Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (‘Old Home’בLouise Bon Jersey’) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
Highlights
One of the biggest challenges for plant biologists has long been to associate genetic variations with phenotypic traits
A total of 73,214 single nucleotide polymorphism (SNP) were predicted by SoapSNP when reads of OH and LBJ were aligned to the genome of ‘Bartlett’ using the Soap aligner, corresponding to one SNP per 1079 bases
In addition to the new P. communis pear SNPs developed in this study, we found that 1482 SNP markers derived from apple (19.3% of the total apple SNPs on the International RosBREED SNP consortium (IRSC) array) were polymorphic in pear, and 1031 of them were positioned on the pear genetic maps
Summary
One of the biggest challenges for plant biologists has long been to associate genetic variations with phenotypic traits. NGS enables the inventory of entire sets of DNA variations in genomes, through the re-sequencing of multiple accessions of the same species and alignment of these sequences to the reference genome, for the purpose of in silico detection of DNA polymorphisms [9,10,11,12,13,14,15,16]. Single nucleotide polymorphisms (SNPs) are single base variations in DNA sequences that are abundant in plant genomes and are useful for identifying differences within individuals or populations as well as identifying genetic loci associated with phenotypic variation. Once polymorphisms have been detected by NGS, the challenge is to screen large genetic populations with multiple markers simultaneously. While re-sequencing can be used for both SNP discovery and genotyping of the entire set of polymorphisms of a species [17], high throughput SNP arrays, such as the InfiniumH II assay (Illumina Inc.), are effective technologies for genotyping of large populations
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