Analysis of genetic diversity of Arabica coffee [Coffea arabica L.] in Solok Regency by SRAP molecular markers

Yunita, Rossa; Oktavioni, M; Chaniago, Irawati; Syukriani, Lily; Jamsari, J

doi:10.1088/1755-1315/497/1/012018

Cited by 5 publications

(2 citation statements)

References 8 publications

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“…Similar results were reported previously by (Aga et al, 2003;Tesfaye et al, 2014) using ISSR markers, where coffee tree samples comprising forest, semi-forest and farmers' cultivars collected from different parts of Ethiopia were clustered based on their geographic origin. Such results were also reported from Indonesia, where 73 to 92 % genetic similarity was detected by eight SRAP markers in populations of five arabica coffee varieties collected from different locations (Yunita et al, 2020). This indicates that some genotypes from the same geographic origin are more closely related at the DNA level than those from different origins.…”

Section: Clustering Patterns Of Elite Breeding Linessupporting

confidence: 80%

Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

Benti¹,

Gebre²,

Tesfaye³

et al. 2022

American Journal of Biochemistry and Biotechnology

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Despite being the center of origin and genetic diversity, there has been limited application of molecular markers in arabica coffee breeding in Ethiopia. In this study, the extent of genetic diversity and relationships of 48 elite breeding lines of arabica coffee from different geographical origins were evaluated using 14 SSR markers. The SSR markers amplified 105 alleles of which 104 are polymorphic with an average of 7.4 polymorphic alleles per locus. The average percent of polymorphism and Polymorphic Information Content (PIC) of the SSR markers were 98.81 and 0.79, respectively. The average genetic similarity coefficient among all possible pairs was 0.37 and ranged from 0.39 to 0.46 within the same geographical origin. The Unweighted Pair Group Method Using Arithmetic averages (UPGMA) cluster analysis placed the studied breeding lines into seven clusters with Jaccard's similarity coefficient of <0.44. The results of this study demonstrated the powerfulness of the SSR markers and the presence of a high level of genetic diversity and wide genetic dissimilarity within and among elite breeding lines from the same and different geographical origins. The observed diversity could be utilized in the breeding program to improve productivity and maintain the typical quality profile of origin-based landrace coffees. The SSR markers could be used in future genetic analysis of arabica coffee germplasm to increase the efficiency of the breeding program in Ethiopia. The studied breeding lines could also be conserved and managed as an important source of genetic variability to be used in the future coffee improvement program.

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Section: Clustering Patterns Of Elite Breeding Linessupporting

confidence: 80%

Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

Benti¹,

Gebre²,

Tesfaye³

et al. 2022

American Journal of Biochemistry and Biotechnology

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“…The genetic variability of C. arabica accessions from other countries, such as Costa Rica [94], Mexico [95], Nicaragua [96], India [97][98][99], Indonesia [100], China [101], Kenya [102] and Ethiopia [34,[103][104][105], has also been analyzed using markers such as ISSRs, SSRs, sequence-related amplified polymorphisms (SRAPs), AFLPs, and SNPs. In Ethiopia, different studies have shown the presence of great genetic variability in coffee plants.…”

Section: Genetic Diversity Based On Molecular Markersmentioning

confidence: 99%

Genetic Variation

2021

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Coffea arabica L. is a native coffee species probably originated in Abyssinia, now Ethiopia. The genetic diversity of C. arabica has economic implications directly related to profits by breeding for developing new varieties to a global market. The economic value of C. arabica genetic resources are estimated at US$ 420 million, considered a 10% discount rate. Understanding the extent of traits variability and genetic diversity is essential to guide crosses between genotypes, targeting the development of new varieties with high economic value. This chapter will present the C. arabica economic importance, primarily to Brazil, the most significant world producer; we will outline the origin and dispersion of arabica coffee and briefly show the leading germplasm banks. We will also point out contribution of genetic diversity studies based on morphological, agronomic traits, and molecular markers supporting the development of new varieties. Finally, we present an outline for the future.

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Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau

2023

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Background The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits. Methods This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform. Results The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality. Conclusions The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role.

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Analysis of genetic diversity of Arabica coffee [Coffea arabica L.] in Solok Regency by SRAP molecular markers

Cited by 5 publications

References 8 publications

Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

Genetic Variation

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau

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