Combining linkage and association mapping to search for markers linked to the flat fruit character in peach

Abstract

The character of flat versus round fruit shape is controlled by a single gene (S/s) on chromosome 6 in peach [Prunus persica (L.) Batsch], with the flat fruit phenotype produced by the S/s heterozygous genotype. We used 16 simple sequence repeat (SSR) markers at the S/s region and physically mapped them in the peach sequence. Seven were mapped in the new F1 population from a cross between the two flat fruit cultivars 'UFO-3' and ‘Sweet Cap’ that segregated for the S/s gene. Fourteen of the SSRs were mapped in the Prunus reference map (T×E), of which seven had already been mapped and seven were added within this work. Our results confirmed the position of S/s on the distal part of chromosome 6. Thirteen of the initial 16 markers were also studied in a collection of flat (66) and round (39) cultivars, where some of the alleles were associated to the character and one of them, the 131 bp allele of marker UDP98-412, predicted in 98.4 % of the cases the flat shape. This allele was highly predictive of the flat fruit character in an additional collection of 100 cultivars, and is an useful tool for marker-assisted selection of flat peaches and nectarines, a trait that is becoming of increasing interest in breeding programs as consumption of these fruits is growing in the European market.