High-density multi-population consensus genetic linkage map for peach

Abstract

Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.

Fig 1. The improved SNP-based genetic linkage map of ‘Zin Dai’ × ‘Crimson Lady’ (ZC²) progeny.

Marker names are listed at the right side of each LG and the genetic position (in cM) is listed at the left of each marker.

Fig 2. Alignment of the ZC² linkage map and the peach genome sequence v2.0.

Peach genome scaffolds and ZC² linkage groups are shown on the left and right of each pair, respectively.

Fig 3. Peach consensus linkage map built using four previously published bi-parental linkage maps, PI91459(‘NJ Weeping’) × ‘Bounty’ (WB) [18], ‘O’Henry’ × ‘Clayton’ (OC) [19], ‘Venus’ × ‘Venus’ (VxV) [20] and ‘Texas’ × ‘Earlygold’ (T×E) [56], and an improved ‘Zin Dai’ × ‘Crimson Lady’² map developed in this study with LPMerge algorithm.

Marker names are listed at the right side of each LG and the genetic position (in cM) is listed at the left of each marker.