An Introduction to Genomic Technology

December 21, 2016 1:34 pm

What is Genomics?

Genomics is the term given to describe a range of DNA based technologies concerned with the structure, function, evolution, and mapping of genomes, being the complete set of genes present in an organism.
In layman’s terms, genomics refers to technologies that provide information about an animal’s genetics by analysing and interpreting the animal’s DNA.

Common current applications of genomics include:

    • parentage verification
    • management of genetic conditions
    • change in qualitative traits (coat colour, polledness)
    • genetic improvement in production traits
    • assessment of breed composition

     
     
     

    What is DNA?

    Deoxyribonucleic acid (DNA) is an exceptionally important molecule found in the nucleus of all bovine cells. It is often described as the ‘blueprint’ of an organism because it codes the instructions for how that organism will develop, function and appear. In a breeding context, DNA is important as it contains an animal’s genes.

    In beef animals, DNA is bundled into chromosomes. Beef cattle have 30 chromosome pairs, with each pair including one chromosome inherited from the sire and one from the dam. Because the progeny inherit chromosomes from both parents, the genetic ‘blueprint’ is passed on from one generation to the next.
     

    What is DNA imagre

     
     
     

    Structure of DNA

    DNA looks like a long twisted ladder, or double helix. The sides of the ladder are made up of alternating sugar and phosphate molecules, with the rungs connecting the sugar molecules and being known as nitrogenous bases.

    There are four different nitrogenous bases, Adenine (A), Thymine (T), Guanine (G) and Cytosine (C), with each rung of DNA being made up of two bases linked together, either G to C or T to A. There are approximately 3 billion base pairs in bovine DNA, with the sequence of base pairs determining the ‘message’ or functionality of DNA.

    Of importance for genomics, the sequence of base pairs differs between individuals, with differences in the base pair sequence providing the basis for genetic variation between individuals. All current applications of genomics in a beef enterprise involve analysis and interpretation of an animal’s base pair sequence.
     

    DNA structure

     
     
     

    What is a Gene?

    A gene is a base pair sequence at a particular location on the chromosome which codes for a specific product. It is estimated there are between 22,000 and 28,000 genes contained within a beef animal’s DNA. Genes are separated on chromosomes by areas of ‘non-coding DNA’ for which no function has been identified, but still makeup part of the animal’s genotype.

    For each gene there may be 2 or more variations, known as alleles, which can result in different phenotypes or observable characteristics. For example one of the genes influencing coat colour has three alleles, the “e” allele for red coat colour, the ED allele for black coat colour and a “Wild type” E+ allele. Which alleles the animal has, and how those alleles interact with each other determines the coat colour of the animal.
     
     
     

    What is a Gene Marker (or DNA Marker)?

    A gene or DNA marker is a known, heritable base pair sequence which is associated with a particular gene. The DNA marker sequence does not necessarily have to be part of the gene that codes for the trait but only associated with it, therefore the value of the genetic marker will vary.

    There are several types of DNA markers, but those most commonly being used in the beef industry are microsatellites, indels and SNPs (pronounced “snips”).
     
     
     

    What is a Microsatellite?

    A microsatellite is a repeat of a particular base pair sequence, usually two or three base pairs, at a specific location in an animal’s DNA. (e.g. CACACACA). The number of base pair repeats differs between animals. Microsatellites form the basis for traditional DNA parent verification, which use multiple microsatellites to determine a calves’ parentage through the exclusion of possible candidates which do not have the same microsatellites.
     
     
     

    What is an Indel?

    An indel is an insertion or deletion of a particular base pair sequence at a specific location in an animal’s DNA. Indels are often associated with undesirable recessive genetic conditions, and are used to identify animals who appear normal but possess (or carry) an undesirable recessive allele within their DNA.
     
     
     

    What is a SNP?

    Single Nucleotide Polymorphisms (SNPs) are markers where there is a difference in a single base pair. For example, in the figure on the left, the top animal has a “C & G” base pair at the particular location in the DNA, whereas the bottom animal has a “T & A” base pair.

    While early DNA technology only evaluated an animal’s DNA for a relatively small number of SNPs, SNP chips now routinely evaluate animals at many thousands of individual SNPs. For example, DNA chips with 7,000 (i.e. 7K), 50,000 (ie. 50K) or 800,000 (ie. 800K) SNPs on them are now available.

    SNPs are the most common form of DNA marker and are now utilised within the Angus breed for parentage verification, for identification of animals carrying undesirable alleles for some genetic conditions, and as the basis for the calculation of genomic predictions for production traits.
     
     
     

    What is a Genomic Prediction?

    As each production trait is influenced by many genes, inferring genetic merit for a particular trait requires the accumulated effects of many markers. Genomic predictions take the genotype of an animal as collected using dense SNP chips (e.g. 50,000 SNPs), to estimate the animal’s breeding value based on the known effect of each SNP on the respective trait of interest.

     

    snp

     
     
     

    Genomic Testing in Practice

    In broad terms, genomic testing of beef animals involves several main processes.

    • Collection of a DNA sample from the animal. Tail hairs and semen are the most common sample types currently collected on Angus animals.
    • DNA Extraction: Use of specialised laboratory equipment to extract the DNA from the nucleus of the cells present within the DNA sample.
    • Genotyping: Laboratory analysis of the DNA to determine the animal’s genotype, being the base pair sequence (or DNA marker) that the animal possesses at specific locations within its DNA.
    • Interpretation of the animal’s genotype: Software analysis of the animal’s genotype to provide informative information about the animal’s genetics.

    For example, comparison of an animal’s genotype with the genotype of prospective parents to determine parentage, or utilisation of an animal’s genotype to predict its breeding value.
     
     
     

    Further Information

    To further discuss genomic technology, please contact Andrew Byrne, Breed Development & Extension Manager, on (02) 6773 4618 or andrew@angusaustralia.com.au. Additional information regarding the utilisation of genomics in an Angus beef breeding enterprise is also available from the Angus Australia website.
     
     
     

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