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Christopher M. Seabury - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle
BMC Genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Background Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. Results GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level ( P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1 , NCAPG , LCORL , ARRDC3 , STC2 ). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold ( P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Conclusions Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle.
BMC genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
J K Bertrand - One of the best experts on this subject based on the ideXlab platform.
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Multi-breed genetic evaluation in a Gelbvieh population.
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie, 2007Co-Authors: Andres Legarra, J K Bertrand, R. L. Sapp, T. Strabel, Juan Sánchez, Ignacy MisztalAbstract:A multi-breed model was presented for the genetic evaluation of growth traits in beef cattle. In addition to the fixed effects, random direct and maternal genetic effects, and random maternal permanent environmental effects are considered; the model also fits direct and maternal heterosis and direct and maternal breed-of-founder (BOF) x generation group effects using a Bayesian approach that weights prior literature estimates relative to information supplied by the dataset to which the model will be applied. The multi-breed evaluation procedures also allow the inclusion of external evaluations for animals of other breeds. The multi-breed model was applied to a dataset provided by the American Gelbvieh Association. Different analyses were conducted by varying the weights given to the prior literature relative to the information provided by the dataset. Large differences were observed for the heterosis estimates, the BOF x generation group effect estimates, and the predicted breeding values across breeds due to the weights posed on prior literature estimates versus estimates derived directly from data. However, the rankings within breed were observed to be relatively robust to the different weights on prior information.
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Joint longitudinal modeling of age of dam and age of animal for growth traits in beef cattle
Journal of animal science, 2005Co-Authors: Kelly R. Robbins, Ignacy Misztal, J K BertrandAbstract:Two methods to jointly model age of dam (AOD) and age of animal in random regression analyses of growth in Gelbvieh cattle were examined. The first method (M1) was analogous to the multiple-trait analysis and consisted of AOD as a nested class variable and a cubic polynomial regression on age nested within birth, weaning, and yearly weights. The second method (M2) used two-dimensional splines, with age knots at 150, 205, 270, 340, and 390 d. The AOD knots were placed at 725, 1,464, and 2,189 d. These selected knots were used to form a two-dimensional grid containing 15 knots, each representing a specific age and AOD combination. A data set containing Gelbvieh growth records was split along contemporary groups into two data sets. Data set 1 contained 316,078 records and was used for prediction by mixed-model equations. Data set 2 contained 164,167 records and was used for cross validation. In the complete data set, only 90 and 30% of animals with birth weight had records on weaning and yearling weights, respectively. Models were evaluated based on R 2 , average squared error (ASE), percent bias, and plots of solutions. The ASE for weights associated with birth weight, weaning weight, and yearling weight for Ml were 15, 505, and 703 kg2. With M2, large jumps in fixed-effect estimates were observed outside the two-dimensional grid. To eliminate this problem, weighted one-dimensional splines were used for extrapolation beyond the two-dimensional grid. For M2 with weighted spline extrapolation, the ASE were 15, 542, and 777 kg2 for birth weight, weaning weight, and yearling weight, respectively. Creation of optimal two-dimensional splines is difficult when data are clustered. Despite such difficulties, the two-dimensional spline was capable of jointly and continuously modeling AOD and age of animal.
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Genetic parameters estimated with multitrait and linear spline-random regression models using Gelbvieh early growth data.
Journal of animal science, 2005Co-Authors: Hiroaki Iwaisaki, Ignacy Misztal, Shogo Tsuruta, J K BertrandAbstract:Estimates of direct and maternal genetic parameters in beef cattle were obtained with a random regression model with a linear spline function (SFM) and were compared with those obtained by a multitrait model (MTM). Weight data of 18,900 Gelbvieh calves were used, of which 100, 75, and 17% had birth (BWT), weaning (WWT), and yearling (YWT) weights, respectively. The MTM analysis was conducted with a three-trait maternal animal model. The MTM included an overall linear partial fixed regression on age at recording for WWT and YWT, and direct-maternal genetic and maternal permanent environmental effects. The SFM included the same effects as MTM, plus a direct permanent environmental effect and heterogeneous residual variance. Three knots, or breakpoints, were set to 1, 205, and 365 d. (Co)variance components in both models were estimated with a Bayesian implementation via Gibbs sampling using flat priors. Because BWT had no variability of age at recording, there was good agreement between corresponding components of variance estimated from both models. For WWT and YWT, with the exception of the sum of direct permanent environmental and residual variances, there was a general tendency for SFM estimates of variances to be lower than MTM estimates. Direct and maternal heritability estimates with SFM tended to be lower than those estimated with MTM. For example, the direct heritability for YWT was 0.59 with MTM, and 0.48 with SFM. Estimated genetic correlations for direct and maternal effects with SFM were less negative than those with MTM. For example, the direct-maternal correlation for WWT was -0.43 with MTM and -0.33 with SFM. Estimates with SFM may be superior to MTM due to better modeling of age in both fixed and random effects.
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A practical longitudinal model for evaluating growth in Gelbvieh cattle.
Journal of animal science, 2005Co-Authors: Kelly R. Robbins, Ignacy Misztal, J K BertrandAbstract:Genetic evaluation of growth in Gelbvieh beef cattle was examined by multiple-trait (MTM) and random regression (RRM) analysis. The data set comprised 541,108 animals with 1,120,086 records. Approximately 15% of the animals in the data set had at least one record measured outside of the accepted MTM age ranges for weaning weight (Wwt) and yearling weight (Ywt). Fourteen percent of Wwt records and 19% of Ywt records were measured outside the accepted ranges for MTM analysis, and thus were excluded from MTM evaluations. Two RRM evaluations were performed using cubic Legendre polynomials (RRML) and linear splines (RRMS) with three knots at 1, 205, and 365 d of age. Data Set 1 (d1) utilized all available records, whereas Data Set 2 (d2) included only records measured within MTM ranges (1 d, 160 to 250 d, and 320 to 410 d). The RRML models did not reach convergence until diagonalization was imposed. After diagonalization, it was found that all longitudinal models required fewer iterations to converge than the MTM. Correlations between the MTM, RRML-d2, and RRMS-d2 evaluations were >or=0.99 for all three traits, indicating that these models were equivalent when predicting breeding values from data within the MTM age ranges. Correlations between MTM, RRML-d1, and RRMS-d1 were >0.99 for Bwt and >0.95 for Wwt and Ywt. The lower correlations for Wwt and Ywt indicate that the added information does affect breeding value prediction. The RRM has the capability to incorporate records measured at all ages into genetic evaluations at a computing cost similar to the MTM.
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Teat scores in first-parity Gelbvieh cows: relationship with suspensory score and calf growth traits.
Journal of animal science, 2004Co-Authors: R. L. Sapp, Romdhane Rekaya, J K BertrandAbstract:Teat and udder suspensory scores from 9,418 first-parity Gelbvieh cows and growth records from 19,119 calves were used to estimate genetic and environmental parameters for teat and suspensory score and to investigate the relationship of teat and suspensory score with calf growth traits and maternal genetic growth effects. First-parity cows did not have multiple records within 280 d, gave birth to one calf, were 4 yr of age or younger at first-calving, and were at least 50% Gelbvieh. Producers scored cows within 24 h of parturition. Teat score (T), a subjective measure of teat size, ranged from 0 (very large) to 50 (very small), and suspensory score (S), a subjective score of udder support, ranged from 0 (very pendulous) to 50 (very tight). Unadjusted birth weight (BW), weaning weight, and yearling weight of the calves, born in the first three parities to cows with first-parity T and S records, were used to calculate pre- and postweaning ADG (WG and YG, respectively). A mixed model was used for the multiple trait analysis of T, S, BW, WG, and YG, which included herd-year, month of calving, age of cow at calving, and sex of calf (included only for BW, WG, and YG) as systematic effects; regression on the percentage of Gelbvieh; and additive animal and maternal genetic of dam (included only for BW and WG), maternal permanent environment (included only for BW and WG), and residual as random effects. The genetic correlation between T and S was 0.95, suggesting that T and S are basically the same trait in this dataset. The genetic correlations between T (S) with direct BW, WG, and YG and with maternal BW and WG were -0.18 (-0.06), 0.38 (0.31), 0.09 (-0.01), -0.16 (-0.16), and -0.47 (-0.55), respectively, suggesting that cows with smaller teats and tighter udders produced less milk and raised calves that had higher genetic growth potential for WG. Further, the Pearson correlations between predicted breeding values of T and S with maternal WG indicated that animals with extremely large teats or pendulous udders may produce more milk, but that the calf may have trouble accessing it. Conversely, with extremely small teats or tight udders, smaller amounts of milk would be produced and there may be a problem producing enough milk to maintain the growing calfs maintenance requirements. Therefore, it may be more beneficial for producers to select animals that have intermediate breeding values for T and S.
Johanna L. Smith - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle
BMC Genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Background Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. Results GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level ( P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1 , NCAPG , LCORL , ARRDC3 , STC2 ). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold ( P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Conclusions Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle.
BMC genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
Sara M. Nilson - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle
BMC Genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Background Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. Results GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level ( P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1 , NCAPG , LCORL , ARRDC3 , STC2 ). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold ( P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Conclusions Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle.
BMC genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
Miranda L. Wilson - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle
BMC Genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Background Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. Results GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level ( P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1 , NCAPG , LCORL , ARRDC3 , STC2 ). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold ( P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Conclusions Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle.
BMC genomics, 2019Co-Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker, Christopher M. SeaburyAbstract:Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.