ORIGINAL ARTICLE Quantitative trait loci (QTL) mapping of blush skin and flowering time in a European pear (Pyrus communis) progeny of ‘Flamingo’ × ‘Abate Fetel’ Solomon M. Ntladi 1,2 & Jan P. Human 1 & Cecilia Bester 1 & Jessica Vervalle 2 & Rouvay Roodt-Wilding 2 & Kenneth R. Tobutt 1 Received: 9 March 2018 /Revised: 25 July 2018 /Accepted: 7 August 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Blush skin and flowering time are agronomic traits of interest to the Agricultural Research Council (ARC) Infruitec-Nietvoorbij pear breeding programme. The genetic control of these traits was investigated in the pear progeny derived from ‘Flamingo’ (blush cultivar) × ‘Abate Fetel’ (slightly blush) made up of 121 seedlings. Blush skin was scored phenotypically over three seasons and flowering time was scored over two seasons. A total of 160 loci from 137 simple sequence repeat (SSR) markers were scored in the progeny and used to construct parental genetic linkage maps. Quantitative trait loci (QTL) analysis revealed two QTLs for blush skin, a major QTL on linkage group (LG) 5 in ‘Flamingo’, and a major QTL on LG9 in ‘Abate Fetel’. Two SSR markers, NB101a and SAmsCO865954, were closely linked with the major QTL on LG5 in ‘Flamingo’, with alleles 139 bp and 462 bp in coupling, respectively. These markers were present in approximately 90% of the seedlings scored as good blush (class 4) based on the average data set. These two markers were used to genotype other pear accessions to validate the QTL on LG5 with the view of marker-assisted selection. Two candidate genes, MYB86 and UDP-glucosyl transferase, were associated with the QTL on LG5 and MYB21 and MYB39 were associated with the QTL on LG9. QTL analysis for flowering time revealed a major QTL located on LG9 in both parents. Marker GD142 with allele 161 bp from ‘Flamingo’ was present in approximately 88% of the seedlings that flowered earlier than either parent, based on the average data set. The QTLs and linked markers will facilitate marker-assisted selection for the improvement of these complex traits. Keywords European pear . Blush skin . Flowering time . Candidate genes . SSRs . QTLs Introduction The European pear (Pyrus communis L.) is an economically important rosaceous fruit crop of temperate regions and is grown in South Africa, with about half of the crop being exported. Traits of interest in pear breeding at the Agricultural Research Council (ARC) include blush skin colour (Human 2013) and adaptation to mild winter, e.g. early flowering time. Blush pear cultivars fetch a higher price than fully red or green pears in overseas fresh markets (Human 2013). The blush skin colour in pear is manifested as red pigmen- tation, often covering more than a third of the surface of mature fruit well exposed to the sun. Traditional blush pear cultivars include ‘Bella di Giugno’, ‘Colorée de Juillet’, ‘Corella’, ‘Forelle’, ‘Nordhäuser Winterforelle’ and ‘Seckel’, all chance seedlings. Some recent blush pear cultivars released from var- ious pear breeding programmes include ‘Cheeky’ (parentage not confirmed) (Human and von Mollendorff 2009) from South Africa; ‘Celina’ (‘Coloree de Juillet’ × ‘Williams’) from Norway (Hjeltnes 2015); and ‘Deliza’ (‘Corella’ × ‘Doyenne du Comice’) and ‘Lanya’ (‘Butirra Precoce Morettini’ × ‘Corella’) from Australia (Turpin et al. 2016). The blush skin Communicated by D. Chagné Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11295-018-1280-y) contains supplementary material, which is available to authorized users. * Rouvay Roodt-Wilding roodt@sun.ac.za 1 Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa 2 Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag XI, Stellenbosch 7602, South Africa Tree Genetics & Genomes (2018) 14:70 https://doi.org/10.1007/s11295-018-1280-y