Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed

Abstract

With regard to potential applications of genomic selection in small numbered breeds, we evaluated genomic models and focused on potential candidate gene annotations for weight and meat quality traits in the local Rotes Höhenvieh (RHV) breed. Traits included 6,003 birth weights (BWT), 5,719 200 d-weights (200dw), 4,594 365 d-weights (365dw) and 547 records for intramuscular fat content (IMF). A total of 581,304 SNP from 370 genotyped cattle with phenotypic records were included in genomic analyses. Model evaluations focused on single- and multiple-trait models with direct and with direct and maternal genetic effects. Genetic relationship matrices were based on pedigree (A-matrix), SNP markers (G-matrix) or both (H-matrix). Genome-wide association studies (GWAS) were carried out using linear mixed models to identify potential candidate genes for the traits of interest. De-regressed proofs (DRP) for direct and maternal genetic components were used as pseudo-phenotypes in the GWAS. Accuracies of direct breeding values were higher from models based on G or on H compared to A. Highest accuracies (> 0.89) were obtained for IMF with multiple-trait models using the G-matrix. Direct heritabilities with maternal genetic effects ranged from 0.62 to 0.66 for BWT, from 0.45 to 0.55 for 200dW, from 0.40 to 0.44 for 365dW and from 0.48 to 0.75 for IMF. Maternal heritabilities for BWT, 200dW and 365dW were in a narrow range from 0.21 to 0.24, 0.24 to 0.27 and 0.21 to 0.25, respectively, and from 0.25 to 0.65 for IMF. Direct genetic correlations among body weight traits were positive and favorable, and very similar from different models but showed a stronger variation with 0.31 (A), -0.13 (G) and 0.45 (H) between BWT and IMF. In gene annotations, we identified 6, 3, 1 and 6 potential candidate genes for direct genetic effect on BWT, 200dW, 365dW and IMF traits, respectively. Regarding maternal genetic effects, four (SHROOM3, ZNF609, PECAM1 and TEX2) and two (TMEM182 and SEC11A) genes were detected as potential candidate genes for BWT and 365dW, respectively. Potential candidate genes for maternal effect on IMF were GRHL2, FGA, FGB and CTNNA3. As the most important finding from a practical breeding perspective, a small number of genotyped RHV cattle enabled accurate breeding values for high heritability IMF.

Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits

“…In Duroc pigs, [32] using a model similar to model 5 of the present study, slightly higher estimates of maternal heritability were reported for IMF (0.13). In the Rotes Höhenvieh cattle breed, a similar h 2 m (0.25) was found by applying a model equal to model 2 [37].…”

“…Nevertheless, in this study a negative direct-maternal genetic correlation ranging from −0.18 to −0.49 was found using different models [37]. Regarding the litter effect (C 2 ), a posterior mean value of 0.18 was found with model 3, which decreased to 0.14 when model 4 including maternal genetic effects was used.…”

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

“…SMARCAL1 (SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1) is an SNF2 family member and can increase 8-cell development in human, mice, and cattle embryos [ 29 ]. Zhe et al identified EPHB2 (EPH receptor B2) as a candidate gene associated with litter weight during weaning in Duroc pigs [ 30 ]. Based on a large-scale GWAS using 294,079 first-lactation Holstein cows, BTBD11 (BTB domain-containing 11) was identified as a candidate gene with a major additive effect on the daughter pregnancy rate [ 31 ].…”

Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity

“…Additionally, it has been identified as a gene coding for proteins influential in plasma urea concentrations 39 . HS3ST1 gene, on the other hand, has been linked to feed efficiency through transcriptome analysis 40 , 41 and is suggested to play a role in immunity across species as well 42 .…”