Pyramiding bean anthracnose and root rot resistance genes into susceptible market class common bean varieties using scar markers

Bean anthracnose, caused by Colletotrichum lindemuthianum (Sacc. et. Magn) Lams.Scrib., is one of the most widespread and economically important fungal diseases of the common bean. It has a high genetic variability which renders single gene resistance inadequate since it is easily broken down. Root rots on the otherhand are caused by a complex of fungal pathogens of which the Pythium spp is the most abundant. This study, therefore, sought to address four objectives namely a) Determine the virulence diversity of Colletotrichum lindemuthianum in Uganda, b) Develop and evaluate advanced common bean lines with multiple resistance genes to anthracnose and Pythium root rot using sequence characterized amplified regions (SCAR) markers, c) Assess the effectiveness of pyramided genes in conferring broad resistance to bean anthracnose, and d) Determine the effect of gene pyramiding of anthracnose and Pythium resistance genes on plant agronomic characters. To determine virulence diversity of Colletotrichum lindemuthianum in Uganda, 51 isolates collected from eight purposively selected districts were used to inoculate 12 differential cultivars under controlled conditions. Disease severity scores were used to designate races using the binary nomenclature system ANOVA revealed that variation due to cultivar and isolate effects was highly significant (P≤0.001). Race designation grouped the 51 isolates into 27 races. The highland districts of Sironko Mbale and Kabarole respectively had the highest race diversity. Races 2047 and 4095 were the most frequentRace 4095 had the broadest spectrum of virulence followed by 2479, 2047 and 2045 respectively. Cultivar G2333 showed the broadest resistance followed by Cornell, TU, and AB136 respectively. Therefore, C. lindemuthianum in Uganda was found to be diverse with 27 races samples from eight districts. A cascading pedigree gene pyramiding scheme was used to pyramid three anthracnose and one Pythium resistance genes in four susceptible bean varieties K132, NABE4, NABE13 and NABE14. SCAR markers were used to facilitate the process through marker assisted selection (MAS). Sixty nine (69) F4:6 families possessing different number of genes in different combinations were obtained. Out of these, three families inherited all the three anthracnose and one Pythium resistance genes. 14 families inherited two anthracnose and one Pythium resistance genes. Four C. lindemuthianum races namely 2047, 713, 767 and 352 were used to screen for resistance among the pyramided lines. Genotypes possessing all three anthracnose resistance genes Co-42, Co-5 and Co-9 showed high level of resistance towards the four races. Three of four genotypes possessing Co-42 and Co-5 genes were resistant to all four races. Two of four genotypes possessing Co-5 and Co-9 were resistant to the four races. Therefore, pyramided lines were successfully developed using SCAR markers and pyramided genes conferred broad resistance to C. lindemuthianum although some pyramid groups were more effective than others. To determine the effectiveness of pyramided genes in conferring broad resistance to bean anthracnose, races 352, 713, 767 and 2047 were used to inoculate 40 F6 lines using the detached leaf method. Five gene pyramid groups namely Co-42+Co-5+Co-9, Co-42+ Co-5, Co-42+Co-9, Co-5+Co-9, Co-43+Co-9 and four single gene group means were compared using Tukey’s test. Results showed that the five pyramid group means were significantly different from each other (P<0.01). Of these, Co-42+Co-5+Co-9 and Co-42+Co-5 exhibited both a high degree and broad spectrum nature of resistance. The group Co-43+Co-9 was the least effective. The single-gene groups were significantly different from each other (P<0.01). The Co-42 and Co-5 single genes conferred resistance to all the four races. The single gene Co-42was not significantly different from the best pyramid groups Co-42+Co-5+Co-9 and Co-42+Co-5 (P<0.01) while the Co-5 was not significantly different from Co-42+Co-5, Co-42+Co-9 and Co-5+Co-9 gene pyramid groups (P<0.01). The study revealed that single genes may be as effective as pyramided genes in conferring broad resistance to anthracnose although pyramided genes may be more effective at suppressing disease symptoms. To determine effect of pyramided genes on plant agronomic characters correlation and path coefficient analysis were carried out. Results showed that number of pyramided genes was significantly negatively correlated with seed weight per plant (0.17, P<0.01) number of pods per plant (-0.24, P<0.05), number of seeds per plant (-0.19, P<0.1). Path coefficient analysis revealed that only number of seeds per plant and 100-seed weight had significant positive direct effects on seed weight per plant. Number of pyramided genes had a significant negative indirect effect (-0.25) on seed weight per plant via number of seeds per plant. Therefore, a yield penalty may be incurred in gene pyramiding programs.