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Millet CP, Allinne C, Vi T, Marraccini P, Verleysen L, Couderc M, Ruttink T, Zhang D, Sanchéz WS, Tranchant-Dubreuil C, Jeune W, Poncet V. Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity. PLoS One 2024; 19:e0299493. [PMID: 38625928 PMCID: PMC11020479 DOI: 10.1371/journal.pone.0299493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/11/2024] [Indexed: 04/18/2024] Open
Abstract
Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.
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Affiliation(s)
- Claude Patrick Millet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
| | - Clémentine Allinne
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
- GECO, Université Montpellier, CIRAD, Montpellier, France
- CIRAD, UPR GECO, F-34398, Montpellier, France
| | - Tram Vi
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Pierre Marraccini
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- CIRAD, UMR DIADE, Montpellier, France
| | - Lauren Verleysen
- Faculty of Sciences, Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- ILVO, Melle, Belgium
| | - Marie Couderc
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
| | - Tom Ruttink
- ILVO, Melle, Belgium
- Ghent University, Ghent, Belgium
| | - Dapeng Zhang
- USDA-ARS, SPCL, Beltsville, Maryland, United States of America
| | | | | | - Wesly Jeune
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- AVSF, Pétion-Ville, Haïti
| | - Valérie Poncet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
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Description of an Arabica Coffee Ideotype for Agroforestry Cropping Systems: A Guideline for Breeding More Resilient New Varieties. PLANTS 2022; 11:plants11162133. [PMID: 36015436 PMCID: PMC9414076 DOI: 10.3390/plants11162133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations’ access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.
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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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Krishnan S, Pruvot-Woehl S, Davis AP, Schilling T, Moat J, Solano W, Al Hakimi A, Montagnon C. Validating South Sudan as a Center of Origin for Coffea arabica: Implications for Conservation and Coffee Crop Improvement. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.761611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cultivated Arabica coffee outside Ethiopia is plagued by low genetic diversity, compromising disease resistance, climate resiliency and sensory potential. Access to the wider genetic diversity of this species may circumvent some of these problems. In addition to Ethiopia, South Sudan has been postulated as a center of origin for Arabica coffee, but this has never been genetically confirmed. We used simple sequence repeat (SSR) markers to assess the genetic diversity of wild and cultivated populations of Arabica coffee from the Boma Plateau in South Sudan, against farmed accessions (of wild origin) from Ethiopia, Yemen, and global cultivars. Our results not only validate Boma Plateau as part of the natural distribution and as a center of origin for Arabica coffee but also indicate that wild populations in South Sudan are genetically distinct from Ethiopian Arabica. This newly identified genetic diversity within Arabica could have the potential for crop improvement through selection and use in breeding programs. Observations and analyses show that the extent and health of the wild population of Arabica in South Sudan have declined. Urgent action should be taken to conserve (in situ and ex situ) the unique, remaining genetic diversity of wild Arabica populations in South Sudan.
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