A pipeline for high throughput detection and mapping of SNPs from EST databases

Abstract

Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users.

Towards F1 Hybrid Seed Potato Breeding

“…To this end, a subset was selected per F 3 population of 24 informative SNP markers derived from the 100 PotSNP marker loci (Anithakumari et al 2010) covering all 24 chromosome arms of potato. DNA extractions were done using Klear Gene DNA Extraction Kits and PotSNP marker analyses by KASP SNP genotyping system (http://www.kbioscience.co.uk).…”

Understanding the genetic basis of potato development using a multi-trait QTL analysis

“…Single nucleotide polymorphism (SNP) markers scored in a core set of C9E (Anithakumari et al 2010) were added to the maps of parents C and E as described in Hurtado et al (2012). Together with the SNP markers, AFLP, SSR and CAPS with expected segregation ratios 1:1 and 1:1:1:1, respectively, were used to construct more saturated maps of parent C and E (additional file 1).…”

Development and application of a 20K SNP array in potato

“…The SNPs from these genotyping studies are publically available and have a fixed location on the reference genome of potato (PGSC 2011). Subsequently these SNP can be used in several types of flexible genotyping platforms, such the Golden Gate system (Anithakumari et al 2010), the KASP genotyping platform (http:// www. kbioscience.…”

“…The map-positions of these marker systems are difficult to compare between studies and difficult to compare with the reference genome of potato and are therefore not straightforward to implement in potato breeding. The study of Anithakumari et al (2010) firstly uses SNPs (single nucleotide polymorphisms) on important mapping populations such as SH 83-92-488 x RH 89-039-16, used in Van Os et al (2006) and C x E used in (van Eck et al 1993;van Eck et al 1994;Werij et al 2007;Kloosterman et al 2010;Wolters et al 2010). They mined available EST (expressed sequence tags) sequences, to identify SNPs.…”

“…Genomic selection however does not rely on such information, but for both strategies the implementation of SNP arrays is urgent, to allow sufficient data collection to improve breeding efficiency. One of the first examples of highly parallel marker studies in potato made use of methods such as the Golden Gate assay (Anithakumari et al 2010), the KASP SNP genotyping system (http://www. kbioscience.co.uk) (Lindhout et al 2011) and more recently a SNP array with 8303 markers was developed (Felcher et al 2012;Hamilton et al 2011), which is currently widely used in potato research (Hirsch et al 2013;Manrique-Carpintero et al 2014;Prashar et al 2014).…”