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

Warburton, Christie L.; Engle, Bailey N.; Ross, Elizabeth M.; Costilla, Roy; Moore, Stephen S.; Corbet, Nicholas J.; Allen, Jack M.; Laing, Alan R.; Fordyce, Geoffry; Lyons, Russell E.; McGowan, Michael R.; Burns, Brian M.; Hayes, Ben J.

doi:10.1186/s12711-020-00547-5

Genetics Selection Evolution

Table 2 Variance components for Smart Futures heifers for reproductive maturity score (RMS) estimated on the 800 K marker panel with standard errors

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

GRM	Analysis	Vp (se)	Va (se)	Ve (se)	h² (se)	WGS Va (se)	WGS h² (se)	Total h² (se)
SGRM	CONTROL	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	TOP GWAS	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	TOP META	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	COJO GWAS 100	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	COJO GWAS 250	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	GWAS COJO CHR	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	COJO META 100	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	COJO META 250	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
	META COJO CHR	1.11 (0.01)	0.22 (0.01)	0.89 (0.01)	0.20 (0.01)	–	–	–
MGRM	TOP GWAS	1.11 (0.00)	0.20 (0.01)	0.90 (0.02)	0.18 (0.01)	0.012 (0.002)	0.012 (0.002)	0.19 (0.011)
	TOP META	1.13 (0.01)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	0.042 (0.007)	0.036 (0.008)	0.21 (0.012)
	COJO GWAS 100	1.11 (0.01)	0.20 (0.01)	0.89 (0.01)	0.18 (0.01)	0.010 (0.000)	0.012 (0.002)	0.20 (0.010)
	COJO GWAS 250	1.11 (0.01)	0.19 (0.01)	0.89 (0.01)	0.17 (0.01)	0.028 (0.007)	0.024 (0.005)	0.20 (0.010)
	GWAS COJO CHR	1.11 (0.01)	0.20 (0.01)	0.89 (0.01)	0.18 (0.01)	0.014 (0.007)	0.010 (0.006)	0.20 (0.010)
	COJO META 100	1.11 (0.01)	0.20 (0.01)	0.89 (0.01)	0.18 (0.01)	0.022 (0.002)	0.018 (0.002)	0.20 (0.012)
	COJO META 250	1.11 (0.01)	0.18 (0.01)	0.89 (0.01)	0.16 (0.01)	0.034 (0.002)	0.032 (0.002)	0.20 (0.011)
	META COJO CHR	1.10 (0.00)	0.20 (0.01)	0.90 (0.01)	0.18 (0.01)	0.016 (0.002)	0.012 (0.002)	0.19 (0.010)
BAYES	CONTROL	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	TOP GWAS	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	TOP META	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	COJO GWAS 100	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	COJO GWAS 250	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	GWAS COJO CHR	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	COJO META 100	1.09 (0.00)	0.19 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	COJO META 250	1.09 (0.00)	0.18 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–
	META COJO CHR	1.09 (0.00)	0.18 (0.01)	0.90 (0.01)	0.17 (0.01)	–	–	–

Estimated phenotypic variance (Vp), additive variance (Va), environmental variance (Ve) and heritability (h²) estimated for single GRM (SGRM), Bayes R (BAYES) analyses and multi-GRM (MGRM) analyses. Whole-genome sequence (WGS) variants additive variance (WGS Va), WGS variants heritability (WGS h²) and total heritability (total h²) estimated in the multiple genomic relationship matrix (MGRM) analyses in the Smart Futures heifers 800 K marker panel (standard errors (se) in parentheses)

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