Breeding for resistance to stem rust in bread wheat

Stem rust disease caused by Puccinia graminis f. sp. tritici (Eriks and E. Henn) poses the greatest threat to global wheat production due to the emergence of a highly virulent race of the Puccinia graminis f. sp. tritici Ug99 race and its variants. This study was set out to a) to identify sources of resistance to stem rust in bread wheat b) to determine the genetics of the stem rust resistance genes in bread wheat and c) to identify molecular markers and the genomic regions (quantitative trait loci, QTL) harbouring the stem rust resistance genes in bread wheat. Twenty-five wheat genotypes designated as “KSL”were evaluated for both field and seedling resistance at Kenya Agricultural Research Institute (KARI), Njoro. The most resistant wheat genotypes KSL-2, KSL-3 and KSL-20 also exhibited the pseudo black chaff (PBC) trait suggesting presence of the Sr2 gene. The presence of trace responses in field tests and resistant infection types during the seedling tests suggested involvement of major genes in conditioning the stem rust resistance. For the inheritance studies, five promising stem rust resistant parents namely KSL-2, KSL-3, KSL-5, KSL-12 and KSL-19 were crossed in a partial diallel to the susceptible parent CACUKE and advanced into F2 derived F3 families. The purpose of the inheritance study was to establish the number and mode of inheritance of the stem rust resistance genes among these parents. The Chi square analysis revealed that the segregation data for KSL-2 consistently followed the 1:2:1 genetic ratio in two seasons implying that one dominant gene conditioned the stem rust resistance in this parent. The parents KSL-3 and KSL-19 consistently followed a 12:3:1 genetic ratio implying that two epistatic genes conditioned the resistance to stem rust. The knowledge of the nature and the number of genes revealed among the wheat parents form a core component of the wheat breeding program in ensuring an efficient breeding strategy. In conclusion, the resistance genes associated with this resistance could be identified through further dissection of the QTLs to elucidate the exact gene effects and their chromosomal locations. The population could also be advanced further into recombinant inbred lines (RILs) for marker assisted selection (MAS) and quantitative trait loci (QTL) mapping. The QTL mapping of PBW343/Juchi F6 recombinant inbred line (RIL) population for adult plant resistance to stem rust involved the use of Diversity Array genotyping Technology (DArTs). The resistance to stem rust in PBW343/Juchi was conditioned by both epistatic and additive genes and this could be exploited through MAS, gene pyramiding and other breeding strategies to transfer these QTLs into elite wheat backgrounds. In this research, three new DArT markers namely wPt-9493, tPt9767 and tPt-6872 were identified and these markers could be used in the co-selection and improvement of important traits through MAS.The QTL mapping also revealed eight QTLs flanked by different DArT markers. Positional cloning of genes and QTLs through fine mapping within the gene-rich regions of bread wheat could lead to identification of more Adult plant resistance (APR) QTLs for better detection, mapping and estimation of gene effects. Also, the QTLs could be used to develop reliable markers for marker assisted breeding.