The aim of this article is to provide an overview of the current situation of coffee genetic resources that are dwindling at an alarming rate in Ethiopia, the centre of diversity of Coffea arabica. Firstly, we describe the coffee growing systems (forest coffee, semi-forest coffee, garden coffee and plantation coffee) and recent research on the genetic diversity of the coffee planting material associated with those systems. Whilst the maximum genetic diversity revealed by DNA-based markers is found in the forest coffees of the south-western highlands, the natural habitat of C. arabica, the taxonomy of coffee landraces is particularly rich in garden coffee systems located in ancient growing zones such as Harerge in eastern Ethiopia. After reviewing the factors involved in the genetic erosion of the Ethiopian genepool, we give an update on the status of coffee genetic resources conserved ex situ in the field genebank of the Jimma Agricultural Research Centre, with 4,780 accessions spread over 10 research stations located in the main production areas, and in the main genebank of the Institute of Biodiversity Conservation located in Choche (Limu) with 5,196 accessions conserved. Lastly, we mention the in situ conservation operations currently being implemented in Ethiopia. Improving our knowledge of the genetic structure of Ethiopian forest and garden coffee tree populations as well as genetic resources conserved ex situ will help to plan the future conservation strategy for that country. To this end, modern tools as DNA-based markers should be used to increase our understanding of coffee genetic diversity and it is proposed, with the support of the international scientific community and donor organizations, to undertake a concerted effort to rescue highly threatened Arabica coffee genetic resources in Ethiopia.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relativesThe International Center for Tropical Agriculture (CIAT) believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture.CIAT is committed to creating and sharing knowledge and information openly and globally. We do this through collaborative research as well as through the open sharing of our data, tools, and publications. Citation:Sarah For more information, please contact CIAT Library at CIAT-Library@cgiar.org. Accepted ArticleThis article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1755-0998.12587 This article is protected by copyright. All rights reserved. Accepted ArticleThis article is protected by copyright. All rights reserved. AbstractWe produced a unique large dataset of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11eudicots. All contigs were annotated using BLAST, prot4EST, and Blast2GO. A strong originality of the dataset is that each crop is associated with close relative species, which will permit whole genome comparative evolutionary studies between crops and their wild related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.