Table 4 SNP efficiency of markers validated using KASP assay.

From: A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea)

 

Concordant allelesa

Discordant alleles

Not validated

SNP efficiency (validation %)

AA [S]

BB [R]

AB

AA [S]

BB [R]

AB

A01_9192862

49

63

0

0

6

5

17

91.1

A01_9530252

46

68

0

1

5

6

14

90.5

A01_9604392

46

66

0

0

5

8

15

89.6

  1. Concordant allele calls were the ones which confirmed the in-silico SNP call in the KASP validation. Discordant allele calls were the ones which showed mismatch of in-silico and KASP genotyping. Overall, the SNP efficiency was ~90% for each SNP. Some of the markers could not be assigned any genotype in KASP assay were therefore considered not validated.
  2. aAA represent homozygous markers from the susceptible parent (Sun Oleic 97R); BB represents the homozygous markers from the resistant parent (NC 94022); AB represents the rare heterozygous call.
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