Genetic diversity of ex-situ conserved Arabica cofee (Coffea arabica L.) accessions in Ethiopia as revealed by simple sequence repeats markers
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Aug 27, 2023
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So far, there has been limited use of molecular markers in arabica coffee breeding program in Ethiopia. The objectives of this study were to explore the effectiveness of simple sequence repeats markers (SSRs) in detecting polymor- phism and to assess the extent of genetic diversity and relationships among ex-situconserved Arabica coffee accessions. Sixty-two forest coffee accessions planted in the experimental plot of the Ethiopian coffee breeding program were evaluated using 14 SSR markers. These markers amplified a total of 100 alleles, varying from four to ten alleles per locus, with an average of 7.2 across all loci. The rate of polymorphism ranged from 75 to 100, with a mean value of 96.4 across the accessions. The polymorphic information content (PIC) varied from 0.26 to 0.92, with a mean value of 0.70. The genetic similarity coefficient values between 72% possible pair-wise combinations ranged from 0.18 to 0.50, with overall mean value of 0.44.The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on Jaccard’s genetic similarity grouped the accessions into five main clusters and two singletons at <0.47 similarity coefficient value. These results indicate the effectiveness of the SSR markers in detecting polymorphism and the presence of a high level of genetic diversity and distant relatedness among the studied coffee accessions. The observed diversity could be exploited in the future coffee breeding program to develop heterotic hybrid coffee varieties through crossing of divergent parental lines. The highly informative SSRs markers can be also used in genetic analysis of Arabica coffee germplasm conserved in the field gene bank at Jimma Agricultural Research Center (JARC) to establish core collections for effective conservation, management and utilization purposes
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Benti, T., Gebre, E., Tesfaye, K., Berecha, G., Lashermes, P., Kyallo, M., & Yao, N. (2023). Genetic diversity of ex-situ conserved Arabica cofee (Coffea arabica L.) accessions in Ethiopia as revealed by simple sequence repeats markers. Pelita Perkebunan (a Coffee and Cocoa Research Journal), 39(2), 79-94. https://doi.org/10.22302/iccri.jur.pelitaperkebunan.v39i2.544
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References
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Aga E.; E. Bekele and T. Bryngelsson. (2005). Inter-simple sequence repeats (ISSR) variation in forest coffee trees (Coffea arabica L.) populations from Ethiopia. Genetica. 124: 213–221.
Al-Murish Tm.; A.A. Elshafei; A.A. Al-Doss and M.N. Barakat (2013). Genetic diversity of coffee (Coffea arabica L.) in Yemen via SRAP, TRAP, and SSR markers. J Food Agric Environ, 11(2), 411-416. https://doi.org/10.1234/4.2013.4315
Ameha M. and B. Bellachew (1983). Heterosis in cross of indigenous coffee selected for yield and resistance to Coffee Berry Disease II-first three years. EJAS. 1: 13–21.
Anthony F; B. Bertrand; O. Quiros; A. Wilches; P. Lashermes; J. Berthaud, and A. Charrier (2001). Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers. Euphytica. 118: 53–65.
Anthony F.; M.C. Combes; C. Astorga; B. Bertrand, G. Graziosi and P. Lashermes (2002). The origin of cultivated Coffea arbica L. varieties revealed by AFLP and SSR markers. Theory of Applied Genetics 104: 894– 900.
Baltazar M.D and J.M.O. Fabella (2020). Genetic Diversity of Philippine Arabica Coffee. Philippine Journal of Science. 149 (3-a): 993-1003.
Benti T. 2017. Progress in arabica coffee breeding in Ethiopia: Achievements, challenges and prospects. International Journals of Sciences: Basic and Applied Research (IJSBAR). 33 (2): 15-25.
Benti T.; G. Endale; T. Kassahun; B. Gezahegn; P. Lashermes; K. Martina and K.Y. Nasser (2021). Genetic diversity among commercial arabica coffee (Coffea arabica L.) varieties in Ethiopia using simple sequence repeat markers. Journal of crop improvement 35(2): 147-168. Doi.10.1080/15427528.2020.1803169.
Benti T; G. Endale; T. Kassahun; B. Gezahegn; P. Lashermes, K. Martina and K.Y. Nasser (2022). Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers. American Journal of Biochemistry and Biotechnology 18 (4): 394.404. doi: 10.3844/ajbbsp.2022.394.404.
Bertrand B.; H. Etienne; C. Cilas; A. Charrier and P. Baradat (2005). Coffea arabica hybrid performance for yield, fertility and bean weight. Euphytica. 141: 255–262.
Borsch T; K.W. Hilu; D. Quandt; V. Wilde; C. Neinhuis and W. Barthlott (2003). Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J. Evol. Biol 16: 558-576.
Botestein D; R.L. White; M. Skolnick and R.W. Devis (1980). Construction of genetic linkage map in man using ristrictin fragment length polymorphisms. The American Journal of Human Genetics, 32: 314-331
Davis A.P.; J. Tosh; N. Ruch and M. Fay (2011). Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc. 167:357- 377. https://doi.org/10.3389/fpls. 2017.00138.
Dessalegn Y.; L. Herselman and M.T. Labuschagne (2008). AFLP analysis among Ethiopian arabica coffee genotype. African Journal of Biotechnology. 7 (18): 3193-3199.
Dessalegn Y.; L. Herselman; and M.T. Labuschagne (2009). Comparison of SSR and AFLP analysis for genetic diversity assessment of Ethiopian arabica coffee genotypes. South African Journal of Plant and Soil. 2009; 62 (2): 119-125. doi:10.1080/02571862.
FAO. 1968a. Food and Agriculture organization of the United Nations. Coffee mission to Ethiopian 1964 –1965.
Garrido-Cardenas J.A; C. Mesa-Valle and F. Manzano-Agugliaro (2018). Trends in Plant Research Using Molecular Markers. Planta, 247:543.
Ghaderi A. A.W. Adams and A.M. Nassib (1984). Relationship between genetic distance and heterosis for yield and morphological traits in dry edible bean and faba bean. Crop Science 24:37-42.
Guillaumet J.L and F. Halle (1978). Sampling of Coffea arabica material harvested in Ethiopia. Bulletin – IFCC. 14: 13-18. http://www.documentation.ird.fr/hor/fdi:03820.
Jaccard P. (1908). Nouvelles researches sur la distribution florale. Bulletin de la Société vaudoise des sciences naturelles. 44: 223-270.
Jingade P.; A.K. Huded; B. Kosaraju and M.K. Mishra (2019) Diversity Genotyping of Indian Coffee (Coffea Arabica L.) Germplasm Accessions by Using SRAP Markers. Journal of Crop Improvement. 33: 327–345. doi:doi.10.1080/15427528.2019.1592050.
Lemi B.; A. Ashenafi and B. Tadesse (2017). Correlation and path coefficient analysis for yield and yield components in some Ethiopian accessions of Arabica Coffee. International Journal of Plant Breeding and Crop Science. 4(2): 178-186.
Lemi B.; B. Tadesse and M.W. Getachew (2021). Phenotypic Diversity of Ethiopian Coffee (Coffea arabica L.) Accessions Collected from Limmu Coffee Growing Areas Using Multivariate Analysis. American Journal of BioScience. 9 (3): 79-85. doi: 10.11648/j.ajbio.20210903.12.
Masreshaw Y.; G.S. Wosene and T. Abush (2020). Estimate of genetic variability components via quantitative traits in coffee (Coffea arabica L.) germplasm in Ethiopia. J. Agri. Sci. Res. 8(5): 492-504.
Mekbib Y.; K. Tesfaye; X. Dong J.K. Saina; G.W. Hu and Q.F. Wang (2022). Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC Plant Biology, 22(1), 1-9. https://doi.org/10.1186/s12870-022-03449-4.
Moncada P. and S. Mccouch (2004). Simple sequence repeats diversity in diploid and tetraploid Coffea species. Genome. 47: 501-509.
Montagnon C.; A. Mahyoub; W. Solano and F. Sheibani (2021). Unveiling a unique genetic diversity of cultivated Coffea arabica L. in its main domestication center: Yemen. Genetic Resources and Crop Evolution, 68 (6), 2411-2422. http://doi.org/10.1007/s10722-021-01139-y.
Pruvot-Woehl S.; S. Krishnan; W. Solano; T. Schilling; L. Toniutti; B. Bertrand and C. Montagnon (2020). Authentication of Coffea arabica Varieties through DNA Fingerprinting and its Significance for the Coffee Sector. Journal of AOAC International, 103(2), 325-334. https://doi.org/10.1093/jaocint/qsz003.
Silveira S.R.; P.M. Ruas; C.F. Ruas; T. Sera; V.P. Carvalho and A.S.G. Coelho (2003). Assessment of genetic variability within and among progenies and cultivars of coffee using RAPD markers. Genet Mol Biol. 26: 329–336.
Silvestrini M.; Junqueira M.G.; A.C. Favarin; O. Guerreiro-Filho; M.P. Maluf; M.P. Silvarolla and C.A. Colombo (2007). Genetic diversity and structure of Ethiopian, Yemen and Brazilian Coffea arabica L. accessions using microsatellites markers. Genet Res Crop Evol. 54: 1367–1379.
Steiger D.L.; C. Nagai; P.H. Moore; C.W. Morden; R.V. Osgood and R. Ming (2002). AFLP Analysis of Genetic Diversity within and among Coffea Arabica Cultivars. Theoretical and Applied Genetics. 105: 209–215. doi:10.1007/s00122-002-0939-8.
Tesfaye K.; K. Govers; E. Bekele and T. Borsch (2014). ISSR fingerprinting of Coffea arabica throughout Ethiopia reveals high variability in wild populations and distinguishes them from landraces. Plant Syst Evol. DOI 10.1007/s00606-013-0927-2.
Teressa A; C. Dominique; P. Vincent and B. Pier (2010). Genetic diversity of Arabica coffee (Coffea arabicaL.) Collections. EJAST. 1(1): 63-79.
Tiago V.S; E.T. Caixeta; E.R. Alkimim, A.C.B. De Oliveira; A.A. Pereira; L. Zambolim and N.S. Sakiyama (2017). Molecular Markers Useful to Discriminate Coffea Arabica Cultivars with High Genetic Similarity. Euphytica, 213 (3), DOI:10.1007/s10681-017-1865-9.
World Coffee Research (WCR) 2014. Assessment of genetic diversity in Coffea arabica. World Coffee Research Annual Report, Texas, USA.
Aga E.; E. Bekele and T. Bryngelsson. (2005). Inter-simple sequence repeats (ISSR) variation in forest coffee trees (Coffea arabica L.) populations from Ethiopia. Genetica. 124: 213–221.
Al-Murish Tm.; A.A. Elshafei; A.A. Al-Doss and M.N. Barakat (2013). Genetic diversity of coffee (Coffea arabica L.) in Yemen via SRAP, TRAP, and SSR markers. J Food Agric Environ, 11(2), 411-416. https://doi.org/10.1234/4.2013.4315
Ameha M. and B. Bellachew (1983). Heterosis in cross of indigenous coffee selected for yield and resistance to Coffee Berry Disease II-first three years. EJAS. 1: 13–21.
Anthony F; B. Bertrand; O. Quiros; A. Wilches; P. Lashermes; J. Berthaud, and A. Charrier (2001). Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers. Euphytica. 118: 53–65.
Anthony F.; M.C. Combes; C. Astorga; B. Bertrand, G. Graziosi and P. Lashermes (2002). The origin of cultivated Coffea arbica L. varieties revealed by AFLP and SSR markers. Theory of Applied Genetics 104: 894– 900.
Baltazar M.D and J.M.O. Fabella (2020). Genetic Diversity of Philippine Arabica Coffee. Philippine Journal of Science. 149 (3-a): 993-1003.
Benti T. 2017. Progress in arabica coffee breeding in Ethiopia: Achievements, challenges and prospects. International Journals of Sciences: Basic and Applied Research (IJSBAR). 33 (2): 15-25.
Benti T.; G. Endale; T. Kassahun; B. Gezahegn; P. Lashermes; K. Martina and K.Y. Nasser (2021). Genetic diversity among commercial arabica coffee (Coffea arabica L.) varieties in Ethiopia using simple sequence repeat markers. Journal of crop improvement 35(2): 147-168. Doi.10.1080/15427528.2020.1803169.
Benti T; G. Endale; T. Kassahun; B. Gezahegn; P. Lashermes, K. Martina and K.Y. Nasser (2022). Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers. American Journal of Biochemistry and Biotechnology 18 (4): 394.404. doi: 10.3844/ajbbsp.2022.394.404.
Bertrand B.; H. Etienne; C. Cilas; A. Charrier and P. Baradat (2005). Coffea arabica hybrid performance for yield, fertility and bean weight. Euphytica. 141: 255–262.
Borsch T; K.W. Hilu; D. Quandt; V. Wilde; C. Neinhuis and W. Barthlott (2003). Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J. Evol. Biol 16: 558-576.
Botestein D; R.L. White; M. Skolnick and R.W. Devis (1980). Construction of genetic linkage map in man using ristrictin fragment length polymorphisms. The American Journal of Human Genetics, 32: 314-331
Davis A.P.; J. Tosh; N. Ruch and M. Fay (2011). Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc. 167:357- 377. https://doi.org/10.3389/fpls. 2017.00138.
Dessalegn Y.; L. Herselman and M.T. Labuschagne (2008). AFLP analysis among Ethiopian arabica coffee genotype. African Journal of Biotechnology. 7 (18): 3193-3199.
Dessalegn Y.; L. Herselman; and M.T. Labuschagne (2009). Comparison of SSR and AFLP analysis for genetic diversity assessment of Ethiopian arabica coffee genotypes. South African Journal of Plant and Soil. 2009; 62 (2): 119-125. doi:10.1080/02571862.
FAO. 1968a. Food and Agriculture organization of the United Nations. Coffee mission to Ethiopian 1964 –1965.
Garrido-Cardenas J.A; C. Mesa-Valle and F. Manzano-Agugliaro (2018). Trends in Plant Research Using Molecular Markers. Planta, 247:543.
Ghaderi A. A.W. Adams and A.M. Nassib (1984). Relationship between genetic distance and heterosis for yield and morphological traits in dry edible bean and faba bean. Crop Science 24:37-42.
Guillaumet J.L and F. Halle (1978). Sampling of Coffea arabica material harvested in Ethiopia. Bulletin – IFCC. 14: 13-18. http://www.documentation.ird.fr/hor/fdi:03820.
Jaccard P. (1908). Nouvelles researches sur la distribution florale. Bulletin de la Société vaudoise des sciences naturelles. 44: 223-270.
Jingade P.; A.K. Huded; B. Kosaraju and M.K. Mishra (2019) Diversity Genotyping of Indian Coffee (Coffea Arabica L.) Germplasm Accessions by Using SRAP Markers. Journal of Crop Improvement. 33: 327–345. doi:doi.10.1080/15427528.2019.1592050.
Lemi B.; A. Ashenafi and B. Tadesse (2017). Correlation and path coefficient analysis for yield and yield components in some Ethiopian accessions of Arabica Coffee. International Journal of Plant Breeding and Crop Science. 4(2): 178-186.
Lemi B.; B. Tadesse and M.W. Getachew (2021). Phenotypic Diversity of Ethiopian Coffee (Coffea arabica L.) Accessions Collected from Limmu Coffee Growing Areas Using Multivariate Analysis. American Journal of BioScience. 9 (3): 79-85. doi: 10.11648/j.ajbio.20210903.12.
Masreshaw Y.; G.S. Wosene and T. Abush (2020). Estimate of genetic variability components via quantitative traits in coffee (Coffea arabica L.) germplasm in Ethiopia. J. Agri. Sci. Res. 8(5): 492-504.
Mekbib Y.; K. Tesfaye; X. Dong J.K. Saina; G.W. Hu and Q.F. Wang (2022). Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC Plant Biology, 22(1), 1-9. https://doi.org/10.1186/s12870-022-03449-4.
Moncada P. and S. Mccouch (2004). Simple sequence repeats diversity in diploid and tetraploid Coffea species. Genome. 47: 501-509.
Montagnon C.; A. Mahyoub; W. Solano and F. Sheibani (2021). Unveiling a unique genetic diversity of cultivated Coffea arabica L. in its main domestication center: Yemen. Genetic Resources and Crop Evolution, 68 (6), 2411-2422. http://doi.org/10.1007/s10722-021-01139-y.
Pruvot-Woehl S.; S. Krishnan; W. Solano; T. Schilling; L. Toniutti; B. Bertrand and C. Montagnon (2020). Authentication of Coffea arabica Varieties through DNA Fingerprinting and its Significance for the Coffee Sector. Journal of AOAC International, 103(2), 325-334. https://doi.org/10.1093/jaocint/qsz003.
Silveira S.R.; P.M. Ruas; C.F. Ruas; T. Sera; V.P. Carvalho and A.S.G. Coelho (2003). Assessment of genetic variability within and among progenies and cultivars of coffee using RAPD markers. Genet Mol Biol. 26: 329–336.
Silvestrini M.; Junqueira M.G.; A.C. Favarin; O. Guerreiro-Filho; M.P. Maluf; M.P. Silvarolla and C.A. Colombo (2007). Genetic diversity and structure of Ethiopian, Yemen and Brazilian Coffea arabica L. accessions using microsatellites markers. Genet Res Crop Evol. 54: 1367–1379.
Steiger D.L.; C. Nagai; P.H. Moore; C.W. Morden; R.V. Osgood and R. Ming (2002). AFLP Analysis of Genetic Diversity within and among Coffea Arabica Cultivars. Theoretical and Applied Genetics. 105: 209–215. doi:10.1007/s00122-002-0939-8.
Tesfaye K.; K. Govers; E. Bekele and T. Borsch (2014). ISSR fingerprinting of Coffea arabica throughout Ethiopia reveals high variability in wild populations and distinguishes them from landraces. Plant Syst Evol. DOI 10.1007/s00606-013-0927-2.
Teressa A; C. Dominique; P. Vincent and B. Pier (2010). Genetic diversity of Arabica coffee (Coffea arabicaL.) Collections. EJAST. 1(1): 63-79.
Tiago V.S; E.T. Caixeta; E.R. Alkimim, A.C.B. De Oliveira; A.A. Pereira; L. Zambolim and N.S. Sakiyama (2017). Molecular Markers Useful to Discriminate Coffea Arabica Cultivars with High Genetic Similarity. Euphytica, 213 (3), DOI:10.1007/s10681-017-1865-9.
World Coffee Research (WCR) 2014. Assessment of genetic diversity in Coffea arabica. World Coffee Research Annual Report, Texas, USA.