Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee

Abstract

Coffee is an important beverage crop in the world and has a significant contribution to Kenya's economy. Here, we analyzed the genome-wide distribution of microsatellites in the Coffea canephora genome. A total of 159,041 SSRs were identified, with an overall density of 308 SSRs per Mb. Tetra-nucleotide repeats are the most abundant, accounting for 32 % of the total SSRs. AT-rich motifs are dominant across all SSR repeat units, while GC-rich motifs were generally rare. A set of 100 SSRs was selected to amplify 96 coffee accessions, including 10 wild accessions collected from Mt. Marsabit (Kenya). Of these SSRs, 33 % generated clear polymorphic bands among all tested accessions, with an average of 3.9 alleles per SSR locus. Wild coffee species from Mt. Marsabit showed a close genetic similarity with cultivated accessions in Kenya, suggesting that the wild species in Mt. Marsabit played an important role in the domestication of cultivated coffee in Kenya. Significantly low pairwise genetic divergence was observed between cultivated and wild accessions in Kenya, suggesting a relatively narrow level of genetic basis among coffee germplasm in Kenya. In addition, cultivated and wild coffee accessions in Kenya show a great divergence from those in other countries. Our results not only provide molecular tools for genetic studies in coffee but are also helpful for conservation and coffee breeding programs in Kenya.

Development and Utilization of Microsatellite Markers to Assess Genetic Variation Coupled with Modelling Range Shifts of Dodonaea Viscosa in Isolated Taita Hills and Mount Kenya Forests

“…The SSR density detected in this study is nearly similar with Jujube (321.56 SSRs/Mb) [49]. Plants exhibit variation of SSRs Repeat units within their genomes, for example, in Paleosuchus trigonatus, di-nucleotide repeat motif predominated [50], whereas tetra-nucleotide repeats were the most frequent in Coffea canephora [51], and tri-nucleotide repeat motifs being most frequent in Hyalessa fuscata [52]. The mono-nucleotide repeat motifs predominated in our study, which is similar to Alibertia edulis [53].…”

Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae)

“…Coming from coding regions, these markers are more conserved among populations of the same species and congeners, thus, enabling cross-amplification and allowing the characterization of molecular marker sets for species which have not been well characterized genetically [ 18 – 22 ]. Several EST-SSR markers have been identified for a diverse range of crops, such as maize [ 23 ] and tomato [ 24 ], arboreal crops as coffee [ 25 , 26 ], cacao [ 27 ] and, the first work involving EST-SSR from T . grandiflorum [ 28 ].…”

Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora

“…A total of 23 C. canephora including 18 cultivated and five wild accessions used in this study are maintained at Spice and Beverage Research Institute of Chinese Academy of Tropical Agricultural Sciences (Hainan, China). Cultivated accessions were selected based on our previously published polymorphic data (Ogutu et al, ; Yan et al, ). Seeds were randomly collected at mature stage, immediately frozen in liquid nitrogen, and then stored at −80°C until use.…”

“…Seeds were randomly collected at mature stage, immediately frozen in liquid nitrogen, and then stored at −80°C until use. Total DNA was isolated from twenty‐three freshly frozen coffee seeds using our previously described modified protocol (Ogutu et al, ). PCR primers were designed for specific sequencing regions (Table ).…”