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Table 4 Evidence for selection and quantitative trait loci (QTL) at major loci affecting complex traits (type 2 loci)

From: Selection for complex traits leaves little or no classic signatures of selection

  Locus Evidence for selection* Evidence for dairy QTL**  
Within breed Differentiation between breeds3
PLAG1 Holstein1,2 1. Jersey with all other breeds NA. Figure 2
Charolais1,2 2. Limousin with all breeds, except Hereford
Shorthorn1,2 3. Hereford with all breeds, except Limousin and Angus
Angus1 4. Murray Grey with all breeds, except Shorthorn and Holstein
Murray Grey1
DGAT1 Limousin1,2 1. Holstein or Jersey with Charolais, Limousin, Hereford and Shorthorn Holstein and Jersey: Milk yield, fat yield, protein yield, FPC and PPC. Additional file 3: Figure S8
Angus1 2. Murray Grey with Hereford
Murray Grey1
GHR Holstein1,2 1. Holstein with Jersey, Charolais & Limousin Holstein: Milk yield, fat yield, protein yield, FPC and PPC. Additional file 3: Figure S9
Jersey2 2. Angus with Jersey, Charolais & Murray Grey Jersey: Milk yield, FPC and PPC.
3. Jersey with Holstein, Angus & Shorthorn
ABCG2 *** Jersey1,2 1. All contrasts between Jersey, Hereford and Charolais Holstein: Fat yield, protein yield and PPC. Additional file 3: Figure S10
Charolais1,2 Jersey: Stature.
MSTN Limousin1 1. Limousin with all other breeds NA. Additional file 3: Figure S11
  1. *windows encompassing loci and identified in the top 5% of within or between breed measures of selection. Measures of selection were 1haplotype homozygosity (HAPH), 2integrated haplotype score (|iHS|) and 3F ST .
  2. **traits in Holstein and Jersey dairy cattle are milk yield (litres per lactation), fat yield (kg per lactation), protein yield (kg per lactation), FPC (fat percentage in milk), PPC (protein percentage in milk) and stature.
  3. ***within breed selection for Charolais at ABCG2 is probably for NCAPG (at 38.78 Mbp).
  4. NA = not applicable, QTL not expected to segregate in Holstein and Jersey cattle.