Table 2.
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.