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Table 1 Summary of major candidate regions identified from XP-EHH and XP-CLR in each breed comparison (see Additional files 2 and 3 for summary values of all candidate genes)

From: The genome landscape of indigenous African cattle

Gene CHRa Max XP-EHHb XP-EHH P valuec XP-CLR Association Candidate SNP position Selected breed
HCRTR1 2 - - 597.3 Circadian rhythm, feeding behavior   N’Dama
STOM 8 - - 525.0 Anemia 112665146
(p.Met48Val)
N’Dama
SLC40A1 2 3.32 0.0002 831.1 Anemia - N’Dama
SBDS 25 2.91 0.0024 - Anemia - N’Dama
EPB42 10 - - 511.1 Anemia 38523031
(p.Arg503His)
N’Dama
RPS26 6 - - 562.8 Anemia - N’Dama
KIT 6 1.80 0.0050 - Coat color - Ankole
MITF 22 1.90 0.0032 - Coat color - Ankole
PDGFRA 6 2.56 0.0001 319.3 Coat color - Ankole
FGF18 20 - - 182.3 Horn development - Ankole
MC1R 18 - - 295.0 Coat color   Ankole
SOD1 1 - - 333.31 Thermoregulation 3116044
(p.Ile95Phe)
B. indicus
- - 186.33 African
PRLH 3 1.49 0.0014 - Thermoregulation 117646610
(p.Arg76His)
B. indicus
1.17 0.0039 - African
BOLA 23 1.19 0.003 110.13 Tick resistance - African
  1. Dash (–) indicates non-significant results
  2. aChromosome
  3. bMaximum (positive) XP-EHH score of all SNPs within a window
  4. cRank-based empirical P value of genomic region