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

BMC Genomics

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

Locus	Evidence for selection^*		Evidence for dairy QTL^**
Locus	Within breed	Differentiation between breeds³	Evidence for dairy QTL^**
PLAG1	Holstein^1,2	1. Jersey with all other breeds	NA.	Figure 2
	Charolais^1,2	2. Limousin with all breeds, except Hereford
	Shorthorn^1,2	3. Hereford with all breeds, except Limousin and Angus
	Angus¹	4. Murray Grey with all breeds, except Shorthorn and Holstein
	Limousin¹
	Hereford¹
	Murray Grey¹
DGAT1	Limousin^1,2	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
	Charolais¹
	Hereford¹
	Murray Grey¹
	Shorthorn¹
GHR	Holstein^1,2	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.
	Jersey²	3. Jersey with Holstein, Angus & Shorthorn	Jersey: Milk yield, FPC and PPC.
ABCG2 ^***	Jersey^1,2	1. All contrasts between Jersey, Hereford and Charolais	Holstein: Fat yield, protein yield and PPC.	Additional file 3: Figure S10
	Charolais^1,2		Jersey: Stature.
	Limousin²		Jersey: Stature.
MSTN	Limousin¹	1. Limousin with all other breeds	NA.	Additional file 3: Figure S11

^*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.
^**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.
^***within breed selection for Charolais at ABCG2 is probably for NCAPG (at 38.78 Mbp).
NA = not applicable, QTL not expected to segregate in Holstein and Jersey cattle.

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