Genomic predictions combining SNP markers and copy number variations in Nellore cattle

Hay, El Hamidi A.; Utsunomiya, Yuri T.; Xu, Lingyang; Zhou, Yang; Neves, Haroldo H. R.; Carvalheiro, Roberto; Bickhart, Derek M.; Ma, Li; Garcia, Jose Fernando; Liu, George E.

doi:10.1186/s12864-018-4787-6

BMC Genomics

Table 2 Pearson’s correlations between dEBVs and DGVs of 9 traits for different models using SNP markers only and combining SNP and CNV information

From: Genomic predictions combining SNP markers and copy number variations in Nellore cattle

	BayesA	BayesA+CNV			Bayes B	BayesB+CNV			GBLUP	GBLUP+CNV
Trait	SNPs^a	del^b	All del^c	All^d	SNPs^a	del^b	All del^c	All^d	SNPs^a	del^b	All del^c	All^d
BW	0.21 (±0.03)	0.22 (±0.02)	0.21 (±0.04)	0.24 (±0.02)	0.17 (±0.02)	0.23 (±0.02)	0.23 (±0.03)	0.22 (±0.06)	0.20 (±0.03)	0.20 (±0.02)	0.20 (±0.02)	0.20 (±0.04)
CW	0.12 (±0.01)	0.10 (±0.01)	0.10 (±0.01)	0.10 (±0.03)	0.15 (±0.01)	0.15 (±0.04)	0.13 (±0.04)	0.14 (±0.02)	0.15 (±0.04)	0.16 (±0.01)	0.14 (±0.04)	0.14 (± 0.05)
CY	0.23 (±0.03)	0.23 (± 0.04)	0.22 (±0.03)	0.20 (±0.02)	0.22 (±0.03)	0.19 (±0.02)	0.19 (±0.05)	0.19 (±0.02)	0.24 (±0.01)	0.22 (±0.01)	0.21 (±0.02)	0.22 (± 0.03)
MW	0.36 (±0.01)	0.34 (± 0.01)	0.33 (±0.02)	0.36 (±0.01)	0.34 (±0.01)	0.39 (± 0.02)	0.38 (±0.03)	0.38 (±0.03)	0.40 (±0.02)	0.39 (±0.01)	0.39 (±0.04)	0.40 (± 0.04)
MY	0.54 (±0.05)	0.53 (± 0.06)	0.50 (±0.03)	0.53 (±0.04)	0.51 (±0.04)	0.56 (±0.02)	0.54 (±0.04)	0.54 (±0.04)	0.54 (±0.03)	0.52 (±0.04)	0.50 (±0.02)	0.55 (± 0.02)
PW	0.38 (±0.02)	0.36 (±0.03)	0.34 (±0.05)	0.36 (±0.01)	0.37 (±0.03)	0.38 (±0.01)	0.34 (±0.04)	0.40 (±0.02)	0.38 (±0.04)	0.36 (±0.03)	0.32 (±0.03)	0.36 (± 0.05)
PWG	0.27 (±0.02)	0.24 (±0.04)	0.23 (±0.03)	0.23 (±0.03)	0.30 (±0.01)	0.26 (±0.02)	0.26 (±0.03)	0.26 (±0.04)	0.30 (±0.01)	0.26 (±0.03)	0.24 (±0.02)	0.27 (± 0.02)
PY	0.58 (±0.04)	0.58 (±0.03)	0.58 (±0.04)	0.58 (±0.04)	0.62 (±0.02)	0.57 (±0.02)	0.56 (±0.03)	0.58 (±0.05)	0.57 (±0.03)	0.59 (±0.04)	0.59 (±0.04)	0.59 (± 0.04)
WG	0.28 (±0.05)	0.22 (±0.04)	0.20 (±0.03)	0.21 (±0.05)	0.30 (±0.03)	0.21 (±0.03)	0.20 (±0.03)	0.22 (±0.06)	0.30 (±0.01)	0.22 (±0.04)	0.22 (±0.05)	0.22 (± 0.03)

^aOnly SNPs
^bSNPs and only common deletions with frequency greater than 5% were included in the model (55 CNVs)
^cSNPs and all deletions were included in the model (72 CNVs)
^dSNPs and all deletions and biallelic duplications (173 CNVs)

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com