GENOMICS- Genetic selection potential (parasites, disease and production parameters)
By Dr Mackie Hobson BSc(Agric),BVSc

1. Reproduction

How can we as a Mohair industry use genomics?

• Parent verification
• Trace animals and their products
• Genomic selection

Roundworms and coccidiosis are 2 parasites that have a massive impact on the Angora goat and Mohair industry. Anthelmintic resistance is becoming a major issue in maintain the health and welfare of the Angora goat so as an industry we need to look at alternatives. Management strategies to maintain refugia are common practice but more needs to be done.

Genetic selection for resistance and resilience to parasites has been proved to be effective and identification of these more resistant goats can be achieved. See website Breeding worm resistant angora goats https://www.angoras.co.za/article/breeding-worm-resistant-angora-goats#234

The Identification of these genes in order to rapidly select goats that are more resistant to parasites, certain diseases and production parameters will be vital in the future.

Below is an explanation of the some of the appropriate terms used in genomics.

What is genomics?

Genomics is the study of the complete set of DNA (including all of its genes), all the information that can be derived from the DNA. The genome contains all the information needed for a goat to develop and grow. Studying the genome may help understand certain diseases and may aid in the selection against certain diseases.

Chromosomes carry genes. The gene is a unit of inheritance and an allele is the variation (nucleotide) at a specific location on the chromosome.

The genetic information is contained with DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

What is a SNP (pronounced ‘snip’)

Each SNP (single nucleotide polymorphism) represents a difference in a single DNA building block, called a nucleotide.

Nucleotides are the units of DNA and RNA. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. The four nucleobases in DNA are guanine (G), Adenine (A), cytosine (C) and thymine (T).

In RNA, uracil (U) is used in place of thymine.

An example of a SNP the nucleotide cytosine (C) may be replaced by with the nucleotide Arginine (A) in a certain stretch of DNA.

SNPs occur normally throughout a goat’s DNA.

Each individual goat has a unique combination of nucleotides at these positions. Thus, a SNP profile provides a kind of fingerprint.

An association between the marker (SNP) and the phenotype and then the marker is used to select for the gene (which is still unidentified). This enables us to identify the biological markers that are associated with disease, resistance to parasites or production parameters.

Research is required to identify these SNPs in Angora goats although there has been a SNP50 chip developed for other goat breeds.

Can the SNP50 chip be used in Angora goats?

There is already a goat SNP50 consortium bead chip (developed excluding the Angora goat)

In trials using phenotypic variation, fibre diameter and fleece weight, were genotyped with the goat SNP50 consortium bead chip. Results revealed that 46 983 SNP (88.1%) SNPs were polymorphic
(MAF>0.05)

A final SNP density of 1 SNP/ ~226 kb was determined (SNP density means the average number of SNPs in a sequence). Results indicate that the goat SNP50 bead chip was informative in the Angora goats that were studied, and should be useful in examining the underlying genetic variation.

What is MAF (Minor Allele Frequency)?

MAF provides information to differentiate between common and rare variants in the population. MAF is the frequency at which the second most common allele occurs in a given population. MAF variants which occur only once, known as "singletons", drive an enormous amount of selection.
Allele frequency, or gene frequency, is the relative frequency of an allele (variant of a gene) at a
particular locus in a population expressed as a fraction or percentage.
What is an allele?
Allele is a variation of the same sequence of nucleotides at the same place on a long DNA molecule.  The simplest alleles are single nucleotide polymorphisms (SNP) but can also be insertions and deletions of up to several thousand base pairs.

How many SNP’s do South African Angora goats have?

Approx 46 983 SNPs (88.1%) polymorphic (differences) have been located for the South African Angora goat. This is comparable with the number of polymorphic loci found in other goat breeds.

How would the SNP test work?

A sample of the goat’s DNA is isolated from a blood sample. This is used to identify genetic variations, known as single nucleotide polymorphisms (SNPs). These SNPs will then ideally tell one whether the goat is resistant or not to a specific disease or has a specific trait.

The successful application of SNP arrays depends largely on the degree of polymorphism (differences). An average MAF of 0.25 obtained in the Angora goats which compares well to other animal species.

What are the requirements for Genomic selection?
A reference population is required (need a minimum of 1000 goats).Phenotypes need to be recorded and biological samples (blood) taken and stored.

Selection for worm resistance

• Faecal egg counts (FEC) requires time and may fail to represent all of the factors involved in internal nematode resistance.
• Levels of IgG1, IgE and IgM have been negatively correlated with FEC in some sheep breeds.
• Immunoglobulin IgA, the isotype closely associated with intestinal mucosal immune responses, has also been positively associated with resistance.
• The FAMACHA ©  method was introduced to support parasite control using target selective treatment, based on the principle of the correlation between eye mucous colour and the haematocrit values (level of anaemia).

In New Zealand accuracy of genomic prediction in dual purpose sheep in determining Faecal egg counts (resistance to roundworms) in reference populations over 100 has been 0.63 and 0.7 (Dods et al 2014) while genomic prediction in Australian Merinos have been recorded as 0.26 and 0.1(Swan et al 2014).
The accuracy of the SNP chip in New Zealand dual purpose sheep for faecal egg counts was 0.5 (Pickering et al 2013).

For this reason it is suggested that the Mohair industry start collecting samples with phenotypic data of faecal egg counts along with other data of body weight, fleece weight etc to enable more rapid progress when the industry approves the development of Genomic selection.

REFERENCES
Validation of the 50k Illumina goat SNP chip in the South African Angora goat
 S.F. Lashmar; C. Visser # ; E. van Marle-Köster
Selection methods for resistance to and tolerance of helminths in livestock.
Concepta McManus,Tiago do Prado Paim,Cristiano Barros de Melo,Bruno S. A. F. Brasil, and Samuel R. Paiva