Development of marker based for breeding cassava for resistance to cassava mosaic disease

Abstract

The dreaded cassava mosaic disease (CMD) caused by cassava mosaic virus (es) still remains the major hindrance to production of cassava in many cassava growing areas. Breeding for host resistance to this disease has remained the most cost effective control strategy. However, it has also been worsened by long cropping cycles, recessive nature of the resistance and cassava‟s heterozygous nature. In Uganda, breeding for resistance to CMD aims at improving farmers preferred cultivars using exotic collections with resistance to CMD. Introduced CMD resistant cultivars; TME5, TME14, Nase10, Nase12 and 95/SE00036 were crossed with susceptible farmer-preferred cultivars; Bamunanika, Bao, Kakwale and Nyaraboke to obtain F1 progeny that were further selected under high CMD pressure in Namulonge. When tested for Mendelian segregation, progeny from susceptible and resistant female parents segregated varyingly. Nyaraboke and Bao conformed to the 1:1 ratio as Kakwale and Bamunanika to the 3:1 ratio of segregation. As expected, all families derived from resistant female parents adhered to the 3:1 ratio except Nase10 that remained non-significant at both P=0.05 and P=0.01. To characterise this population for polymorphism associated with resistance to CMD, parents were analysed with 120 SSR markers widely distributed in the cassava genome. Amplifications were performed on GeneAmp PCR system 9700 and products were resolved on ABI3730 capillary electrophoresis. Preliminary analysis was performed using Genemapper and data exported to Microsoft excel for further statistical analyses. Genotyping results from the 120 primers were subjected to cluster analysis using PowerMarker to cluster the parents based on their response to CMD. Two clusters were obtained, one consisting of resistant parents and the other of susceptible parents. The parent 95/SE00036 that is tolerant to infection by CMD was clustered with susceptible

parents, suggested it‟s a different form of resistance, probably highly dependent on the environment. This suggests that it is probably tolerant to disease and not resistant to the pathogen infection and multiplication. The selected parental polymorphic markers used in cluster analysis were validated through bulk segregant analysis (BSA) of the segregating loci. Six Simple Sequence Repeat (SSR) markers SSRY20, SSRY45, SSRY175, SSRY284, NS40 and NS717 located on linkage groups 18, 8, not mapped yet, 5, 7 and 4 respectively were found to segregate with the loci conditioning resistance to CMD. These genetic markers were subsequently used to screen the entire progeny. Linkage analysis was also performed using MAPMAKER to determine the map distance from the resistance loci. Mapping results showed that SSRY20, SSR, located on different linkage groups on the SSR based cassava genetic map are actually in one linkage group. This disparity confirms speculation that the SSR based cassava genetic map still needs to be saturated with molecular markers. Having been generated from open pollination, the population did not have established paternity and mapping information was only obtained from female parents (half sib). Other factors, including paternal contribution, pre and post fertilisation modifications, selective fertilization may also have influenced the genetic map obtained. Further analysis using additional markers and attempts to establish paternity of these progeny may authenticate the mapping results. These findings stress the need for a more homozygous mapping population with fully established parentage and that use of pedigree information (association mapping) may provide the best option for mapping in cassava.