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Table 2 Details of the most strongly associated SNPs  (with a p value < 10−6) in each QTL region with antibody response to F. hepatica

From: Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle

BTA SNP name Pos (bp) p value Gene Favourable allele (freq) Effecta Annotation Start of QTL End of QTL Other genes in the QTL region
14 rs801151638 82,704,197 2.02 × 10−8 – A (0.988) 0.42 Intergenic 80,104,349 83,212,505 RALYL, SNX16, CHMP4C
20 rs382942594 21,005,570 1.77 × 10−7 – T (0.063) 0.19 Intergenic 20,574,362 22,008,166 RAB3C, ENSBTAG00000005229, GAPT, PLK2, ENSBTAG00000026505
6 rs439064316 44,643,846 1.96 × 10−7 – C (0.008) 0.46 Intergenic 44,643,846 44,643,846 –
15 rs134727358 67,661,877 5.12 × 10−7 PRR5L G (0.003) 0.66 Upstream 67,661,877 67,661,877 –
15 rs379765497 23,526,098 5.44 × 10−7 – A (0.008) 0.44 Intergenic 23,515,275 2,3581,425 –
18 rs110443247 4,974,911 6.04 × 10−7 – C (0.375) 0.08 Intergenic 4,974,911 5,158,840 NUDT7, VAT1L
  1. BTA: Bos taurus chromosome number, SNP: name of the single nucleotide polymorphism, pos: position of base pair on the chromosome, p value: p value of the SNP, gene: gene name in which the SNP is located, favourable allele (freq): allele with favourable effect (frequency of the favourable allele), effect: effect of the favourable allele, annotation: annotation of the SNP, start of QTL: base pair on the chromosome at the start of the QTL, end of QTL: base pair on the chromosome at the end of the QTL, other genes in the QTL region: protein-coding genes located in the QTL region that the SNP is not located in
  2. aBinary trait (0/1)
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Genetics Selection Evolution

ISSN: 1297-9686