QTL detection was performed using a sparse SNP panel and sire-based mapping, whilst QTL confirmation and estimation of position was performed using a denser SNP panel and dam-based mapping.
The Banshee has five 10-watt speakers and a sparse control panel with a power switch and two volume buttons.
The initial sire-linkage analysis using a sparse SNP panel identified three putative QTL affecting PD resistance, on chromosomes 3, 7 and 23 (Table 2).
The sib-pair (SP) analysis using the same sparse SNP panel also identified the QTL on chromosomes 3 and 4, with the QTL on chromosome 4 reaching genome-wide significance (Table 2).
Survivors from these families were identified, their genomic DNA was extracted (using the Qiagen DNeasy 96 protocol Blood & Tissue kit), and genotyped (by LGC Genomics Ltd) for the same sparse SNP panel used for parentage assignment of mortalities (Supplementary Table 2).
The QTL on chromosome 3 was confirmed with a dam-linkage analysis using the sparse SNP panel, which also identified a further QTL on chromosome 4 (both were significant at the chromosome-wide level).
A dam-linkage analysis using the same approach and sparse SNP panel (55 dams, resulting in 55 FS families, with average size 23 offspring per family) was also conducted to identify QTL segregating in dams but not sires, recognising that dam-segregating QTL may be missed with sparse markers.
In the second step of QTL mapping, a denser set of SNP markers (36 in total, taken from Lien et al. (2011) and Gonen et al. (2014) and including the sparse marker panel used in step one; Supplementary Table 2) was genotyped for chromosomes identified as containing QTL at chromosome- or genome-wide significance in step one.
This study focuses on alternative low-cost genomic selection methods (IBD-GS) that use selective genotyping with sparse marker panels to estimate identity-by-descent relationships through linkage analysis.
The low-cost approach combines sparse marker panels (or genotyping by sequencing) with selective genotyping of a subsample of the selection candidates and the phenotypically most extreme training sibs of these candidates.
