Genome-wide DNA polymorphisms in two peatland adapted Coffea liberica varieties

Coffea liberica is one of the species within the Coffea genus known for its distinctive flavor and resistance to leaf rust disease. Through breeding approaches, two superior varieties of C. liberica, designated as Liberoid Meranti 1 (Lim 1) and Liberoid Meranti 2 (Lim 2), were introduced in 2015. These varieties are known for their high adaptability in peatlands. The genetic basis of plant adaptability to peatlands remains largely unknown. It is therefore essential to identify genome-wide DNA polymorphisms in Lim 1 and 2 in order to gain insights into its capacity for adaptation in peatlands.

Whole genome sequencing was performed on three plants from each variety (Lim 1 and 2), resulting in 430 million sequencing reads. The mean depth of sequencing for each sample was 36.90x. The reads were mapped to the Coffea canephora genome, with an average mapping rate of 96.34%. The sequencing data revealed the presence of 3,766,805 single-nucleotide polymorphisms (SNPs) and 1,123,683 insertion-deletions (indels) in all six plants. Among the SNPs, there was a notable prevalence of transitions, with a ratio of approximately twofold compared to transversions. The generated data offers invaluable genomic resources for marker development, with significant implications for understanding peatlands adaptability.