Assessment of genetic homogeneity of somatic embryo-derived plants and seed-derived plants of a robusta coffee cultivar using molecular markers and functional genes sequencing

Evaluation of genetic uniformity is important in a perennial plant like coffee propagated through somatic embryogenesis. In this study, we compared the genetic homogeneity of somatic embryo-derived plants and the seed-derived plants obtained from a single mother plant of robusta coffee cultivar by employing Sequence Related Amplified Polymorphism (SRAP) and Start Codon Targeted (SCoT) molecular markers and sequencing four functional genes. The SRAP and SCoT molecular markers revealed 96% genetic similarity between somatic embryo-derived and seed-derived plants with the mother plant. The sequencing analysis has shown the minimum sequence variability in the chloroplast maturase K gene and the highest sequence variability in the zinc finger protein gene compared to NAC25 and UDP-glycosyltransferase genes. The presence of SNP and indels created polymorphism in gene sequences. The percent frequency of SNP varied from 0.0 to 0.45 in matK, 0.36 to 1.40 in NAC25, 0.81 to 2.63 in the UDP-glycosyltransferase gene and 3.30 to 8.70 in the zinc finger protein gene. In the case of NAC25 and UDP-glycosyltransferase genes, the seed-derived plants have shown a higher frequency of SNP compared to somatic embryo-derived plants. However, in the case of zinc finger protein gene, tissue culture-derived plants accumulated a two-fold higher frequency of SNP compared to the seed-derived plants. The sequence characterization of the four genes has revealed the presence of a higher frequency of non-synonymous SNPs compared to synonymous SNPs. This is the first report on the comparative genetic uniformity analysis of somatic embryo-derived and seed-derived plants in robusta coffee cultivar with significant practical implications. Key messageMolecular marker based genetic homogeneity assessment of somatic embryo and seed-derived plantsof Coffea canephora revealed 96% similarity with the mother plant. The SE derived plants exhibited highersequence variability in zinc finger protein gene.