Investigating the diversity of plant-parasitic nematodes associated with coffee in Kenya, using morphological and molecular approaches

Summary Comprehensive surveys in nine coffee-growing counties in Kenya, involving 53 farms and comprising 116 soil and 63 root samples, revealed a total of 12 genera of plant-parasitic nematodes, including: Meloidogyne , Paratylenchus , Pratylenchus , Helicotylenchus , Rotylenchus , Rotylenchulus , Scutellonema , Trophotylenchulus , Xiphinema , Trichodorus , Aphelenchoides and Hemicycliophora. Meloidogyne was the most abundant genus, with densities of up to 210 juveniles (100 ml soil) −1 . Morphological and molecular characterisation enabled the identification of several nematode species including Meloidogyne javanica , M. africana , Rotylenchulus borealis and Trophotylenchulus obscurus . For T. obscurus , the 18S rDNA sequences obtained in this study are the first ever reported for the genus. Additionally, the 18S and D2-D3 of 28S, as well as ITS sequences, marked first for this species. In total, six partial 18S, seven D2-D3 of 28S, four ITS sequences of rDNA, ten COI , and two nad5 gene sequences were generated in this study. In conclusion, our study reveals that our knowledge of plant-parasitic nematode occurrence on important crops even, such as coffee, remains poorly documented and understood, highlighting the potential for new discoveries in such areas.