Root-knot nematodes and coffee in Nicaragua: management systems, species identification and genetic diversity

The coffee production is affected by several limiting factors such as parasitic nematodes. Plant-parasitic nematodes have a substantial economic impact on coffee production in most countries and they are regarded as one of the major limiting factors in coffee production and worldwide coffee losses have been estimated to about 15%. The aim of this thesis is to contribute to the knowledge of the plant-parasitic nematodes associated with coffee production in Nicaragua, by studying the effect of coffee management, identification of Meloidogyne species and determination of the level of genetic diversity in the root-knot nematodes and coffee. This thesis includes results of the effect of coffee management systems on the occurrence of plant-parasitic nematodes, identification of root-knot nematodes using morphological characteristics, SCAR markers and DNA sequences; ISSR based genetic diversity of M. exigua and SSR based genetic diversity of Coffea arabica in Nicaragua.Both Meloidogyne and Pratylenchus species were found in both conventional and organic management systems. A higher population of Meloidogyne spp. occurred under conventional management with no shade and with shade from nitrogen fixer species while higher populations of Pratylenchus spp. occurred in both conventional and organic management, shaded with non-fixer nitrogen species. Analyses of root-knot nematode isolates from Nicaraguan coffee plantations based on perineal patterns, SCAR markers and DNA sequence revealed the presence of Meloidogyne exigua and M. incognita, of which the former has a wider distribution in the country. DNA sequences analysis revealed that this species has unique variable sites within the 18S and 28S rDNA region, which are not present in the rest of the Meloidogyne species including in those sharing similar reproductive mechanisms. These variable sites are useful for developing new species specific SCAR markers that can be used in the diagnosis of M. exigua. The assessment of the genetic diversity of M. exigua populations based on ISSR markers revealed a high genetic diversity in this species. Similarly, the genetic diversity analyses of C. arabica populations using SSR markers revealed a significant variation among different varieties and the highest diversity was obtained in variety Catimor,