Over-dominance in Breeding: Case of Deletion in Exon12 of CSN1S1 in Norwegian Goats

B S D h * G Th ll † S Li *‡ d T Åd ø *

* Department of Animal and Aquacultural Sciences, UMB, Box 5003, N-1432 Ås, Norway † Institute of Animal Breeding and Husbandry, CAU, D-24098 Kiel, Germany

‡ Center for Integrative Genetics, UMB, Box 5003, N-1432 Ås, Norway

B.S. Dagnachew , G. Thaller†, S. Lien ‡ and T. Ådnøy

Introduction Conclusions• The Norwegian deletion has reducing effect on DM content of the milk

• Over-dominance and dominance effects of the deletion allele and its high frequencyin the population, 0.73, reduced the selection pressure of conventional breeding onthe allele.

• Use of molecular information in the national breeding scheme could help to reducethe deletion allele frequency in the population (currently the information is used aspart of genetic evaluation)

In the Norwegian dairy goat population, 39 DNA-polymorphic sites have been identifiedthroughout the four casein loci. A deletion in exon12 of CSN1S1 – so far unique to Norwegiangoats – has been found in high frequency (0.73).The deletion allele has been found associatedwith reduced level of dry matter (DM) content of the milk

Problem statement: the national breeding goal is to increase dry matter content in milk(against the deletion effect), so it is difficult to explain the high frequency (i.e. 73%) of theallele in the population. The purpose of this study is to investigate additive and dominanceeffects of casein SNPs in Norwegian goat population.

Genotype: Blood samples of 575 goats were collected and DNA was isolated from the samplesfollowing standard procedure. Genotyping of possible casein SNPs were accomplished with theSequenom MassARRAY genotyping platform

Phenotype record: Recordings from the Norwegian Dairy Goat Control on milk productiontraits in 2005 were used as phenotypes. 3194 test-days were available for analysis for dailymilk yield (DMY), and 2236 samples of fat content (FC), protein content (PC) and lactose

Model: single trait test-day mixed models with fixed effect of single SNP’s additive anddominance effects were fitted.

Where q contains fixed effects of SNPs, β all other fixed effects, u random effect of individuals, p permanent environment effect and e is random residuals. X, Q and Z are

eZpZuQqXy

Materials and Methods

content (LC).individuals, p permanent environment effect and e is random residuals. X, Q and Z are incidence matrices.

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Figure 1: Casein SNPs additive effect. The horizontal lines indicate 10% experimental wise threshold level and test statistic value above the top-line or bellow the bottom line are taken as significant.

Figure 2: Casein SNPs dominance effect. The horizontal lines indicate 10% experimental wise threshold level and test statistic value above the top-line or bellow the bottom line are taken as significant.

Results and Discussion

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The most frequent SNPs within CSN1S1 have opposite additive effects on milk kg (per test-day) and milk composition(fat %, protein % and lactose %). SNP 14 of CSN1S1 and a cluster of SNPs at CSN3 had significant additive effects onmilk kg, fat % and protein %.

The deletion allele, SNP14, had a positive over-dominance effect on milk kg, negative over-dominance on lactose % anda negative dominance effect on fat % and protein % (Figure 1 and 2). It has been reported that the deletion allele hasnegative effect on DM content of milk (Ådnøy et al. (2003)) and our results also confirmed that the deletion significantlyreduced the protein and fat content of the milk (Figure 1).

Figure 3 presents gene substitution effect (α) of the deletion for the fixed additive (a) and dominance (d) values. It showsFigure 3:Gene substitution effect

that the gene substitution effect decreases when the frequency of the allele increases for milk kg. For the milk content αincreases with higher frequency of the deletion allele.

Variances of gene substitution effects are presented in Figure 4. it shows that at current frequency of the allele in thepopulation, 0.73, the gene substitution effect variances are reduced for all four traits. This might influence the selectionpressure of conventional selection on the allele.

Over-dominance and dominance effects of the Norwegian deletion allele reduced additive genetic variance available forselection in the predominant progeny testing of bucks. The reduced selection pressure of the conventional selection onthe allele might explain why the allele frequency has remained high despite selection being against the effect of thell lallele.

References Ådnøy, T., Vegarud, G., Devold, T.G. et al. (2003). In proc. IWMGQSG, CD-ROM Communication No. 2-17.

Dodds, K.G., McEwan, J.C. & Davis, G.H. (2007). Small Ruminant Res., 70:32-41

Hayes, B., Hagesæther, N., Ådnøy, T. el al. (2006). Genetics, 174:455-464

Acknowledgment

Figure 4:Gene substitution effect variance