Unknown

Dataset Information

0

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


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 8K 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 20K 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 ?3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ?15.8K SNP markers were mapped with an average of ?6.8K 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.

SUBMITTER: Bianco L 

PROVIDER: S-EPMC4193858 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Bianco Luca L   Cestaro Alessandro A   Sargent Daniel James DJ   Banchi Elisa E   Derdak Sophia S   Di Guardo Mario M   Salvi Silvio S   Jansen Johannes J   Viola Roberto R   Gut Ivo I   Laurens Francois F   Chagné David D   Velasco Riccardo R   van de Weg Eric E   Troggio Michela M  

PloS one 20141010 10


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 8K 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 preci  ...[more]

Similar Datasets

| S-EPMC7705664 | biostudies-literature
| S-EPMC4110548 | biostudies-literature
2018-12-25 | GSE115664 | GEO
| S-EPMC4364616 | biostudies-literature
| S-EPMC7911497 | biostudies-literature
| S-EPMC9661974 | biostudies-literature
2014-05-20 | GSE51727 | GEO
| S-EPMC3095355 | biostudies-other
| S-EPMC8836888 | biostudies-literature
| S-EPMC4755197 | biostudies-literature