High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ~3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ~15.8 K SNP markers were mapped with an average of ~6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs

Bianco, L.; Cestaro, A.; Sargent, D.J.; Banchi, E.; Derdak, S.; Di Guardo, M.; Salvi, S.; Viola, R.; Gut, I.; Chagné, D.; Velasco, R.; van de Weg, E.; Troggio, M. (2014). Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus x domestica Borkh). PLOS ONE, 9 (10): e110377. doi: 10.1371/journal.pone.0110377 handle: http://hdl.handle.net/10449/25016

Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus x domestica Borkh)

Bianco, Luca;Cestaro, Alessandro;Sargent, Daniel James;Banchi, Elisa;Di Guardo, Mario;Viola, Roberto;Velasco, Riccardo;Troggio, Michela
2014-01-01

Abstract

High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ~3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ~15.8 K SNP markers were mapped with an average of ~6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs
Settore AGR/07 - GENETICA AGRARIA
2014
Bianco, L.; Cestaro, A.; Sargent, D.J.; Banchi, E.; Derdak, S.; Di Guardo, M.; Salvi, S.; Viola, R.; Gut, I.; Chagné, D.; Velasco, R.; van de Weg, E.; Troggio, M. (2014). Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus x domestica Borkh). PLOS ONE, 9 (10): e110377. doi: 10.1371/journal.pone.0110377 handle: http://hdl.handle.net/10449/25016
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