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.

Rao et al.

Rao et al. BMC Genomics 2012 13:513   doi:10.1186/1471-2164-13-513

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