Abstract
Coffee is a popular beverage in the world and a valuable agricultural export commodity for several developing countries. Coffea arabica is one of the widely cultivated species and is believed to have originated from Ethiopia. Currently, a large number of C. arabica accessions are conserved ex situ in field gene banks in Ethiopia. However, there is no useful molecular barcoding to identify the conserved accessions, which presents a challenge to sustainable utilization of this economic species. To identify polymorphic chloroplast markers for the use in various studies, the complete chloroplast genome sequences of 24 C. arabica accessions were assembled and screened for variable regions in this study. The total length of the individual chloroplast genome sequence varied from 155,059 to 155,192 bp. Genome annotation revealed a total of 114 unique genes, consisting of 80 protein-coding, 30 tRNA, and four rRNA genes in all the 24 genomes. Twenty-four polymorphic regions were identified and developed. Most (71%) of the variable regions were found in non-coding sequence, and 54% of the variations detected are single base pairs. Three non-synonymous SNPs were found in accD, rpoA, and ycf1 genes. The markers developed were able to cluster the majority of the coffee accessions according to their geographical regions of collection. Five out of 24 newly developed markers were validated by assessing the diversity levels that were assessed in five original regions. The southwest region displayed the highest genetic diversity (HE = 0.224; I = 0.370) and might become a potential coffee genetic resource bank. Overall, the polymorphic markers developed and validated in this study could be a useful genomic resource for molecular breeding, identification, and biogeography studies of this commercially important crop.
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Acknowledgments
The authors would like to thank the Ethiopian Biodiversity Institute for providing the coffee leaf samples used in this study. We gratefully acknowledge Jara Negash for his assistance during sample collection and Andrew W. Gichira for his help with the data analysis.
Funding
We thank Sino-Africa Joint Research Center, CAS (SAJC201614), for providing funding for the study.
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Key Message
• Comparative analysis of the newly sequenced 24 chloroplast genome sequences of ex situ conserved Coffea arabica accessions have been conducted.
• Three non-synonymous single-nucleotide polymorphisms were found in accD, rpoA, and ycf1 genes.
• The markers developed could be a useful genomic resource for molecular barcoding, molecular breeding, and biogeography studies.
Electronic Supplementary Material
Table S1
Informations of Coffea arabica accessions used for marker validation and polymorphism levels. (DOCX 17 kb)
Table S2
List of genes encoded by chloroplast genomes of Coffea arabica. (DOCX 14 kb)
Table S3
The twenty-four variable regions identified in the newly sequenced chloroplast genome sequences of Coffea arabica accessions. (DOCX 15 kb)
Table S4
Polymorphism detected across the 24 chloroplast genome sequences of Coffea arabica accessions. (DOCX 22 kb)
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Mekbib, Y., Saina, J.K., Tesfaye, K. et al. Chloroplast Genome Sequence Variations and Development of Polymorphic Markers in Coffea arabica. Plant Mol Biol Rep 38, 491–502 (2020). https://doi.org/10.1007/s11105-020-01212-3
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DOI: https://doi.org/10.1007/s11105-020-01212-3