Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Abstract

BackgroundA whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny.ResultsOf the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence.ConclusionsWe incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

Inheritance of reproductive phenology traits and related QTL identification in apricot

“…These tools have made it possible to design very dense maps in these aforementioned species (Antanaviciute et al 2012;Chagné et al 2012 in apple; Montanari et al 2013 in pear;Eduardo et al 2013;Martínez-García et al 2013;Pirona et al 2013 in peach;Klagges et al 2013 in cherry). Nevertheless, the mapped SNPs already make it possible to anchor the available maps with the peach genome sequences and to identify several QTLs linked to phenology traits in the 'B × C' and 'G × C' populations.…”

Identification of Four New Est-Based Markers on the Apple (MALUS ⋉ DOMESTICA) Genetic Map

“…Mapping of SNPs in the UDP6Deh and the UDPglTra sequences was not successful despite their identification in the genome of both analysed parental forms. In general, SNP markers are known to have low level of transferability (Antanaviciute et al 2012). It is also possible that these unmapped SNPs, as well as the CAPS-derived marker of DHAR gene were transferred during evolution of 'Retina' and 'Topaz' on genome segments which haven't been mapped by us.…”

Identification of QTLs for Flesh Mealiness in Apple (<i>Malus</i> × <i>domestica</i> Borkh.)

“…4C). However, a relatively high rate of errors in the apple genome assembly means that there are some inconsistencies between the positions obtained by genetic mapping and the positional data in the public database (Antanaviciute et al, 2012;Kunihisa et al, 2016). Thus, to confirm the origin of these regions, a r 2 LD analysis of all the significant SNP pairs was conducted.…”