Reaction of Selected Coffee Germplasm to Root-Knot Nematodes in Kenya

Coffee is one of the most important cash crops in Kenya and a leading export earner. Nematodes are among the most important biotic constraint in coffee production in Kenya and crop improvement work has mainly been breeding for resistance to diseases such as coffee berry disease and coffee leaf rust. However resistance has been used successfully in other coffee producing countries and it is one of the most economical and practical nematode management strategies. A greenhouse study was conducted to test the response of local and exotic coffee germplasm to root knot nematodes (RKNs). Ten (10) cultivars provided by Coffee Research Foundation (CRF) were tested for resistance to Meloidogyne incognita under greenhouse conditions (25±2oC). Nematodes were extracted from the roots using Modified Baermann Technique and enumerated using Cobbs slide. After 90 days of plant growth, the disease severity was evaluated and the experiment repeated twice. Galling indices (GI), egg mass indices (EMI) and nematode populations recovered from soil samples indicated a range of responses from resistant to highly susceptible.  Three breeder’s lines including Robusta tree 1, Robusta tree 2 and Robusta tree 3 were rated resistant with galling indices of 1.2-3.0. This study has demonstrated the potential of host resistance as a strategy in the management of nematodes in coffee for increased productivity. Field evaluation needs to be conducted to confirm these findings. The identified resistance sources can be utilized to deploy resistance genes to improve existing varieties that have high commercial value but lack resistance to nematodes.   Key words: Resistance, susceptible, galling indices, nematode population, cultivar

Plant Parasitic Nematodes Associated With Coffee in Kenya and Factors Influencing their Occurrence, Abundance and Diversity

Frequent detection of galls on coffee roots has raised concerns of nematodes in coffee production systems in Kenya. This study aimed at determining the occurrence of nematodes associated with coffee in Kenya and the role of crop management, cultivars, soil properties and agro ecological zones on the abundance and frequency of nematodes. A survey was conducted in the prime coffee growing areas in 10 counties namely; Machakos, Makueni, Kiambu, Embu, Kirinyanga, Nyeri, Meru, Kisii, Nandi and Trans-Nzoia. Nematodes were extracted using a combination of centrifugal floatation and Modified Baermann techniques and identified to genera level.  Nutrient analysis was carried out using the Double Mehlich method. Results showed that nematodes belonging to 30 genera were recovered from coffee agro-ecosystems. Plant parasitic nematodes were the most prevalent with 64% frequency (19 genera) of occurrence followed by bacterial feeders at 24%. The genus Tylenchulus, Meloidogyne and Pratylenchus were the most dominant across all the coffee growing areas. Coffee farms in the coffee-tea zones (Upper Midland 1) harbored the highest numbers of plant parasitic nematodes, followed by Upper Midland 2 and least in the marginal coffee growing zones (Upper Midland 3). Well managed farms had less plant parasitic nematodes compared to neglected farms. K and P significantly contributed to the variation in the nematode community composition. This study demonstrated the prevalence of plant parasitic nematodes, factors that influence their abundance and distribution and justifies need for further management of nematodes in coffee production. Key words: Abundance, agro-ecologial zones, diversity, nematode genera, nutrient

IMa input and nested models files

The IMa.zip contains two files: The input file for IMa and the nested models files needed to test competing hypotheses of gene flow pattern

Data from: Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae

Ecological speciation through host-shift has been proposed as a major route for the appearance of novel fungal pathogens. The growing awareness of their negative impact on global economies and public health created an enormous interest in identifying the factors that are most likely to promote their emergence in nature. In this work, a combination of pathological, molecular and geographic data was used to investigate the recent emergence of the fungus Colletotrichum kahawae (Ck). Ck emerged as a specialist pathogen causing Coffee Berry Disease in Coffea arabica, due to its unparalleled adaptation of infecting green coffee berries. Contrary to current hypotheses, our results suggest that a recent host-jump underlay the speciation of Ck from a generalist group of fungi seemingly harmless to coffee berries. We posit that immigrant inviability and a predominantly asexual behavior could have been instrumental in driving speciation by creating pleiotropic interactions between local adaptation and reproductive patterns. Moreover, we estimate that Ck began its diversification at less than 2,200 yrs leaving a very short time frame since the divergence from its sibling lineage (∼5,600 yrs), during which a severe drop in Ck’s effective population size occurred. This further supports a scenario of recent introduction and subsequent adaptation to C. arabica. Phylogeographic data revealed low levels of genetic polymorphism but provided the first geographically consistent population structure of Ck, inferring the Angolan population as the most ancestral and the East African populations as the most recently derived. Altogether, these results highlight the significant role of host specialization and asexuality in the emergence of fungal pathogens through ecological speciation

Silva2012_alignments

This zip files contain the alignments of the six nuclear markers in NEXUS leave format

*BEAST and Skyride xml files

This .zip file contains the xml input files of the best model for the *BEAST analysis and GMRF Skyride