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Seyum EG, Bille NH, Abtew WG, Munyengwa N, Bell JM, Cros D. Genomic selection in tropical perennial crops and plantation trees: a review. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:58. [PMID: 37313015 PMCID: PMC10248687 DOI: 10.1007/s11032-022-01326-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
To overcome the multiple challenges currently faced by agriculture, such as climate change and soil deterioration, more efficient plant breeding strategies are required. Genomic selection (GS) is crucial for the genetic improvement of quantitative traits, as it can increase selection intensity, shorten the generation interval, and improve selection accuracy for traits that are difficult to phenotype. Tropical perennial crops and plantation trees are of major economic importance and have consequently been the subject of many GS articles. In this review, we discuss the factors that affect GS accuracy (statistical models, linkage disequilibrium, information concerning markers, relatedness between training and target populations, the size of the training population, and trait heritability) and the genetic gain expected in these species. The impact of GS will be particularly strong in tropical perennial crops and plantation trees as they have long breeding cycles and constrained selection intensity. Future GS prospects are also discussed. High-throughput phenotyping will allow constructing of large training populations and implementing of phenomic selection. Optimized modeling is needed for longitudinal traits and multi-environment trials. The use of multi-omics, haploblocks, and structural variants will enable going beyond single-locus genotype data. Innovative statistical approaches, like artificial neural networks, are expected to efficiently handle the increasing amounts of heterogeneous multi-scale data. Targeted recombinations on sites identified from profiles of marker effects have the potential to further increase genetic gain. GS can also aid re-domestication and introgression breeding. Finally, GS consortia will play an important role in making the best of these opportunities. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01326-4.
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Affiliation(s)
- Essubalew Getachew Seyum
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Ngalle Hermine Bille
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Wosene Gebreselassie Abtew
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Norman Munyengwa
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Joseph Martin Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - David Cros
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Univ. Montpellier, Institut Agro, 34398 Montpellier, France
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2
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de Sousa LP, Cipriano MAP, da Silva MJ, Patrício FRA, Freitas SDS, Carazzolle MF, Mondego JMC. Functional genomics analysis of a phyllospheric Pseudomonas spp with potential for biological control against coffee rust. BMC Microbiol 2022; 22:222. [PMID: 36131235 PMCID: PMC9494895 DOI: 10.1186/s12866-022-02637-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background Pseudomonas spp. promotes plant growth and colonizes a wide range of environments. During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. In parallel, several experiments were performed to confirm certain physiological characteristics that could be associated with phyllospheric behavior. Finally, in vivo and in vitro experiments were carried out to verify whether this isolate could serve as a biocontrol agent against coffee rust and how the isolate could act against the infection. Results The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. There was an increase of exopolysaccharides synthesis in response to osmotic stress, which may protect cells from dessication on phyllosphere. Metabolic pathways for degradation and incorporation into citrate cycle of phenolic compounds present in coffee were found, and experimentally confirmed. In addition, MN1F was found to be highly tolerant to caffeine. The experiments of biocontrol against coffee leaf rust showed that the isolate can control the progress of the disease, most likely through competition for resources. Conclusion Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02637-4.
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Affiliation(s)
- Leandro Pio de Sousa
- Instituto Agronômico de Campinas, IAC, Campinas, SP, Brazil.,Programa de Pós-Graduação Em Genética E Biologia Molecular, UNICAMP, Campinas, SP, Brazil
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3
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Portillo OR, Arévalo AC. Caffeine. A critical review of contemporary scientific literature. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.03.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Caffeine is a secondary metabolite extensively studied for its stimulatory properties and presumed association with specific pathologies. This alkaloid is typically consumed through coffee, tea, and other plant products but is also an additive in many medications and confectionaries. Nonetheless, despite its worldwide consumption and acceptance, there is controversial evidence as to whether its effects on the central nervous system should be interpreted as stimulatory or as an addiction in which typical withdrawal effects are canceled out with its daily consumption. The following discussion is the product of an extensive review of current scientific literature, which aims to describe the most salient topics associated with caffeine's purpose in nature, biosynthesis, metabolism, physiological effects, toxicity, extraction, industrial use and current plant breeding approaches for the development of new caffeine deficient varieties as a more economical option to the industrially decaffeinated coffees currently available to caffeine intolerant consumers.
Keywords: biosynthesis, decaffeination, extraction, metabolism, physiological effects, plant breeding.
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Affiliation(s)
- Ostilio R. Portillo
- Faculty of Engineering, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Ana C. Arévalo
- Faculty of Chemistry & Pharmacy, National Autonomous University of Hondura (UNAH), Tegucigalpa, Honduras
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R. Portillo O, Arévalo AC. Coffee's Phenolic Compounds. A general overview of the coffee fruit's phenolic composition. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.03.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Phenolic compounds are secondary metabolites ubiquitously distributed in the plant kingdom which come in a wide array of molecular configurations which confer them a comprehensive set of chemical attributes such as, but not limited to: nutraceutical properties, industrial applications (e.g., dyes, rawhide processing, beer production, antioxidants), and plant self-defense mechanisms against natural enemies also known as the Systemic Acquired Resistance (SAR).However, despite the fact, that there is a large number of phenolic-containing food products (e.g., chocolate, green tea, wines, beer, wood barrel-aged spirits, cherries, grapes, apples, peaches, plums, pears, etc.), coffee remains, in the western hemisphere, as the main source of dietary phenolic compounds reflected by the fact that, in the international market, coffee occupies the second trading position after oil and its derivatives. The following discussion is the product of an extensive review of scientific literature that aims to describe essential topics related to coffee phenolic compounds, especially chlorogenic acids, their purpose in nature, biosynthesis, determination, metabolism, chemical properties, and their effect on cup quality.
Keywords: phenolic acids, caffeoylquinic acid, antioxidant capacity, metabolism, biosynthesis.
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Affiliation(s)
- Ostilio R. Portillo
- Faculty of Engineering, National Autonomous University of Honduras, Tegucigalpa (UNAH), Honduras
| | - Ana C. Arévalo
- Faculty of Chemistry & Pharmacy, National Autonomous University of Honduras, Tegucigalpa (UNAH), Honduras
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José Luis SC, Paulino PR, Bello-Bello JJ, Esteban EP, Víctor Heber AR, Tarsicio CT, Gabino GDLS, Victorino MR. SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm. Mol Biol Rep 2022; 49:4849-4859. [PMID: 35474051 DOI: 10.1007/s11033-022-07339-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Coffee quality is an important selection criterion for coffee breeding. Metabolite profiling and Genome-Wide Association Studies (GWAS) effectively dissect the genetic background of complex traits such as metabolites content (caffeine, trigonelline, and 5-caffeoylquinic acid (5-CQA)) in coffee that affect quality. Therefore, it is important to determine the metabolic profiles of Coffea spp. genotypes. This study aimed to identify Single Nucleotide Polymorphisms (SNPs) within Coffea spp. genotypes through GWAS and associate these significant SNPs to the metabolic profiles of the different genotypes. METHODS AND RESULTS A total of 1,739 SNP markers were obtained from 80 genotypes using the DArTseq™ method. Caffeine, trigonelline, and 5-CQA content were determined in coffee leaves using Ultra-Performance Liquid Chromatography/tandem mass spectrometry (UPLC-MS/MS) analyses. The GWAS was carried out using the Genome Association and Prediction Integrated Tool (GAPIT) software and a compressed mixed linear model. Finally, a total of three significant SNP markers out of ten were identified. One SNP, located in the coffee chromosome (Chr) 8, was significantly associated with caffeine. The two remaining SNPs, located in Chr 4 and 5, were significantly associated with trigonelline and six SNPs markers were associated with 5-CQA in Chr 1, 5 and 10, but these six markers were not significant. CONCLUSIONS These significant SNP sequences were associated with protein ubiquitination, assimilation, and wall receptor kinases. Therefore, these SNPs might be useful hits in subsequent quality coffee breeding programs.
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Affiliation(s)
- Spinoso-Castillo José Luis
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México.
| | - Pérez-Rodríguez Paulino
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - Jericó Jabín Bello-Bello
- CONACYT-Colegio de Postgraduados Campus Córdoba, Carretera Federal Córdoba-Veracruz km 348, Amatlán de los Reyes 94946, Veracruz, México
| | - Escamilla-Prado Esteban
- Universidad Autónoma Chapingo, Centro Regional Universitario Oriente, Carretera Huatusco-Xalapa Km 6, 94100, Huatusco, Veracruz, México
| | - Aguilar-Rincón Víctor Heber
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - Corona-Torres Tarsicio
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - García-de Los Santos Gabino
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - Morales-Ramos Victorino
- Colegio de Postgraduados Campus Córdoba, Carretera Federal Córdoba-Veracruz km 348, Amatlán de los Reyes, 94946, Veracruz, México
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Mekbib Y, Tesfaye K, Dong X, Saina JK, Hu GW, Wang QF. Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC PLANT BIOLOGY 2022; 22:69. [PMID: 35164709 PMCID: PMC8842891 DOI: 10.1186/s12870-022-03449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 06/04/2023]
Abstract
BACKGROUND Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology. RESULTS The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups. CONCLUSIONS Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.
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Affiliation(s)
- Yeshitila Mekbib
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Josphat K Saina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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7
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da Silva Araújo C, Macedo LL, Vimercati WC, Saraiva SH. Spectroscopy Technique Applied to Estimate Sensory Parameters and Quantification of Total Phenolic Compounds in Coffee. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02025-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Li Z, Zhang C, Zhang Y, Zeng W, Cesarino I. Coffee cell walls—composition, influence on cup quality and opportunities for coffee improvements. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The coffee beverage is the second most consumed drink worldwide after water. In coffee beans, cell wall storage polysaccharides (CWSPs) represent around 50 per cent of the seed dry mass, mainly consisting of galactomannans and arabinogalactans. These highly abundant structural components largely influence the organoleptic properties of the coffee beverage, mainly due to the complex changes they undergo during the roasting process. From a nutritional point of view, coffee CWSPs are soluble dietary fibers shown to provide numerous health benefits in reducing the risk of human diseases. Due to their influence on coffee quality and their health-promoting benefits, CWSPs have been attracting significant research attention. The importance of cell walls to the coffee industry is not restricted to beans used for beverage production, as several coffee by-products also present high concentrations of cell wall components. These by-products include cherry husks, cherry pulps, parchment skin, silver skin, and spent coffee grounds, which are currently used or have the potential to be utilized either as food ingredients or additives, or for the generation of downstream products such as enzymes, pharmaceuticals, and bioethanol. In addition to their functions during plant development, cell walls also play a role in the plant’s resistance to stresses. Here, we review several aspects of coffee cell walls, including chemical composition, biosynthesis, their function in coffee’s responses to stresses, and their influence on coffee quality. We also propose some potential cell wall–related biotechnological strategies envisaged for coffee improvements.
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Affiliation(s)
| | | | | | | | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Raharimalala N, Rombauts S, McCarthy A, Garavito A, Orozco-Arias S, Bellanger L, Morales-Correa AY, Froger S, Michaux S, Berry V, Metairon S, Fournier C, Lepelley M, Mueller L, Couturon E, Hamon P, Rakotomalala JJ, Descombes P, Guyot R, Crouzillat D. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Sci Rep 2021; 11:8119. [PMID: 33854089 PMCID: PMC8046976 DOI: 10.1038/s41598-021-87419-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.
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Affiliation(s)
- Nathalie Raharimalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Stephane Rombauts
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Andrew McCarthy
- grid.418923.50000 0004 0638 528XEuropean Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Andréa Garavito
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia ,Centro de Bioinformática y biología computacional de Colombia – BIOS, Ecoparque los Yarumos, Manizales, Caldas, Colombia
| | - Simon Orozco-Arias
- grid.7779.e0000 0001 2290 6370Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia ,grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia
| | - Laurence Bellanger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Alexa Yadira Morales-Correa
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Solène Froger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Stéphane Michaux
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Victoria Berry
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Sylviane Metairon
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Coralie Fournier
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland ,grid.8591.50000 0001 2322 4988Present Address: University of Geneva, CMU-Décanat, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Maud Lepelley
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Lukas Mueller
- grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Emmanuel Couturon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Perla Hamon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Jean-Jacques Rakotomalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Romain Guyot
- grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia ,grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Dominique Crouzillat
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
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Zhang D, Vega FE, Solano W, Su F, Infante F, Meinhardt LW. Selecting a core set of nuclear SNP markers for molecular characterization of Arabica coffee (Coffea arabica L.) genetic resources. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01201-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Quantitative comparison of three main metabolites in leaves of Coffea accessions by UPLC-MS/MS. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03631-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lemos MF, Perez C, da Cunha PHP, Filgueiras PR, Pereira LL, Almeida da Fonseca AF, Ifa DR, Scherer R. Chemical and sensory profile of new genotypes of Brazilian Coffea canephora. Food Chem 2020; 310:125850. [DOI: 10.1016/j.foodchem.2019.125850] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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Identification and Expression Analysis of the NAC Gene Family in Coffea canephora. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9110670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.
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Gamboa-Becerra R, Hernández-Hernández MC, González-Ríos Ó, Suárez-Quiroz ML, Gálvez-Ponce E, Ordaz-Ortiz JJ, Winkler R. Metabolomic Markers for the Early Selection of Coffea canephora Plants with Desirable Cup Quality Traits. Metabolites 2019; 9:E214. [PMID: 31590271 PMCID: PMC6835713 DOI: 10.3390/metabo9100214] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/08/2023] Open
Abstract
Genetic improvement of coffee plants represents a great challenge for breeders. Conventional breeding takes a too long time for responding timely to market demands, climatic variations and new biological threads. The correlation of genetic markers with the plant phenotype and final product quality is usually poor. Additionally, the creation and use of genetically modified organisms (GMOs) are often legally restricted and rejected by customers that demand natural products. Therefore, we developed a non-targeted metabolomics approach to accelerate conventional breeding. Our main idea was to identify highly heritable metabolites in Coffea canephora seedlings, which are linked to coffee cup quality. We employed a maternal half-sibs approach to estimate the metabolites heritability in open-pollinated plants in both leaves and fruits at an early plant development stage. We evaluated the cup quality of roasted beans and correlated highly heritable metabolites with sensory quality traits of the coffee beverage. Our results provide new insights about the heritability of metabolites of C. canephora plants. Furthermore, we found strong correlations between highly heritable metabolites and sensory traits of coffee beverage. We revealed metabolites that serve as predictive metabolite markers at an early development stage of coffee plants. Informed decisions can be made on plants of six months old, compared to 3.5 to 5 years using conventional selection methods. The metabolome-wide association study (MWAS) drastically accelerates the selection of C. canephora plants with desirable characteristics and represents a novel approach for the focused breeding of crops.
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Affiliation(s)
- Roberto Gamboa-Becerra
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Km 9.6 Libramiento Norte Carr. Irapuato-León, Guanajuato, 36824, Mexico.
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Xalapa, Veracruz 91070, Mexico.
| | - María Cecilia Hernández-Hernández
- Laboratorio de Tecnología del Café, Unidad de Investigación y Desarrollo en Alimentos, TNM/Instituto Tecnológico de Veracruz, Veracruz, 9187, Mexico.
| | - Óscar González-Ríos
- Laboratorio de Tecnología del Café, Unidad de Investigación y Desarrollo en Alimentos, TNM/Instituto Tecnológico de Veracruz, Veracruz, 9187, Mexico.
| | - Mirna L Suárez-Quiroz
- Laboratorio de Tecnología del Café, Unidad de Investigación y Desarrollo en Alimentos, TNM/Instituto Tecnológico de Veracruz, Veracruz, 9187, Mexico.
| | - Eligio Gálvez-Ponce
- Agroindustrias Unidas de México S.A. de C.V. (AMSA), Bosque de Alisos 45-A 2do Piso, Bosques de las Lomas, Ciudad de México, 05120, Mexico.
| | - José Juan Ordaz-Ortiz
- Laboratorio de Metabolómica y Espectrometría de Masas, Unidad de Genómica Avanzada, CINVESTAV-IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato, 36824, Mexico.
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Km 9.6 Libramiento Norte Carr. Irapuato-León, Guanajuato, 36824, Mexico.
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15
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Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers. Genetica 2019; 147:205-216. [PMID: 31054007 DOI: 10.1007/s10709-019-00064-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/20/2019] [Indexed: 10/26/2022]
Abstract
Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard's coefficient and population structure in 33 genotypes of C. arabica and of three diploid Coffea species (C. canephora, C. eugenioides and C. racemosa) using 30 SSR markers. A total of 206 alleles were identified, with a mean of 6.9 over all loci. The set of SSR markers was able to discriminate all genotypes and revealed that Ethiopian accessions presented higher genetic diversity than commercial varieties. Population structure analysis indicated two genetic groups, one corresponding to Ethiopian accessions and another corresponding predominantly to commercial cultivars. Thirty-four private alleles were detected in the group of accessions collected from West side of Great Rift Valley. We observed a lower average genetic distance of the C. arabica genotypes in relation to C. eugenioides than C. canephora. Interestingly, commercial cultivars were genetically closer to C. eugenioides than C. canephora and C. racemosa. The great allelic richness observed in Ethiopian Arabica coffee, especially in Western group showed that these accessions can be potential source of new alleles to be explored by coffee breeding programs.
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16
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Quintero FOC, Pinto LG, Barsalobres-Cavallari CF, Arcuri MDLC, Pino LE, Peres LEP, Maluf MP, Maia IG. Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato. PLANT CELL REPORTS 2018; 37:1257-1268. [PMID: 29947954 DOI: 10.1007/s00299-018-2310-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
A seed maturation protein gene (CaSMP) from Coffea arabica is expressed in the endosperm of yellow/green fruits. The CaSMP promoter drives reporter expression in the seeds of immature tomato fruits. In this report, an expressed sequence tag-based approach was used to identify a seed-specific candidate gene for promoter isolation in Coffea arabica. The tissue-specific expression of the cognate gene (CaSMP), which encodes a yet uncharacterized coffee seed maturation protein, was validated by RT-qPCR. Additional expression analysis during coffee fruit development revealed higher levels of CaSMP transcript accumulation in the yellow/green phenological stage. Moreover, CaSMP was preferentially expressed in the endosperm and was down-regulated during water imbibition of the seeds. The presence of regulatory cis-elements known to be involved in seed- and endosperm-specific expression was observed in the CaSMP 5'-upstream region amplified by genome walking (GW). Additional histochemical analysis of transgenic tomato (cv. Micro-Tom) lines harboring the GW-amplified fragment (~ 1.4 kb) fused to uidA reporter gene confirmed promoter activity in the ovule of immature tomato fruits, while no activity was observed in the seeds of ripening fruits and in the other organs/tissues examined. These results indicate that the CaSMP promoter can be used to drive transgene expression in coffee beans and tomato seeds, thus representing a promising biotechnological tool.
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Affiliation(s)
- Fabíola OCampo Quintero
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Layra G Pinto
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Carla F Barsalobres-Cavallari
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Mariana de Lara Campos Arcuri
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Lilian Ellen Pino
- Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Lázaro Eustáquio Pereira Peres
- Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Mirian P Maluf
- Embrapa Coffee and Coffee Center Alcides Carvalho, Agronomic Institute of Campinas, Campinas, Sao Paulo, 13012-970, Brazil
| | - Ivan G Maia
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil.
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17
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Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models. Heredity (Edinb) 2018; 122:261-275. [PMID: 29941997 DOI: 10.1038/s41437-018-0105-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022] Open
Abstract
Genomic selection has been proposed as the standard method to predict breeding values in animal and plant breeding. Although some crops have benefited from this methodology, studies in Coffea are still emerging. To date, there have been no studies describing how well genomic prediction models work across populations and environments for different complex traits in coffee. Considering that predictive models are based on biological and statistical assumptions, it is expected that their performance vary depending on how well these assumptions align with the true genetic architecture of the phenotype. To investigate this, we used data from two recurrent selection populations of Coffea canephora, evaluated in two locations, and single nucleotide polymorphisms identified by Genotyping-by-Sequencing. In particular, we evaluated the performance of 13 statistical approaches to predict three important traits in the coffee-production of coffee beans, leaf rust incidence and yield of green beans. Analyses were performed for predictions within-environment, across locations and across populations to assess the reliability of genomic selection. Overall, differences in the prediction accuracy of the competing models were small, although the Bayesian methods showed a modest improvement over other methods, at the cost of more computation time. As expected, predictive accuracy for within-environment analysis, on average, were higher than predictions across locations and across populations. Our results support the potential of genomic selection to reshape traditional plant breeding schemes. In practice, we expect to increase the genetic gain per unit of time by reducing the length cycle of recurrent selection in coffee.
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18
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Cheng B, Furtado A, Smyth HE, Henry RJ. Influence of genotype and environment on coffee quality. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.09.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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