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INTRODUCTION
Sussex cattle are considered one of the oldest and purest English breeds and were favoured by breeders due to quality of their flesh and fineness of their hides. Breed development was only realized in the early 1800’s, where breeders placed emphasis on the quality of beef acquired from an animal and the red colour coat. In more recent times, emphasis has been placed on carcass conformation, with the main aim producing a maximum of prime meat whilst retaining the inherent genetic qualities and diversity of the breed. Sussex cattle remain a quintessential stud breed, with international pure-bred herds in Australia, New Zealand, South
Africa (SA) and the United States. The first Sussex animals were imported to South Africa in 1903, with the Sussex Cattle Breeders Society of SA being ratified in 1920. Farmers noticed that Sussex cattle are great as a pure breed and for use in both commercial and crossbreeding systems to improve the growth and fertility of their beef herd. An emergence of polled SA Sussex is a consequence of importing polled breeding material from Western Australia over 20 years ago and three British bulls 15 years ago. An investigation into the SA Sussex breed at a genomic level was conducted to identify genetic clustering, firstly at a herd level and secondly at a species level with other cattle breeds.
BREED CLUSTERING THROUGH A “GENEBOX”
A total of 223 Sussex animals have been genomically tested from various herds over the last few years using SA Stud Books Genomic Services. SA Stud Book has the ability to assess the level of genetic relatedness of animals within a breed as well as shared ancestry between the Sussex genotypes and other cattle breed genotypes. To assess any genetic differences between the animals, principal component analysis is used to visualise and explore variation between the vast number of genetic markers in a much simpler format. A “GeneBox” is a three-dimensional tool that allows one to elucidate genetic variances at a simpler level. In order to verify the use of this tool, the investigation was split into 2 scenarios. As we progress from Scenario 1 to Scenario 2, other breeds of different genetic backgrounds are included as this increases the scientific accuracy of this analysis.
Scenario 1 occurs at a herd level, with each animal being colourcoded to the herd they were born in. Table 1 refers to the herd as well as number of animals genotyped.
TABLE 1: NUMBER OF SUSSEX GENOTYPES FOR EACH HERD USED IN THE ANALYSIS.
Table 2 refers to the number of genotypes in each respective breed used in this investigation. For Scenario 2, each breed is distinctly colour-coded in the “Genebox” to easily differentiate between them. The Sussex animal types were colour-coded as black.
The Dairy Bos taurus breed were coded as blue and the Beef Bos taurus breed as brown. The composite breed included were coded as red, while the Sanga breed were made orange with the Zebu indicus type being yellow respectively.
TABLE 2: NUMBER OF GENOTYPES FOR EACH BREED USED IN THE ANALYSIS.
SCENARIO 1
In this scenario, the Sussex genotypes were assessed only within the Sussex breed. As seen in Figure 1, the “Genebox” indicates the level of genetic diversity within the Sussex breed. The animals cluster distinctively together in one large cluster which is an indication that they share common ancestry and a similar genetic composition. Herd 1 (black) constitutes the largest part of the Sussex genomic population, with branches indicating genetic differences and could be attributed to specific lines within this herd. Animals from Herds 2 and 3 (yellow and red) show tighter clustering, indicating high levels of relatedness. The two British bulls (blue) cluster within the SA Sussex cluster, indicating these foreign animals are related to the SA population. The one bull shows a lower degree of relatedness (near the outside of the cluster) which could be attributed to genetic variation within the Sussex breed that is yet to be captured through genotyping.
Figure 1: Scenario 1 of only Sussex animals colour-coded at a herd level.
SCENARIO 2
The Sussex, a Dairy Bos taurus breed and a Beef Bos taurus breed cattle genotypes were collated with a Zebu indicus breed of African origin, a composite breed of American origin and an indigenous Sanga breed. The addition of the breeds with known Bos indicus ancestry increased the variation in genetic composition and allowed for a greater analysis of genetic differences between all the animals in the dataset. As can be seen in Figure 2, the distance between the Taurine breeds decreased due to a data structure that allowed for the identification of genetic differences. Here we can easily observe the distinct breed clusters and we see the greatest difference between the Zebu cluster (yellow) and the Taurine breeds, with the composite and Sanga breed clustering between the Taurine and Zebu breeds. Although all these breeds share ancestry in that they are all of Bos origin, the fact that all the breeds cluster away from each is a sign of the genetic pressures each breed uniquely faces.
Figure 2: A ”Genebox” with the 3 Bos taurus breeds, a composite breed, a Sanga breed and the Zebu indicus breed.
Figure 3 represents a rotation of Figure 2. As this “Genebox” is 3D, it allows for a better assessment of depth in genetic diversity, in comparison to the 2D plot. Here we can assess diversity according to the first principal component (PCA1). The Zebu indicine breed clusters on the left, with the composite breed clustering in the middle, as it is comprised of both Taurine and Indicine ancestry. All three Taurine breeds clustering to the right indicates shared ancestry. It can be seen that the Taurine breeds differ on the second and third principal component (PCA2 and PCA2), with the dairy breed (blue) clustering above the Sussex (black), while the other Taurine beef breed (brown) clusters closer to the Sussex.
Figure 3: The same as Figure 2, just from a different angle
IN SUMMARY
An interesting observation was noticed between the two different Scenarios above. In Scenario 1, the Sussex genotypes were seen to cluster directly in the centre of the “Genebox” with various branches possibly indicating lines within a herd. In Scenario 2 we observe the distinct and tight clustering of animals within their breed of origin. The analysis uses no pedigree information, only the genomic information, and with over 40 000 markers, it makes this analysis highly accurate. One must keep in mind that the Sussex is the smallest genomic population in this analysis. The population size will play a role in the size of the cluster as this is attributed to the amount of genetic diversity within each breed. As not many SA Sussex animals have been genotyped, the amount of genetic diversity here may not be representative of the whole breed. It is recommended to genotype as many animals from numerous herds that have different environmental and selection pressures.