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

Cassia Da Silva Linge,Laura Rossini,Daniele Bassi,Stephen Ficklin,Ksenija Gasic,Asma Abdelghafar,Laima Antanaviciute,Pere Arús

doi:10.1371/journal.pone.0207724

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.

Highlights

A genetic linkage map represents positions and genetic distances of molecular markers on chromosomes allocated based on segregation data and recombination events of individuals in a mapping population [1,2]
Genetic maps are important tools for a vast number of genetic applications and are widely used in plant breeding programs, genetics and genomics studies. These maps are crucial for a better understanding of marker-trait associations through quantitative trait loci (QTL) mapping, discovery of genes associated with economically important fruit quality and disease resistance traits, and successful deployment of molecular markers in plant breeding programs via marker-assisted selection (MAS) [3,4,5]
The construction of the improved SNP-based linkage map was based on heterozygous SNPs observed in this study combined with SNP marker data previously reported by Frett et al [17]

Summary

Introduction

A genetic linkage map represents positions and genetic distances of molecular markers on chromosomes allocated based on segregation data and recombination events of individuals in a mapping population [1,2]. Genetic maps are important tools for a vast number of genetic applications and are widely used in plant breeding programs, genetics and genomics studies. These maps are crucial for a better understanding of marker-trait associations through quantitative trait loci (QTL) mapping, discovery of genes associated with economically important fruit quality and disease resistance traits, and successful deployment of molecular markers in plant breeding programs via marker-assisted selection (MAS) [3,4,5]. High-resolution maps which cover the entire genome with co-segregating, reproducible and high-throughput markers at short intervals are most valuable because of the increased resolution that leads to more effective QTL mapping, candidate gene detection, and more precise estimates of QTL effect [5, 12,13]. Recent advances in next-generation high-throughput sequencing and genotyping techniques, such as development of the IPSC 9K peach array [16], have permitted rapid development of high-quality genetic linkage maps [17,18,19,20]

Methods

Results

Conclusion