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.

High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

“…If no genetic map is available, one will need to be constructed alongside genotypic data curation. The need for a precise genetic position of markers on the 9K peach array prompted development of consensus linkage map for peach [58] that in the future could serve as a reference map to estimate genetic positions of unmapped markers. A mapping approach for pedigreed, multi-parental maps is described by Di Pierro and co-workers (2016) [45].…”

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

“…However, limiting this exercise to just two parents often limits the genetic (allelic) variation and informative markers available, making it difficult to produce high density genetic linkage maps 36 . While larger population sizes are expected to increase the number of detectable recombination events, the use of multiple populations with differing parentage can increase the numbers of markers detected and map density 13 . The value of including multiple populations into mapping projects to capture allelic diversity and increase representation of recombination has been recognised and demonstrated both for inbreeding species such as Arabidopsis 37 and rice 38,39 , as well as outcrossing crops including apple 40,41 , strawberry 42 and peach 13 .…”

“…Genetic linkage maps are a powerful resource that can improve breeding efficiency by identifying the relative chromosomal location of genes underlying key phenotypic traits, and assisting in the development of selective markers, which may be of particular value in perennial crops with long generation times. More specifically, dense linkage maps remain valuable for anchoring and orienting whole-genome sequence scaffolds, mapping of quantitiative trait loci (QTL), and informing comparative genomic and evolutionary studies [11][12][13][14] . Given that linkage maps represent the distribution of chiasmatic crossovers (COs) resulting from parental meiotic recombination, they provide valuable insights into the contribution that each set of parental alleles may make to subsequent progeny.…”

Resynthesis: Marker-based partial reconstruction of elite genotypes in clonally-reproducing plant species

“…As an approximation, if we consider that an individual with 50% IBD has a continuous fragment of half of the length of each chromosome in homozygosis, the probability of a fully homozygous chromosome with a single recombination event increases to 9/32, and the probabilities of having eight or five or more chromosome pairs fully homozygous can be estimated as 3.9×10 -5 and 8.0×10 -3 , respectively (Table 1). For a finer estimation including recombination rates, we know that in peach the number of crossovers per chromosome (co/cs) per meiosis ranges between 1 and 2, and an overall estimation of 1.2-1.5 is reasonable (Arús et al 2005;da Silva Linge et al 2018). We have calculated approximate probabilities of finding a given number of chromosomes in homozygosis (or heterozygosis) considering 1.2 and 1.5 co/cs: 1.2 (80% of the meiosis with a single co/cs and 20% with two) and 1.5 (50% with one co/cs and 50% with two), and 50% IBD (half a chromosome in homozygosis and half in heterozygosis).…”

“…Key elements of their biology are the perennial habit of most species and a long intergeneration period, often accompanied by a juvenile period, which requires as few generations as possible to obtain a new cultivar. Our model, peach, has certain advantages: a relatively short intergeneration period (3-4 years), selfcompatibility, and a compact, diploid and sequenced genome (250 Mbp; x=8) (Verde et al 2013;Arús et al 2012), with a low recombination rate (1.2-1.5 crossovers/chromosome and meiosis) and a high level of homozygosity in the commercial cultivars (Micheletti et al 2015;da Silva Linge et al 2018). In this paper we develop the basic scheme for Resynthesis, and its genetic foundation, and provide experimental data from a trial using the peach 'Sweet Dream' (SD) cultivar.…”