre for Food Security, School of Agriculture, Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading RG6 6AR, UK
| | | | - Marzena Lipska
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | | | - Philip Brain
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - Peter J Gregory
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK Centre for Food Security, School of Agriculture, Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading RG6 6AR, UK
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Campoy JA, Lerigoleur-Balsemin E, Christmann H, Beauvieux R, Girollet N, Quero-García J, Dirlewanger E, Barreneche T. Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars. BMC PLANT BIOLOGY 2016; 16:49. [PMID: 26912051 PMCID: PMC4765145 DOI: 10.1186/s12870-016-0712-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/11/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry. RESULTS A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method. CONCLUSION The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.
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Affiliation(s)
- José Antonio Campoy
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Emilie Lerigoleur-Balsemin
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- Current address: CNRS, UMR 5602 GEODE, Géographie de l'environnement, F-31058, Toulouse, France.
| | - Hélène Christmann
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Rémi Beauvieux
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Nabil Girollet
- INRA, UAR 0415 SDAR, Services Déconcentrés d'Appui à la Recherche, F 33140, Villenave d'Ornon, France.
- Current address: INRA, ISVV, UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, F 33140, Villenave d'Ornon, France.
| | - José Quero-García
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Elisabeth Dirlewanger
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Teresa Barreneche
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
- University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
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Adal A, Demissie Z, Mahmoud S. EST-SSR Analysis and Cross-species Transferability Study in Lavandula. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T. Genomics-assisted breeding in fruit trees. BREEDING SCIENCE 2016; 66:100-15. [PMID: 27069395 PMCID: PMC4780794 DOI: 10.1270/jsbbs.66.100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 05/03/2023]
Abstract
Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.
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Affiliation(s)
- Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
- Corresponding author (e-mail: )
| | - Mai F. Minamikawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Motoyuki Ishimori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Takeshi Hayashi
- Agroinfomatics Division, NARO Agricultural Research Center (NARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
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Bushakra JM, Lewers KS, Staton ME, Zhebentyayeva T, Saski CA. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). BMC PLANT BIOLOGY 2015; 15:258. [PMID: 26499487 PMCID: PMC4620654 DOI: 10.1186/s12870-015-0629-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/28/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. METHODS Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs. Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. RESULTS To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. CONCLUSION This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.
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Affiliation(s)
- Jill M Bushakra
- USDA-ARS, National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR, 97333-2521, USA.
| | - Kim S Lewers
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705-2350, USA.
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 EJ Chapman Drive, 370 PBB, Knoxville, TN, 37996, USA.
| | - Tetyana Zhebentyayeva
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
| | - Christopher A Saski
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
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Adal AM, Demissie ZA, Mahmoud SS. Identification, validation and cross-species transferability of novel Lavandula EST-SSRs. PLANTA 2015; 241:987-1004. [PMID: 25534945 DOI: 10.1007/s00425-014-2226-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
We identified and characterized EST-SSRs with strong discrimination power against Lavandula angustifolia and Lavandula x intermedia . The markers also showed considerable cross-species transferability rate into six related Lavandula species. Lavenders (Lavandula) are important economical crops grown around the globe for essential oil production. In an attempt to develop genetic markers for these plants, we analyzed over 13,000 unigenes developed from L. angustifolia and L. x intermedia EST databases, and identified 3,459 simple sequence repeats (SSR), which were dominated by trinucleotides (41.2 %) and dinucleotides (31.45 %). Approximately, 19 % of the unigenes contained at least one SSR marker, over 60 % of which were localized in the UTRs. Only 252 EST-SSRs were 18 bp or longer from which 31 loci were validated, and 24 amplified discrete fragments with 85 % polymorphism in L. x intermedia and L. angustifolia. The average number of alleles in L. x intermedia and L. angustifolia were 3.42 and 3.71 per marker with average PIC values of 0.47 and 0.52, respectively. These values suggest a moderate to strong level of informativeness for the markers, with some loci producing unique fingerprints. The cross-species transferability rate of the markers ranges 50-100 % across eight species. The utility of these markers was assessed in eight Lavandula species and 15 L. angustifolia and L. x intermedia cultivars, and the dendrogram deduced from their similarity indexes successfully delineated the species into their respective sections and the cultivars into their respective species. These markers have potential for application in fingerprinting, diversity studies and marker-assisted breeding of Lavandula.
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Affiliation(s)
- Ayelign M Adal
- Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC, V1V 1V7, Canada
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Tecle IY, Edwards JD, Menda N, Egesi C, Rabbi IY, Kulakow P, Kawuki R, Jannink JL, Mueller LA. solGS: a web-based tool for genomic selection. BMC Bioinformatics 2014; 15:398. [PMID: 25495537 PMCID: PMC4269960 DOI: 10.1186/s12859-014-0398-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/26/2014] [Indexed: 11/18/2022] Open
Abstract
Background Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders. Results We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs. Conclusions solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0398-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isaak Y Tecle
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA.
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Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA. The Sol Genomics Network (SGN)--from genotype to phenotype to breeding. Nucleic Acids Res 2014; 43:D1036-41. [PMID: 25428362 PMCID: PMC4383978 DOI: 10.1093/nar/gku1195] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.
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Affiliation(s)
| | - Naama Menda
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Jeremy D Edwards
- Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
| | - Surya Saha
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Isaak Y Tecle
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | | | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA
| | | | - Anuradha Pujar
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Hartmut Foerster
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Aimin Yan
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA
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Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly. PLoS One 2014; 9:e109835. [PMID: 25330175 PMCID: PMC4199719 DOI: 10.1371/journal.pone.0109835] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/31/2014] [Indexed: 12/28/2022] Open
Abstract
Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.
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Gesell A, Yoshida K, Tran LT, Constabel CP. Characterization of an apple TT2-type R2R3 MYB transcription factor functionally similar to the poplar proanthocyanidin regulator PtMYB134. PLANTA 2014; 240:497-511. [PMID: 24923676 DOI: 10.1007/s00425-014-2098-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/19/2014] [Indexed: 05/06/2023]
Abstract
The apple MdMYB9 gene encodes a positive regulator of proanthocyanidin synthesis that activates anthocyanidin reductase promoters from apple and poplar via interaction with basic helix-loop-helix proteins. The regulation of proanthocyanidins (PAs, condensed tannins) is of great importance in food plants due to the many benefits of PAs in the human diet. Two candidate flavonoid MYB regulators, MdMYB9 and MdMYB11, were cloned from apple (Malus × domestica) based on their similarity to known MYB PA regulators. Transcript accumulation of both MdMYB9 and MdMYB11 was induced by high light and wounding, similar to the poplar (Populus spp) PA regulator PtMYB134. In transient activation assays with various basic helix-loop-helix (bHLH) co-regulators, MdMYB9 activated apple and poplar anthocyanidin reductase (ANR) promoters, while MdMYB11 showed no activity. Potential transcription factor binding elements were found within several ANR promoters, and the importance of the bHLH binding site (E-box) on ANR promoter activation was demonstrated via mutational analysis. The ability of MdMYB9 and PtMYB134 to reciprocally activate ANR promoters from both apple and poplar and to partner with heterologous bHLH co-factors from these plants confirms the high degree of conservation of PA regulatory complexes across species. The similarity in apple and poplar PA regulation suggests that regulatory genes from poplar could be effectively employed for metabolic engineering of the PA pathway in apple.
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Affiliation(s)
- Andreas Gesell
- Department of Biology & Centre for Forest Biology, University of Victoria, Station CSC, Box 3020, Victoria, BC, V8W 3N5, Canada
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Visser M, Maree HJ, Rees DJG, Burger JT. High-throughput sequencing reveals small RNAs involved in ASGV infection. BMC Genomics 2014; 15:568. [PMID: 24998458 PMCID: PMC4118050 DOI: 10.1186/1471-2164-15-568] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 12/29/2022] Open
Abstract
Background Plant small RNAs (sRNAs) associated with virulent virus infections have been reported by previous studies, while the involvement of sRNAs in latent virus infection remains largely uncharacterised. Apple trees show a high degree of resistance and tolerance to viral infections. We analysed two sRNA deep sequencing datasets, prepared from different RNA size fractions, to identify sRNAs involved in Apple stem grooving virus (ASGV) infection. Results sRNA analysis revealed virus-derived siRNAs (vsiRNAs) originating from two ASGV genetic variants. A vsiRNA profile for one of the ASGV variants was also generated showing an increase in siRNA production towards the 3′ end of the virus genome. Virus-derived sRNAs longer than those previously analysed were also observed in the sequencing data. Additionally, tRNA-derived sRNAs were identified and characterised. These sRNAs covered a broad size-range and originated from both ends of the mature tRNAs as well as from their central regions. Several tRNA-derived sRNAs showed differential regulation due to ASGV infection. No changes in microRNA, natural-antisense transcript siRNA, phased-siRNA and repeat-associated siRNA levels were observed. Conclusions This study is the first report on the apple sRNA-response to virus infection. The results revealed the vsiRNAs profile of an ASGV variant, as well as the alteration of the tRNA-derived sRNA profile in response to latent virus infection. It also highlights the importance of library preparation in the interpretation of high-throughput sequencing data. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-568) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Johan T Burger
- Genetics Department, Stellenbosch University, Stellenbosch, South Africa.
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Würdig J, Flachowsky H, Höfer M, Peil A, Eldin Ali MAMS, Hanke MV. Phenotypic and genetic analysis of the German Malus Germplasm Collection in terms of type 1 and type 2 red-fleshed apples. Gene 2014; 544:198-207. [DOI: 10.1016/j.gene.2014.04.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/08/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
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Kirov I, Van Laere K, De Riek J, De Keyser E, Van Roy N, Khrustaleva L. Anchoring linkage groups of the Rosa genetic map to physical chromosomes with tyramide-FISH and EST-SNP markers. PLoS One 2014; 9:e95793. [PMID: 24755945 PMCID: PMC3995938 DOI: 10.1371/journal.pone.0095793] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/31/2014] [Indexed: 11/29/2022] Open
Abstract
In order to anchor Rosa linkage groups to physical chromosomes, a combination of the Tyramide-FISH technology and the modern molecular marker system based on High Resolution Melting (HRM) is an efficient approach. Although, Tyramide-FISH is a very promising technique for the visualization of short DNA probes, it is very challenging for plant species with small chromosomes such as Rosa. In this study, we successfully applied the Tyramide-FISH technique for Rosa and compared different detection systems. An indirect detection system exploiting biotinylated tyramides was shown to be the most suitable technique for reliable signal detection. Three gene fragments with a size of 1100 pb–1700 bp (Phenylalanine Ammonia Lyase, Pyrroline-5-Carboxylate Synthase and Orcinol O-Methyl Transferase) have been physically mapped on chromosomes 7, 4 and 1, respectively, of Rosa wichurana. The signal frequency was between 25% and 40%. HRM markers of these 3 gene fragments were used to include the gene fragments on the existing genetic linkage map of Rosa wichurana. As a result, three linkage groups could be anchored to their physical chromosomes. The information was used to check for synteny between the Rosa chromosomes and Fragaria.
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Affiliation(s)
- Ilya Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Katrijn Van Laere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
- * E-mail:
| | - Jan De Riek
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Ellen De Keyser
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Nadine Van Roy
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
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Visser M, van der Walt AP, Maree HJ, Rees DJG, Burger JT. Extending the sRNAome of apple by next-generation sequencing. PLoS One 2014; 9:e95782. [PMID: 24752316 PMCID: PMC3994110 DOI: 10.1371/journal.pone.0095782] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/31/2014] [Indexed: 02/07/2023] Open
Abstract
The global importance of apple as a fruit crop necessitates investigations into molecular aspects of the processes that influence fruit quality and yield, including plant development, fruit ripening and disease resistance. In order to study and understand biological processes it is essential to recognise the range of molecules, which influence these processes. Small non-coding RNAs are regulatory agents involved in diverse plant activities, ranging from development to stress response. The occurrence of these molecules in apple leaves was studied by means of next-generation sequencing. 85 novel microRNA (miRNA) gene loci were predicted and characterized along with known miRNA loci. Both cis- and trans-natural antisense transcript pairs were identified. Although the trans-overlapping regions were enriched in small RNA (sRNA) production, cis-overlaps did not seem to agree. More than 150 phased regions were also identified, and for a small subset of these, potential miRNAs that could initiate phasing, were revealed. Repeat-associated siRNAs, which are generated from repetitive genomic regions such as transposons, were also analysed. For this group almost all available repeat sequences, associated with the apple genome and present in Repbase, were found to produce siRNAs. Results from this study extend our current knowledge on apple sRNAs and their precursors significantly. A rich molecular resource has been created and is available to the research community to serve as a baseline for future studies.
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Affiliation(s)
- Marike Visser
- Biotechnology Platform, Agricultural Research Council, Pretoria, Gauteng, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Anelda P. van der Walt
- Central Analytical Facilities, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa
- Infruitec-Nietvoorbij, Agricultural Research Council, Stellenbosch, Western Cape, South Africa
| | - D. Jasper G. Rees
- Biotechnology Platform, Agricultural Research Council, Pretoria, Gauteng, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa
- * E-mail:
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45
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Rusanov K, Kovacheva N, Atanassov A, Atanassov I. Rosa Damascena—Genetics of a Complex Allotetraploid Species and Perspectives for Molecular Breeding. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10818495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Pons C, Martí C, Forment J, Crisosto CH, Dandekar AM, Granell A. A bulk segregant gene expression analysis of a peach population reveals components of the underlying mechanism of the fruit cold response. PLoS One 2014; 9:e90706. [PMID: 24598973 PMCID: PMC3944608 DOI: 10.1371/journal.pone.0090706] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/04/2014] [Indexed: 11/29/2022] Open
Abstract
Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding strategies to better cope with chilling injury.
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Affiliation(s)
- Clara Pons
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Cristina Martí
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Javier Forment
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Carlos H. Crisosto
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Antonio Granell
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
- * E-mail:
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Lauxmann MA, Borsani J, Osorio S, Lombardo VA, Budde CO, Bustamante CA, Monti LL, Andreo CS, Fernie AR, Drincovich MF, Lara MV. Deciphering the metabolic pathways influencing heat and cold responses during post-harvest physiology of peach fruit. PLANT, CELL & ENVIRONMENT 2014; 37:601-16. [PMID: 23937123 DOI: 10.1111/pce.12181] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/30/2013] [Accepted: 08/03/2013] [Indexed: 05/23/2023]
Abstract
Peaches are highly perishable and deteriorate quickly at ambient temperature. Cold storage is commonly used to prevent fruit decay; however, it affects fruit quality causing physiological disorders collectively termed 'chilling injury' (CI). To prevent or ameliorate CI, heat treatment is often applied prior to cold storage. In the present work, metabolic profiling was performed to determine the metabolic dynamics associated with the induction of acquired CI tolerance in response to heat shock. 'Dixiland' peach fruits exposed to 39 °C, cold stored, or after a combined treatment of heat and cold, were compared with fruits ripening at 20 °C. Dramatic changes in the levels of compatible solutes such as galactinol and raffinose were observed, while amino acid precursors of the phenylpropanoid pathway were also modified due to the stress treatments, as was the polyamine putrescine. The observed responses towards temperature stress in peaches are composed of both common and specific response mechanisms to heat and cold, but also of more general adaptive responses that confer strategic advantages in adverse conditions such as biotic stresses. The identification of such key metabolites, which prime the fruit to cope with different stress situations, will likely greatly accelerate the design and the improvement of plant breeding programs.
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Affiliation(s)
- Martin A Lauxmann
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina
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Jung S, Main D. Genomics and bioinformatics resources for translational science in Rosaceae. PLANT BIOTECHNOLOGY REPORTS 2014; 8:49-64. [PMID: 24634697 PMCID: PMC3951882 DOI: 10.1007/s11816-013-0282-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/22/2013] [Indexed: 05/22/2023]
Abstract
Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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Numa H, Itoh T. MEGANTE: a web-based system for integrated plant genome annotation. PLANT & CELL PHYSIOLOGY 2014; 55:e2. [PMID: 24253915 PMCID: PMC3894707 DOI: 10.1093/pcp/pct157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon-intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the Brassicaceae, Fabaceae, Musaceae, Poaceae, Salicaceae, Solanaceae, Rosaceae and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at https://megante.dna.affrc.go.jp/.
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Affiliation(s)
| | - Takeshi Itoh
- *Corresponding author: E-mail, ; Fax, +81-29-838-7065
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Immanen J, Nieminen K, Duchens Silva H, Rodríguez Rojas F, Meisel LA, Silva H, Albert VA, Hvidsten TR, Helariutta Y. Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica. BMC Genomics 2013; 14:885. [PMID: 24341635 PMCID: PMC3866579 DOI: 10.1186/1471-2164-14-885] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/27/2013] [Indexed: 01/01/2023] Open
Abstract
Background Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species. Results Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses. Conclusions In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ykä Helariutta
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland.
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