Genetic diversity and signatures of selection in Anglo-Arabian racehorses based on medium-density genotype data

Figures & data

Figure 1. Number of runs of homozygosity (ROH) and average length in Mb across the 31 horse autosomes.

Table 1. Inbreeding divided based on runs of homozygosity (ROH) length classes to differentiate ancient and recent inbreeding.

Class (Mbp)	Mean	SD	Min	Max
0.5-1	0.042	0.004	0.031	0.052
1-2	0.039	0.005	0.019	0.053
2-4	0.041	0.008	0.003	0.060
4-8	0.042	0.012	0.007	0.070
8-16	0.029	0.012	0.004	0.072
>16	0.017	0.012	0.007	0.072
Total	0.211	0.030	0.054	0.320

Figure 2. Violin plots showing inbreeding based on runs of homozygosity (ROH) across the 31 horse autosomes.

Figure 3. Correlation between inbreeding based on genotype and pedigree data.

Figure 4. Runs of homozygosity (ROH) islands on ECA1, ECA5, ECA7 and ECA17 in the Anglo Arabian (AA) horse breed. The x-axis represents the chromosome position in Mb and the y-axis represents the number of horses showing an ROH in each chromosome position. A dotted line shows significance level which was set as over 70% of the horses showing a ROH in a specific position.

Table 2. Runs of homozygosity (ROH) islands shared in over 70% of the Anglo Arabian (AA) horses, with genomic coordinates and a list of known QTLs located within each ROH island.

ECA	N. SNP	From	To	Length (Mb)	QTL
1	17	755781	1566092	0.81	–
1	43	21890990	23080884	1.18	Withers height
1	28	44925797	45836010	0.91	Withers height
5	16	55293804	55821027	0.52	Osteochondrosis dissecans
7	13	39673370	40287274	0.61	–
7	7	42399298	42896952	0.49	Navicular bone morphology
7	15	43077400	43752457	0.67	–
7	18	44216713	44953345	0.73	Navicular bone morphology
7	12	45336546	45714817	0.37	Navicular bone morphology, Chronic progressive lymphedema
7	18	46030873	46569541	0.53	–
17	15	20698671	21391864	0.69	Racing performance

Figure 5. Effective population size (Ne) based on linkage disequilibrium (LD) in a 20 generations time-period in the Anglo Arabian (AA) breed.

Figure 6. Principal Component analysis and breeds differentiation. AA means Anglo Arabian horses, ARR Arabian and TB thoroughbred.

Figure 7. Discriminant Analysis of Principal Components plot of linear discriminant function 1 (LD1) and linear discriminant function 2 (LD2). AA means Anglo Arabian horses, ARR Arabian and TB thoroughbred.

Data availability statement

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