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Table 2 Genotyping 8 no hit markers using three different genotyping strategies

From: A duck RH panel and its potential for assisting NGS genome assembly

 

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. Controls 4 or Mean pos 5

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

  1. 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.