novel approaches to expression and detection of oestrus in dairy cows

CHAPTER 3 – Single Nucleotide Polymorphisms and
Their Association with Oestrous Expression
3.1 INTRODUCTION
Oestrous detection is becoming increasingly difficult in the modern dairy
cow as oestrous expression is diminished. Cows display a shorter and less
intense oestrus (Van Eerdenburg et al., 1996;Dransfield et al., 1998), with
fewer cows standing to be mounted (Dobson et al., 2008). Therefore poor
expression of oestrus leads to more difficult detection of oestrus (Lucy,
2001). It is possible that genomics might provide a novel solution to the
problem.
Using a genomic approach to improve oestrous expression involves
investigating the possible associations of single nucleotide polymorphisms
(SNPs) with phenotypic traits that denote oestrus. A SNP is a single base
pair change in the sequence of DNA which causes variation in the
genotype. A SNP can take on two allelic forms, interacting with other SNPs
at different loci, causing common variants among the population, and thus
differences in the phenotype of animals in many traits (Berglund, 2008).
These polymorphisms in DNA can affect gene expression, translation and
transcription which in turn can affect protein function. With rapid
development of genomics dense SNP arrays were invented working on the
principle of 1000s of SNPs approximately 1cm apart in the genome. It is
expected that there will always be a SNP in close proximity to a gene or
DNA fragment of interest inherited by linkage disequilibrium (Meuwissen et
al., 2001). The BovineSNP50 provides a low cost, high density, genome
wide genotyping in cattle to enhance selection (Illumina, 2011). However,
use of SNP chips is based on associations of sequence variation and not on
understanding the biological information to make more informed decisions
based on phenotypic information. There are many effects of SNPs and so a
relationship must be determined between each SNP and a functional trait
(Ibeagha-Awemu et al., 2008). Studying genomic information allows links
to be made between SNP variants and physiological data (Berglund, 2008),
which is beneficial for selection as gains in fertility can be achieved using
genomic selection whilst sustaining high milk production (Veerkamp et al.,
2000).
A number of SNPs have been reported for their association with
reproductive traits and associations with fertility. SNPs in FGF2 and STAT5A
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