Analysis of AFLP Markers for Screening Resistance to Common Bean Roots Rot (Pythium spp.)

Abstract

Aims: To investigate AFLPs for suitability as potential markers for identification of sources of Pythium resistance in bean genotypes preferred by poor small holder farmers. Place and Duration of Study: Department of biological sciences Masinde Muliro University of Science and Technology, Kenya and Bangor University, North Wales, United Kingdom, between September 2010 and December 2012. Methodology: 45 common bean accessions comprising 35 seed samples collected from farmers, market centers, as well as seed stockists and ten common bean lines generated from a conventional breeding program with differential resistance to the pathogen Pythium were subjected to AFLP analysis. Genetic characterization using cluster and principal component analysis were conducted to determine segregating patterns of bean accessions in relation to tolerant and Original Research Article Maryrose et al.; AJEA, 5(4): 374-391, 2015; Article no.AJEA.2015.039 375 susceptible bean lines. Average genetic distances were calculated and similarity coefficients subjected to unweighted pair group method of arithmetic averages to generate dendograms. Results: Two informative AFLP primer combinations yielded 194 polymorphic loci. Genetic distance of bean samples from KARI Kakamega had 56 to 414 base pairs with a variability index of 0.63 to 0.90. Combined analysis of bean accessions from KARI breeding program and market class common bean samples revealed a variability index range of 0.62 to 0.90 with 56 to 420 base pairs. PCA contributed about 51.58% on the genetic variation. Cluster analysis of the 10 KARI-Kakamega bean lines revealed that resistant bean varieties were genetically different from the susceptible bean varieties. The dendogram generated revealed four sub-groups and with the exception of Alulu, a mildly resistant cultivar, that segregated alongside resistant cultivars, resistant varieties clustered differently from susceptible cultivars. However, screening with farmers’ germplasm produced a dendogram that revealed a mixture of distinct and relatively non-distinct categorization with regard to resistance. Only resistant cultivars AN1062, R2075, R719 and R1946 and susceptible cultivars GLP2 and GLP585 clustered together as expected. The others segregated randomly alongside the farmers’ germplasm. Resistant varieties AND1062, R2075, R719, R1946 and SCAM80 were more genetically related to marketable class of beans. R1946 R719, R2075 and AND1062 are closely related genetically compared to Mw001, KK15, Alulu and GLP2. Conclusion: AFLP is a relatively informative technique that has a great potential of delineating susceptible and resistant Pythium root rot dry bean varieties, and can be used as a preliminary guide to carry out further analysis. It is notable that the AFLP markers used were not able to clearly distinguish all the cultivars comprehensively and should not be used alone in determining resistance levels. The information generated in this study will contribute to the propagation of acceptable market class bean lines with resistance to Pythium root rot for improved livelihood and increased food security.