Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers

Table 1 Description of whole genome sequence (WGS) SNP pre-selection methods

Analysis	Description
CONTROL^a	Analysis of marker panel only, 6 K, 50 K or 800 K
GWAS SNP pre-selection
TOP GWAS	All significant variants (P ≤ 5.0e−06) from the WGS from each of the beef CRC populations
COJO^b GWAS 100	COJO selecting the 100 most significant variants from each of the beef CRC GWAS analyses
COJO^b GWAS 250	COJO selecting the 250 most significant variants from each of the beef CRC GWAS analyses
GWAS COJO^b CHR	COJO analysis performed within chromosome where significant (P ≤ 5.0e−03) variants were selected from each beef CRC GWAS analyses
META SNP pre-selection
TOP META	All significant (P ≤ 5.0e−06) variants from the WGS meta analyses of the beef CRC populations
META COJO^b 100	COJO of meta analyses of the beef CRC populations selecting the 100 most significant variants
META COJO^b 250	COJO of meta analyses of the beef CRC populations selecting the 250 most significant variants
META COJO^b CHR	COJO analysis performed within chromosome where significant (P ≤ 5.0e−03) variants were selected from meta-analysis of beef CRC populations

From both single cohort genome wide association study (GWAS) and meta-analysis genome wide association study (META) output
^aCONTROL = marker panel analysis only, with no WGS variants included in analyses
^bCOJO = conditional or joint analysis in GCTA

ISSN: 1297-9686