Ahmad, Sausan
(2011)
Application of BLUP in prediction of breeding values and estimation of SNP effects in dairy cattle.
PhD thesis, University of Nottingham.
Abstract
Genetic selection for higher milk production has unavoidably resulted in a decline in fertility of dairy cattle in the UK due to the antagonistic correlation existing between fertility and milk yield. This trend in fertility has necessitated broadening the breeding programme to include fertility traits. However, the heritability of fertility traits currently used in the UK are of low heritability (h2<0.05). Therefore, one approach is to use molecular markers in order to identify animals with the highest genetic merit for fertility.
The first aim of this project was therefore to test single nucleotide polymorphisms (SNPs) in candidate genes for their possible associations with fertility PTAs. A group of 408 dairy cows and bulls were genotyped at different loci (GnRH receptor, FSH receptor, LH receptor, activin receptor, and neuropeptide Y receptor Y2 (NPYRY2)). Seven SNPs were identified in the GnRH receptor gene. These were in the promoter and coding regions at positions -331, -108, 206, 260, 341, 383 and 410 relative to the translation start site. Two groups of SNPs were found to be in linkage disequilibrium, the SNPs at positions 206 and 383 being inherited together, as were those at -108, 260, 341 and 410. An association study between these SNPs and fertility PTAs revealed that the -108 SNP group was associated with favourable effects on fertility, reducing PTA for DFS by about 0.4 day. However, when GnRHR gene function was evaluated by measuring circulating LH level after administration of GnRH in pre-pubertal animals, no significant associations of the SNPs with LH levels were detected. Furthermore, five SNPs were identified in the FSHR at residues 502, 669, 596, 658, and 685, four of which (at positions 502, 669, 658, and 685), had deleterious effects on fertility PTAs, increasing CI and DFS, while decreasing NR56.
Inaccurate heat detection has been identified as a major contributor to low fertility in dairy cattle, and therefore the second aim of this project was to investigate oestrus expression traits for which BLUP breeding values were estimated. Electronic tags (Fullwood and Lily) were used to measure behavioural activities at oestrus in two separate groups of animals. The first group comprised 103 cows in their first parity. Oestrus behaviour traits were: the number of steps at oestrus (STEPS) and the percentage increase in the number of steps at oestrus (STEPS%) relative to the number of steps over the 10 days preceding oestrus (BASE). Cows in this group were genotyped at 10 genes (GnRHR, LHR, FSHR, oestrogen receptors α and β (ESR), activin receptor, leptin, ghrelin, neuropeptide Y (NPY) and NPYRY2 for SNP identification. Of these SNPs, only those located in the GnRHR, oestrogen receptor α and NPY were found to have statistically significant effects on oestrus traits. The second group consisted of 189 cows with 995 oestrus behaviour records. Oestrus traits were: the number of activity units (AU) at oestrus (ACTIVITY) and the percentage increase in the number of AU at oestrus (ACTIVITY%) over baseline activity (BASE) determined over a 4 day rolling average. In addition to the above mentioned 10 genes, these cows were genotyped at signal transducer and activator of transcription 1 and 5A (STAT1, STAT5A), growth hormone receptor (GHR), prolactin, and prolactin receptor genes. In this study SNPs in the GnRHR, LHR, FSHR, ESRα, GHR, activin receptor, STAT1, and STAT5 were found to have significant effects on oestrus expression. The genetic basis for oestrus behaviour was also investigated applying various animal models in this group. ACTIVITY, ACTIVITY% and BASE had moderate heritabilities of 0.19 to 0.24, 0.16, and 0.25 respectively. The breeding values of the cows were shown to be normally distributed, and ranged between -19 to 27, -18 to 20, and -20 to 28 for ACTIVITY, ACTIVITY%, and BASE respectively. These values are significant in terms of the ability of the stockman to reliably detect cows in heat.
There have in the past been few genetic analyses of oestrus behaviour characteristics, and there are few studies of SNP associations with fertility traits of the kind described here. Therefore these studies make a significant contribution to our understanding of the genetics of fertility in dairy cattle, and can be used by breeders as a means to improving fertility in the national dairy herd.
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