Sequence-based GWAS meta-analyses for beef production traits

Table 3 Software and reference population used for whole-genome sequence imputation

Population	Imputation software		Reference population		Number of animals	Number of biallelic variants
Population	Step 1 50k-HD	Step 2 HD-WGS	Step 1 50k-HD	Step 2 HD-WGS	Number of animals	Number of biallelic variants
INRAE_CHA_cows	Fimpute3	Minimac4	672 CHA	1479 incl. 82 CHA	7999	25,050,323
INRAE_CHA_cows	Fimpute3	Minimac4	672 CHA	1479 incl. 82 CHA	8501	25,050,323
INRAE_MON_bulls	Fimpute3	Minimac4	530 MON	1479 incl. 63 MON	3226	25,050,323
INRAE_NOR_bulls	Fimpute3	Minimac4	551 NOR	1479 incl. 44 NOR	2749	25,050,323
INRAE_CHA_steers	Fimpute3	Minimac4	672 CHA	1479 incl. 82 CHA	4354	25,050,323
INRAE_MON_steers	Fimpute3	Minimac4	530 MON	1479 incl. 63 MON	4163	25,050,323
INRAE_NOR_steers	Fimpute3	Minimac4	551 NOR	1479 incl. 44 NOR	2730	25,050,323
INRAE-ULIM_CHA	Fimpute3	Minimac4	672 CHA	1479 incl. 82 CHA	1059	25,050,323
INRAE-ULIM_LIM	Fimpute3	Minimac4	462 LIM	1479 incl. 64 LIM	1209	25,050,323
INRAE-ULIM_BLA	Fimpute3	Minimac4	327 BLA	1479 incl. 41 BLA	939	25,050,323
ETH_bulls	Beagle5	Beagle5	1166 BSW and OBV	372 BSW and OBV	10,419	27,214,878
ETH_cows	Beagle5	Beagle5	1166 BSW and OBV	372 BSW and OBV	20,185	27,214,878
FBN_bulls	Beagle5	Beagle5	133 HOL and CHA F0 and F1 parents	1568 incl. 844 HOL and 144 CHA	1043	19,590,361
FBN_cows	Beagle5	Beagle5	133 HOL and CHA F0 and F1 parents	1568 incl. 844 HOL and 144 CHA	1043	19,590,361
UAL	Beagle5	Beagle5	4059 multi-breed	3093 Bos taurus	7552	47,833,012

CHA Charolais, MON Montbéliarde, NOR Normande, LIM Limousine, BLA Blonde d’Aquitaine, BSW Brown Swiss, OBV Original Braunvieh

ISSN: 1297-9686