Molecular distinction of C × R hybrid (Coffea congensis × Coffea canephora) from morphologically resembling male parent using rbcL and matK gene sequences

Interspecific C × R hybrid (Coffea congensis × Coffea canephora) in India is cultivated as mixed population with male parent C. canephora as this species is an efficient pollen donor for enhanced yield. But distinction of C × R hybrid from C. canephora in old plantation is difficult due to varying plant sizes of C × R hybrid and often resembles with C. canephora. C × R hybrid cultivated under different agroclimatic conditions show distinct vegetative growth pattern with varying yields. Thus development of DNA marker for identification of C × R hybrid is important for clonal propagation and seed preparation from selective individuals. In this study, two DNA bar coding loci of chloroplast genome (rbcL and matK) of parents, F1 hybrid and its back cross progeny were partially sequenced to identify SNPs as DNA marker for distinction of C × R hybrid from C. canephora. Seven SNPs in the matK gene sequence and three nucleotides in the rbcL gene sequence were identified as DNA markers for the genetic identity of C. congensis. These SNPs were found in F1 and advanced progenies of C × R hybrid due to maternal inheritance. Large number of samples of C × R hybrids with varying morphological features revealed no polymorphism among C × R hybrid and C. congensis. Thus, the SNPs in C. congensis can be used as DNA markers for precise identification of C × R hybrid for production of clones besides tagging the chloroplast inheritance in advanced progenies.