Genetic study of scores for limb conformation, breed traits, sexual traits, eye pigmentation, and navel size in Hereford and Braford cattle

Souza, Juliana Salies; Silveira, Daniel Duarte da; Teixeira, Bruno Borges Machado; Boligon, Arione Augusti

doi:10.37496/rbz5320220139

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Breeding and genetics • R. Bras. Zootec. 53 • 2024 • https://doi.org/10.37496/rbz5320220139 copy

Genetic study of scores for limb conformation, breed traits, sexual traits, eye pigmentation, and navel size in Hereford and Braford cattle

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

Data from 83,088 Hereford and Braford cattle were used to compare parameters and breeding values obtained using linear and threshold models for visual scores of limb conformation (LCW and LCY), breed traits (BTW and BTY), sexual traits (STW and STY), eye pigmentation (EPW and EPY), and navel size (NSW and NSY) at weaning and yearling, respectively. Additionally, principal component analysis was applied to investigate the relationship among the estimated breeding values. Higher direct heritability were estimated using the threshold model (ranging from 0.134±0.021 to 0.194±0.023) compared with the linear model (ranging from 0.085±0.008 to 0.120±0.009). Rank correlations between breeding values predicted using linear and threshold models ranged from 0.61 to 0.88 (LCW), 0.53 to 0.91 (BTW), 0.66 to 0.87 (STW), 0.80 to 0.96 (EPW), 0.87 to 0.95 (NSW), 0.70 to 0.92 (LCY), 0.49 to 0.93 (BTY), 0.56 to 0.95 (STY), 0.88 to 0.97 (EPY), and 0.80 to 0.95 (NSY). The low genetic variability of the studied traits suggests a small genetic gain in the morphology and adaptation. According to the results obtained in the rank correlation, the percentage of coincident animals and the cross-validation analyses, it is recommended to use the threshold model for limb conformation, breed, and sexual traits. For eye pigmentation and navel size scores, both models can be used. In practical terms, the producer will be able to carry out his own selection, considering other traits that are not currently incorporated in the selection indexes, but that can lead to simultaneous gains in the morphology and adaptation of Hereford and Braford cattle.

Keywords:
heritability; linear model; morphological traits; principal components; rank correlation; threshold model

Trait		Number of animals	Median	Number of sires	Number of dams	Number of contemporary groups	Means±SD age at measurement (days)	Means±SD cow age at calving (years)
Limb conformation
	Weaning	82,433	3	7,509	39,758	3,317	193.82±39.28	8.73±5.03
	Yearling	42,015	3	4,004	25,753	2,642	535.58±51.33	9.73±4.86
Breed traits
	Weaning	83,088	3	7,546	40,031	3,365	193.86±39.29	8.72±5.03
	Yearling	42,063	3	4,006	25,769	2,649	535.58±51.31	9.72±4.86
Sexual traits
	Weaning	82,405	3	7,505	39,746	3,318	193.82±39.29	8.73±5.03
	Yearling	42,062	3	4,006	25,770	2,649	535.59±51.31	9.72±4.86
Eye pigmentation
	Weaning	75,308	4	6,504	36,452	3,104	193.11±39.76	8.75±5.02
	Yearling	37,649	4	3,454	23,390	2,473	534.88±50.60	9.78±4.87
Navel size
	Weaning	75,221	1	7,370	36,040	2,995	192.24±39.38	8.71±5.02
	Yearling	37,840	1	3,841	23,506	2,649	535.59±51.31	9.72±4.86

	Linear model					Threshold model
	LC	BT	ST	EP	NS	LC	BT	ST	EP	NS
	Weaning visual score
Direct additive genetic variance	0.013 (±0.001)	0.031 (±0.003)	0.012 (±0.001)	0.138 (±0.013)	0.025 (±0.002)	0.075 (±0.011)	0.340 (±0.038)	0.092 (±0.015)	0.407 (±0.053)	0.068 (±0.008)
Maternal genetic variance	0.002 (±0.001)	0.005 (±0.002)	0.002 (±0.001)	0.008 (±0.005)	0.002 (±0.001)	0.014 (±0.008)	0.087 (±0.032)	0.033 (±0.013)	0.028 (±0.014)	0.009 (±0.004)
Maternal permanent environmental variance	0.006 (±0.001)	0.003 (±0.002)	0.003 (±0.001)	0.008 (±0.005)	0.009 (±0.002)	0.031 (±0.008)	0.058 (±0.021)	0.032 (±0.009)	0.030 (±0.018)	0.009 (±0.005)
Residual variance	0.135 (±0.001)	0.245 (±0.002)	0.127 (±0.001)	0.825 (±0.009)	0.256 (±0.002)	0.458 (±0.011)	1.423 (±0.035)	0.579 (±0.015)	1.835 (±0.167)	0.355 (±0.007)
Direct heritability	0.086 (±0.010)	0.111 (±0.012)	0.089 (±0.011)	0.120 (±0.009)	0.085 (±0.008)	0.134 (±0.021)	0.194 (±0.023)	0.141 (±0.025)	0.171 (±0.017)	0.150 (±0.017)
Highest posterior density (95%)	0.086 to 0.087	0.111 to 0.112	0.089 to 0.090	0.120 to 0.121	0.085 to 0.086	0.134 to 0.135	0.194 to 0.195	0.141 to 0.142	0.171 to 0.172	0.150 to 0.151
Maternal heritability	0.001 (±0.001)	0.018 (±0.009)	0.017 (±0.008)	0.007 (±0.004)	0.009 (±0.003)	0.025 (±0.015)	0.050 (0.019)	0.051 (±0.021)	0.012 (±0.007)	0.020 (±0.009)
Highest posterior density (95%)	0.001 to 0.002	0.018 to 0.019	0.017 to 0.018	0.007 to 0.008	0.009 to 0.010	0.025 to 0.026	0.050 to 0.051	0.051 to 0.052	0.012 to 0.013	0.020 to 0.021
	Yearling visual score
Direct additive genetic variance	0.005 (±0.001)	0.007 (±0.001)	0.001 (±0.001)	0.163 (±0.015)	0.029 (±0.003)	0.039 (±0.009)	0.110 (±0.023)	0.027 (±0.010)	0.584 (±0.106)	0.097 (±0.011)
Residual variance	0.124 (±0.001)	0.172 (±0.002)	0.094 (±0.001)	0.738 (±0.012)	0.264 (±0.003)	0.431 (±0.013)	0.998 (0.032)	0.669 (±0.023)	2.402 (±0.381)	0.398 (±0.011)
Direct heritability	0.042 (±0.008)	0.038 (±0.008)	0.011 (±0.005)	0.181 (±0.015)	0.101 (±0.010)	0.084 (±0.019)	0.099 (±0.002)	0.039 (±0.015)	0.195 (±0.018)	0.196 (±0.021)
Highest posterior density (95%)	0.042 to 0.043	0.038 to 0.039	0.011 to 0.012	0.181 to 0.182	0.100 to 0.101	0.084 to 0.085	0.099 to 0.100	0.039 to 0.040	0.195 to 0.196	0.196 to 0.197

Proportion of selected	Weaning score					Yearling score
Proportion of selected	LC	BT	ST	EP	NS	LC	BT	ST	EP	NS
	Animals with phenotypic measures
50%	0.81 (90%)	0.84 (92%)	0.79 (90%)	0.96 (96%)	0.93 (92%)	0.90 (93%)	0.90 (94%)	0.91 (92%)	0.97 (96%)	0.94 (91%)
20%	0.67 (76%)	0.79 (81%)	0.70 (76%)	0.90 (91%)	0.91 (91%)	0.74 (86%)	0.74 (86%)	0.82 (87%)	0.91 (92%)	0.88 (89%)
10%	0.61 (68%)	0.74 (78%)	0.69 (68%)	0.87 (87%)	0.90 (88%)	0.84 (75%)	0.65 (78%)	0.84 (76%)	0.88 (89%)	0.85 (86%)
2%	0.73 (48%)	0.53 (63%)	0.66 (57%)	0.80 (82%)	0.91 (90%)	0.83 (79%)	0.50 (64%)	0.56 (80%)	0.91 (88%)	0.80 (80%)
	Sires, parents of animals with phenotypic measures
50%	0.88 (86%)	0.91 (93%)	0.87 (86%)	0.95 (96%)	0.88 (80%)	0.92 (84%)	0.93 (89%)	0.88 (80%)	0.97 (96%)	0.82 (77%)
20%	0.87 (85%)	0.88 (91%)	0.85 (88%)	0.93 (92%)	0.93 (93%)	0.91 (91%)	0.92 (90%)	0.91 (90%)	0.94 (93%)	0.92 (96%)
10%	0.79 (88%)	0.82 (88%)	0.82 (85%)	0.93 (91%)	0.91 (90%)	0.85 (88%)	0.87 (90%)	0.86 (89%)	0.91 (92%)	0.91 (88%)
2%	0.67 (72%)	0.74 (71%)	0.76 (76%)	0.82 (83%)	0.89 (85%)	0.83 (76%)	0.66 (75%)	0.79 (86%)	0.91 (82%)	0.89 (86%)
	Sires, parents of animals with phenotypic measures and with accuracy above 0.40
50%	0.80 (90%)	0.84 (93%)	0.84 (89%)	0.96 (95%)	0.93 (92%)	0.87 (95%)	0.90 (95%)	0.83 (89%)	0.97 (96%)	0.95 (94%)
20%	0.66 (79%)	0.77 (81%)	0.81 (78%)	0.91 (91%)	0.88 (90%)	0.80 (85%)	0.71 (83%)	0.87 (87%)	0.91 (94%)	0.91 (87%)
10%	0.68 (67%)	0.69 (76%)	0.75 (75%)	0.83 (88%)	0.87 (86%)	0.78 (79%)	0.68 (75%)	0.95 (82%)	0.88 (88%)	0.90 (89%)
2%	0.65 (52%)	0.58 (71%)	0.68 (72%)	0.90 (82%)	0.95 (87%)	0.70 (70%)	0.49 (73%)	0.80 (100%)	0.93 (92%)	0.83 (87%)

Trait	Score	Linear model			Threshold model
Trait	Score	β	R²	AIC	β	R²	AIC
LCW	1	37.8500	0.6414	13183.1981	36.7433	0.7243	11285.4322
	2	95.3766			94.0984
LCY	1	80.8786	0.5986	6628.6482	54.1883	0.6522	6151.7508
	2	171.6434			116.8844
BTW	1	25.0839	0.5629	17183.9675	22.4090	0.6567	14565.5300
	2	58.6915			57.6876
BTY	1	44.7137	0.4879	8171.4525	25.8461	0.5699	7354.5209
	2	119.6410			73.8047
STW	1	46.9900	0.6556	12267.4521	41.3299	0.7056	11208.0771
	2	104.5344			94.2097
STY	1	120.2734	0.5600	6443.2820	68.3476	0.6435	5803.4583
	2	318.6265			176.8270
EPW	1	13.8785	0.5374	42702.1062	13.7692	0.5382	42684.3839
	2	25.3333			25.0685
	3	37.3390			37.2126
	4	49.5344			49.4444
EPY	1	6.3018	0.5120	18314.7107	6.1688	0.5140	18299.1047
	2	13.7844			13.5542
	3	25.7001			25.6168
	4	37.8306			37.7114
NSW	1	23.3872	0.6188	25536.0257	23.3012	0.6197	25532.9625
	2	34.4748			34.3056
	3	45.9213			45.7254
	4	56.2391			56.0187
NSY	1	18.8594	0.5946	12861.8468	18.7953	0.5969	12858.7174
	2	31.8844			31.3435
	3	39.1432			39.0174
	4	46.6823			46.2975

Trait	Principal component
Trait	First	Second	Third	Fourth	Fifth
LCW	−0.617	−0.089	0.180	−0.107	0.628
BTW	−0.612	−0.044	0.362	−0.476	−0.224
STW	−0.712	−0.112	0.175	−0.188	0.383
EPW	−0.165	0.874	0.132	−0.029	−0.004
NSW	−0.633	0.081	−0.666	−0.018	−0.060
LCY	−0.378	−0.015	0.236	0.749	0.171
BTY	−0.555	−0.181	0.344	−0.104	−0.283
STY	−0.566	−0.129	0.100	0.516	−0.306
EPY	−0.099	0.875	0.162	0.043	−0.040
NSY	−0.577	0.102	−0.712	−0.024	−0.081

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E-mail: rbz@sbz.org.br

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[1] *Corresponding author: ju_salies@hotmail.com