Skip to main content
. 2012 Sep 28;13:513. doi: 10.1186/1471-2164-13-513

Table 2.

Genotyping 8 no hit markers using three different genotyping strategies

  WGA-PCR
 WGA-FLDMqPCR
 Pre-ampFLDMqPCR
 BLAST to duck assembly
WGA Duck1 Duck2 No. pos3 WGA Duck1 Duck2 No. pos3 Duck2 No. pos3 BLAST hit (scaffold name) Scaffold length (bp)
EstCtg11412
 +
 +
 11
 +
 +
 3
 +
 25
 sca4924
 26 914
EstCtg23833
 -
 +
 0
 -
 +
 0
 +
 25
 C19155564
 548
EstCtg2805
 +
 +
 18
 -
 +
 3
 +
 24
 sca12946
 245
EstCtg293
 +
 +
 24
 +
 +
 16
 +
 30
 sca271
 23 394
EstCtg727
 +
 +
 14
 -
 +
 1
 +
 44
 nohit
 NA
EstCtg8099
 -
 +
 1
 -
 +
 2
 +
 29
 C18154597
 159
Y03G5XE5
 +
 +
 7
 -
 +
 0
 +
 25
 nohit
 NA
Y04H5QRB
 +
 +
 13
 +
 +
 11
 +
 43
 sca1017
 95 902
Nb. Controls4or Mean pos5
 6/8
 8/8
 11
 3/8
 8/8
 4.5
 16/16
 30.6
 NA
 NA
Mean retentions (%) NA NA 12 NA NA 5 NA 34 NA NA

The 8 no hit markers were genotyped using either of three methods (see Material and Methods): (i) WGA-PCR: the WGA-amplified panel and conventional agarose genotyping; (ii) WGA-FLDMqPCR: the WGA-amplified panel and genotyping with the Fluidigm BioMark gene expression dynamic array, without the pre-amplification with a mix of all primer pairs or (iii) Pre-ampFLDMqPCR: the non-amplified panel and genotyping with the Fluidigm BioMarkTM IFC Dynamic ArrayTM with a pre-amplification step using a mix of all primer pairs. 1WGA Duck: WGA-amplified duck genomic DNA as positive control; 2Duck: duck genomic DNA as positive control; 3No. Pos: number of hybrids positive for the assay (out of 90 hybrids tested); 4 Nb. Controls: total number of controls which are positive over the number of controls tested; 5Mean pos: mean number of positive hybrids observed over the whole panel; NA: not applicable.