University of Debrecen Centre for Agricultural and Applied Economics Science Faculty of Agricultural and Food Sciences and Environmental Management Effect of Stearoyl-COA desaturase genepolymorphism on milk production traits of Hungarian Holstein Friesian cows By : Tegegn Gudeta, Jaleta (MSc thesis) Debrecen , Hungary, May 2012
IntroductionMarker Assisted selection in modern dairyNumber of studies conducted in large scale on candidate genes in dairy breedingSCD is hypothesiszed candidate gene It catalyze Cis∆-9 desaturation Mapped to chromosome 26 in bovine SCD 1 and SCD5 Associated with milk fatty acid compositionStudies of SCD gene not conducted in HHF
Objectives of the studyTo estimating allele and genotype frequencies of SCD gene polymorphism(878 C/T)To determining the effect of SCD gene polymorphism on cows milk production traits
Materials and Methods1) Animals and Milk data Hair root samples (8-10) were collected from 277 HHF in Tedej Dairy Farm located 15 km north of Debrecen One lactation milk record data were collected for 277 HHF cows-305 day average milk yield (kg), fat yield (kg), fat percentage(%), protein yield (kg), protein percentage (%) and SCC (10,000 cell/ml)
2) Study Methods Molecular Laboratory of UD DNA isolation from Hair root 3-5 hair root+ 100 µL Lysis buffer+1.5 ProteinK Water bath for 60 min at 60 0c , for 20 min at 95 oc water bath, stored at -20 oc Spectrophotometrical Analysis-Nanodrop Spectrophotometer RT-PCR 7300
Amplification and Sequencing protocol Initial steps: Activation at 950C for 10 minutes (AmpliTaq Gold DNA polymerase), Melting for 15 sec at 920C, Annealing/Extension at 600C for 1 minute (40 cycles). The SNP 878 C/T was used in this study and the nucleotide substitution was identified according to Tanguichi et al., (2004).
4.) Data Analysisa)Descriptive Statistics using R software (Version: R- 2.14.2)b)Hardy-Weinberg Equationc) Analysis of Variance (ANOVA) using R software (Version: R-2.14.2)
Results and Discussion1. Genotypes and Allele Frequencies of SCD gene Polymorphisms Amplification curve for CC(left) and CT(right) genotypes
Result of amplification curve for TT genotype (Green line)
Allelic discrimination of SCD genotypes (Blue-CC, Green-CT, and Red-TT)
Genotype and allele frequencyy of the SCD gene in the investigated Hungarian Holsteins cow population No of Animals (Genotype SCD P value X2 Frequencies in %) Allele % CC CT TT 0.04695 3.947Observed 94(34) 148(53) 35(13) C(0.61)Expected 102(37) 132(48) 43(15) T(0.39)
2. Effects of SCD Genotypes on Recorded Milk Production Traits Parameter Genotype CC CT TT P value Fat (%) 3.76±0.41 3.8±0.43 3.7±0.38 0.2272 Protein (%) 3.22±0.178 3.22±0.178 3.23±0.14 0.998 SCC(X103 cell/ml) 136±106.4 116±70.2 119±72.7 0.2264 305 MY (kg) 8277.5±1301 8468.5±1542 8463.4±1294 0.5805 305 FY (kg) 310.6±52.4 321.9±55.2 313±50.6 0.2505 305 PY (kg) 266.1±38.5 272.1±45.8 272.3±36.2 0.5315Mean and standard deviation of milk production traits and its association withSCD genotypes.
Conclussions Higher C allele(0.61) frequency and lower T allele (0.39) frequency was reported in this study The SCD genotypes frequency in HHF herds under this study were not in Hardy-Weinberg equilibrium, the possible reason for this result may be small numbers of animals included in this study and indicating the herds were not in a random mating system SCD-878 C/T locus cannot be considered as candidate gene in milk production traits Further studies will be necessary on large number of animals to confirm the current result