Evaluation of potential effects and genetic parameters in conformational limb defects in Pura Raza Española horses

Figures & data

Figure 1. Conformational limb defects in Pura Raza Española horses. Lines of aplomb in the colour red.

Table 1. Number and proportions of Pura Raza Española horses according to the class of conformational limb defects and the significance level for the difference within unaffected (class 0) vs affected animals (class 1 + 2).

			Number of horses (%)
Limbs conformational defects		Total	Class 0	Class 1	Class 2	Class 1 + 2	p-value
Hock defects	Closed	31,040	24,184 (77.91%)^b	4786 (15.42%)	2070 (6.67%)	6856 (22.09%)^a	<.0001
	Open	36,502	24,184 (66.25%)^b	9109 (24.95%)	3209 (8.79%)	12,318 (33.75%)^a	<.0001
	Convergent	40,570	10,498 (25.88%)^b	21,379 (52.70%)	8693 (21.43%)	30,072 (74.12%)^a	<.0001
	Divergent	13,286	10,498 (79.02%)^b	1956 (14.72%)	832 (6.26%)	2788 (20.98%)^a	<.0001
Knee defects	Buck	32,556	30,431 (93.47%)^b	1699 (5.22%)	426 (1.31%)	2125 (6.53%)^a	<.0001
	Calf	39,503	30,431 (77.03%)^b	7190 (18.20%)	1882 (4.76%)	9072 (22.97%)^a	<.0001
	Bench	30,879	29,858 (96.69%)^b	820 (2.66%)	201 (0.65%)	1021 (3.31%)^a	<.0001
	Knock	40,607	29,858 (73.53%)^b	8323 (20.50%)	2426 (5.97%)	10,749 (26.47%)^a	<.0001

Class 0 = absence of the defect; class 1 = slight presence of the defect; class 2= the most pronounced degree of defect; class 1 + 2= affected animals.

^a,bDifferent superscript letters indicate significant difference between groups (p < .05).

Table 2. Generalised Non-Linear Model (GLZ) between conformation limb defects and effects, using a multinomial logic test (Wald Statistic).

	Defects	Age	Gender	Coat	Birth	Geographical	Inbreeding	Proportionality
				Colour	stud size	área	Coefficient	Index
Hock defects	Closed	0.0510	0.0300	0.0020	<0.0001	<0.0001	<0.0001	<.0001
	Open	0.0150	<0.0001	<0.0001	0.2040	<0.0001	0.0190	<.0001
	Convergent	<0.0001	<0.0001	<0.0001	<0.0001	<0.0001	0.7800	<.0001
	Divergent	<0.0001	0.0130	0.0090	0.1940	<0.0001	0.7920	<.0001
Knee defect	Buck	0.6300	<0.0001	0.1780	<0.0001	<0.0001	<0.0001	<.0001
	Calf	<0.0001	<0.0001	<0.0001	0.0600	<0.0001	0.1250	<.0001
	Bench	0.0710	<0.0001	0.0167	0.0185	<0.0001	0.5280	<.0001
	Knock	<0.0001	<0.0001	<0.0001	<0.0001	<0.0001	0.6320	<.0001

Table 3. Total number of observations and percentage of Pura Raza Española horses affected by conformation limb defects (horses in classes 1 and 2), according to the effects, after an association frequency analysis of all the effects (Maximum-Likelihood Chi-square).

Effects			Population affected hock defects (%)				Population affected knee defects (%)
		N	Closed	Open	Conv.	Diver	Buck	Calf	Bench	Knock
Age	Young (<4)	22,403	16.14 ^a	28.50^b	70.09^b	7.26^b	5.07^a	22.61^b	2.43^a	27.10^b
	Adult (≥4)	20,955	15.46^a	28.32^a	68.58^a	5.54^a	5.14^a	20.93^a	2.48^a	24.46^a
Gender	Stallions	14,331	16.14^b	26.91^a	67.46^a	6.63^b	6.81^b	20.01^a	2.07^a	28.17^b
	Female	29,027	15.65^a	29.15^b	70.30^b	6.33^a	4.27^a	22.67^b	2.64^b	24.67^a
Coat	Bay	15,963	15.72^b	29.29^b	70.02^b	6.35^a	5.26^a	21.27^a	2.37^a,b	25.75^b,c
Colour	Chestnut	2863	13.13^a	34.06^c	70.63^a,b	6.39^a	5.41^a	19.87^a	1.90^a	23.77^a,b
	Black	5404	14.17^a	29.15^b	67.02^a	7.85^b	5.64^a	21.40^a,b	2.75^b	23.55^a
	Grey	19,128	16.75^c	26.63^a	69.28^a,b	6.10^a,b	4.77^a	22.64^b	2.52^b	26.85^c
BSS	<3	7177	13.21^a	29.34^a	68.78^a	5.71^a	4.45^a	21.98^a	2.79^b	24.70^a
	3–9	21,863	15.63^b	28.68^a	68.33^a	6.48^a	5.05^ab	22.15^a	2.56^b	26.42^b
	>9	14,318	17.39^c	27.52^a	71.22^b	6.72^a	5.51^b	21.16^a	2.12^a	25.47^a,b
G.Area	Spain	28,151	15.82^c	29.33^b	71.94^c	4.76^a	5.34^bc	21.29^a	2.13^a	25.97^b
	Europe	4138	11.26^a	31.56^b	67.79^bc	5.39^b	5.85^c	20.54^a	2.45^a	23.85^a
	S.A.+ C.A.	2809	14.03^b	29.19^b	57.42^a	12.46^c	4.58^ab	25.12^c	3.61^b	23.47^a
	USA + Mex	826	18.68^d	23.41^a	65.41^b	10.59^b	4.17^a	22.90^b	3.10^b	27.12^b
F (%)	<3.125	977	11.98^a	30.71^b	68.58^a	5.02^a	7.51^b	21.14^a	2.90^a	24.89^a
	≥3.125 to < 6.25	23,517	15.28^b	28.43^c	69.47^a	6.48^a	5.00^a	21.75^a	2.44^a	25.37^a
	≥6.25 to < 12.50	13,988	16.14^c	28.75^b,c	69.32^a	6.48^a	4.92^a	21.69^a	2.51^a	26.03^a
	≥12.50	4876	18.21^d	26.87^a	69.09^a	6.36^a	5.64^a	22.43^a	2.27^a	27.54^a
P.I.	<98	5905	21.64^c	27.57^a	68.45^a	5.61^ab	3.48^a	29.06^b	3.08^b	32.02^c
	98–100	20,721	15.44^b	29.64^b	70.68^b	6.61^a	4.62^b	21.04^a	2.25^a	22.53^b
	>100	16,732	14.22^a	27.18^a	68.04^a	6.50^b	6.29^c	20.12^a	2.48^a	27.72^a

N: Number of observations; Conv.: Convergent hock; Diver.: Divergent hock; BSS: Birth stud size; G.Area: Geographical area; S.A.: South America; C.A.:Central America; Mex:México; F: Inbreeding coefficient; P.I.: Proportionality index.

^a,b,cDifferent superscript letters indicate significant difference between groups (p < .05).

Table 4. Heritability coefficient (h²), genetic correlations (r_g) and their standard deviations (s.d.) for hock defects and knee defects in Pura Raza Española horses.

	Approach	Defects	h^2 (s.d.)	Defects	rg (s.d.)
Hock defects	1	Closed	0.40 (0.017)	Closed vs Convergent	0.51 (0.038)
		Open	0.27 (0.015)	Closed vs Divergent	0.38 (0.137)
		Convergent	0.26 (0.010)	Open vs Convergent	0.29 (0.037)
		Divergent	0.42 (0.025)	Open vs Divergent	0.28 (0.070)
	2	Closed/Open hock	0.21 (0.060)
		Convergent/Divergent hock	0.24 (0.031)
Knee defects	1	Buck	0.33 (0.024)	Buck vs Bench	0.42 (0.203)
		Calf	0.32 (0.014)	Buck vs Knock	0.13 (0.061)
		Bench	0.25 (0.036)	Calf vs Bench	0.20 (0.133)
		Knock	0.38 (0.013)	Calf vs Knock	0.70 (0.276)
	2	Buck/Calf kneed	0.14 (0.057)
		Bench/Knock kneed	0.18 (0.069)

Table 5. Genetic correlations and their standard deviations (in parenthesis) between hock defects and knee defects of Pura Raza Española horses.

	Hock defects
	Closed	Open	Convergent	Divergent
Knee defects
Buck	0.10 (0.079)	0.41 (0.055)	−0.06 (0.051)	0.39 (0.094)
Calf	0.39 (0.043)	−0.18 (0.049)	0.15 (0.034)	0.23 (0.080)
Bench	−0.25 (0.160)	0.25 (0.123)	0.12 (0.106)	0.07 (0.025)
Knock	0.59 (0.033)	−0.14 (0.042)	0.21 (0.029)	0.20 (0.069)

Table 6. Percentage of coincident animals within the upper 5 and 20 percentile of the estimated breeding values (EBV), with a reliability greater or equal than 0.20 and 0.60, between the genetic models used in Approaches 1 and 2.

	Reliability ≥ 0,20		Reliability ≥ 0,60
	EBV 5%	EBV 20%	EBV 5%	EBV 20%
Hock defects
Closed	67.35	69.12	62.50	57.14
Open	95.89	93.69	75.00	77.77
Convergent	75.25	78.74	66.66	70.10
Divergent	69.02	71.02	25.00	35.00
Knee defects
Buck	32.86	45.59	33.33	50.00
Calf	37.59	46.63	6.60	20.39
Bench	27.75	31.89	33.33	50.00
Knock	94.12	91.17	92.85	96.43

Approach_1: scale from 0 to 2; approach_2: scale from −2 to 2.

Data availability statement

The data that support the findings of this study are available from the corresponding author, MRL, upon reasonable request.