Yellow (stripe) rust (YR) caused by the fungus Puccinia striiformis f. sp. tritici, is a major disease threat to UK winter wheat (WW). Genetic resistance in varieties can be an effective way for growers to prevent or limit disease. However, the presence of resistance genes may come at the expense of successful growth and development in a variety. As part of a previous collaborative project4 novel loci associated to YR resistance were identified. For these to be successfully utilized by marker-assisted selection (MAS), breeders need to know their effectiveness and any associated unwanted agronomic effects. This project aimed to quantify the effectiveness of the Yr genes at these loci and investigate if they have any pleiotropic effect on yield, in a breeding programme environment. Four crosses, Basset x Reflection (BxR), W282 x Siskin (WxS), Kerrin x Hardwicke and Jackal x Reflection were selected from the KWS UK Ltd WW breeding programme. Crosses were selected based on segregating combinations of YR resistance at the marker loci and lines were developed from these using Double Haploid technology. All lines were genotyped for 14 different YR resistance-associated KASP markers. Two years of disease data was collected from field nurseries inoculated with prevalent races. Additionally, lines were chosen which segregated for different resistances from two of the crosses, BxR and WxS, and sown in a replicated fungicide treated yield trial to estimate yield potential. Genotypes containing combinations of published YR genes Yr11, Yr37, Yr15 and Yr3 were associated with significantly lower YR infection compared to sibling lines without those genes, whereas Yr5, Yr8 and Yr9 did not significantly effect YR score. There was no significant difference between the dry grain yield of different combinations of resistances in the BxR cross. In the WxS cross a marker associated to Yr5 had a significant negative effect on yield. As this marker was also identified as having no significant effect on YR resistance, the results suggest that this resistance locus is of negative value in a UK breeding programme. Whilst most loci implicated in YR resistance were confirmed to decrease infection, there was evidence for additional resistance factors elsewhere on the genome, therefore we have still not characterised all the current UK WW resistance. This study demonstrates how the use of MAS should consider the benefit of each resistance before assuming that all resistances are of equal value to a variety’s overall performance.