Thesis Projects (work in progress)

Abebe, Abiye Shenkut, 2013 (SLU): Analysis of the genetic diversity of local Swedish chicken breeds using microsatellite markers

The aim of the present study was to analyse the genetic diversity, genetic relationship and breed structure of ten local Swedish chicken breeds. A total of 127 chickens from ten breeds were genotyped using 24 autosomal microsatellite markers. Genotyping was performed by amplifying the genomic DNA using multiplex PCR kits and fragment analysis was carried out using genetic analyzer. A total of 124 alleles were detected in all populations, with a mean number of 5.17 alleles per locus. Within breeds, the observed and expected heterozygosities ranged from 0.219 to 0.417 and 0.231 to 0.559 respectively, and three breeds (Gotlandshöna, Hedemorahöna and Skånsk blommehöna) showed significant deviations from Hardy-Weinberg expectations. Similarly, 6 of the 24 loci were significantly deviated from Hardy-Weinberg. Inbreeding within breeds (FIS) was generally high with the overall across loci and breed being 0.181. Due to small sample sizes in 50% of the breeds, the genetic relationship between breeds shown in the neighbor-joining tree was supported by low bootstrap values. The results of the breed structure analysis revealed that the Gotlandshöna, Hedemorahöna, Öländsk Dvärghöna and Svarthöna breeds formed their own distinct clusters, but breeds with small sample sizes (Skånsk blommehöna, Åsbohöna, Kindahöna, Ölandshöna, Gammelsvensk Dvärghöna and Orusthöna) clustered together. The results of the current study can be used as baseline genetic information that can be assimilated with genetic conservation programs, for instance, to control inbreeding within breeds and to implement further genetic studies in local Swedish chickens.

Babigumira, Brian Martin (WUR): Comparing different approaches to pedigree reconstruction in commercial broodstocks of Common sole, Solea solea (L., 1756)

In this study exclusion-based and likelihood-based approaches were compared using Family Assignment Program (FAP) and CERVUS. The criteria used to compare FAP and CERVUS were: (1) the overlap in the performance of the assignment programs and (2) the heritability estimates generated using Residual Maximum Likelihood (REML) for each reconstructed pedigree. Parentage analysis using the genotyping dataset generated based on ten microsatellite loci showed that 95.5% of the assignments made by FAP concurred with those made by CERVUS. However, genetic analysis using REML revealed a marked difference in the heritability estimates. Based on these results we concluded that though there may be strong agreement in the assignments by both approaches, appreciable differences may be expected in genetic analysis.

Babigumira, Brian Martin (APT): Molecular mechanisms of cortisol production in pigs

The response to stress is mediated by glucocorticoid release via hypothalamic-pituitary- adrenocortical (HPA) axis stimulation. However, the genes involved in the variation in HPA axis activity are unknown. The aim of this association study was to discover single nucleotide polymorphisms (SNPs) in HPA axis functional candidate genes and analyze their association with basal cortisol production in 100 animals from a LW by MS advanced intercross. We found significant associations of single nucleotide polymorphisms (SNPs) in the corticotrophin releasing hormone receptor type 1 gene (CRHR1), glucocorticoid receptor gene (NR3C1) and cyclic adenosine monophosphate (cAMP) response element modulator gene (CREM) with cortisol production and cortisol-related traits.

Chakkingal Bhaskaran, Bimal, 2009 (SLU): Selection on DRD4 haplotypes in a natural great tit population in relation to personality

Variations in neurotransmitter-related genes are reported to be associated with personality traits among humans. One of the genes, the dopamine receptor (Drd4) gene showed a relation with novelty-seeking behaviour or curiosity traits. Moreover, in human, the dopamine receptor is the target site for drugs used in treating Parkinson’s disease and schizophrenia. Non human vertebrates and free living species can provide better understanding of the genotype personality relationships as they can be measured under standardized selection experiments. The great tit (Parus major) is one such model species used in these types of studies. Temperamental traits are heritable as well as linked to fitness traits, which makes it important in the study of ecology and evolution. A recent study by Fidler et al (2007) detected 73 polymorphisms (66 SNPs and 7 indels) in the great tit Drd4 orthologue (GenBank: DQ006801.1) The objectives of the current study were i) to amplify and sequence selected regions in dopamine receptor gene in two lines (slow and fast) of great tit, including from the wild and ii) to identify SNPs and haplotypes within this gene. iii) To develop a strategy for typing the different haplotypes within a large population (> 1000 animals).
Two different lines of a great tit population, selected for slow and fast Early Exploratory Behaviour (EEB) were considered for the experiment. These birds were reared under captive conditions at Netherlands Institute of Ecology (NIOO). A total of 19 birds from the fast line and 21 birds from the slow line were used in the study. Apart from the captive population of these two lines, a wild population (N=10) representing an out-group was also tested to identify the pattern followed under natural selection. Twelve regions within the dopamine receptor gene (Fig 1) were selected based on either SNP density or their proximity to indels.
Six haplotype blocks were identified within the gene. The SNPs constituting these blocks had, on an average, a MAF of 0.2 and were in high LD, which would eventually make it easier to find them and thereby enable to genotype a larger population using these six haplotype blocks. A significant association of SNPs 79 and 81 with the slow phenotype was observed, suggestive of a region which could be in association with this trait. SNP 76, which was reported (Fidler et al, 2007) to be associated with novelty seeking behaviour was found to be not significant. However, these SNPs are in close correlation (r2=0.69) with SNP 76 and hence indicate a region of strong association with the trait. The effect of introns, rather than the coding regions, in gene regulation could be the possible reason for this strong association. Further, a low level of LD within the gene supports the speculation that the causative mutation is within the dopamine receptor gene. The results from the wild out group weren’t significant owing to their small number but a highly similar trend was noticed suggestive of an association with the trait. A more detailed study could explain the trends followed in natural selection and evolution.

Dagnachew, Binyam, 2009 (NMBU): Casein SNPs and haplotypes: Effect on milk production and quality in Norwegian goats

The pantophysin (Pan I) locus reveals differences between Norwegian coastal cod (NCC) and Northeast Arctic cod (NEAC) populations that are highly significant, temporally stable and larger than for any other genetic marker. However, the biochemical basis for selection and the functional role of pantophysin in fishes are unknown. The observed polymorphism might be related to different expression levels and/or function of Pan I genotypes.
Since pantophysin expression in fish has not yet been investigated, this study provides the first characterization of the Pan I and synaptophysin-like2 (Sypl2) spatio-temporal expression patterns in Atlantic cod. Using quantitative PCR analysis, expression of Pan I and Sypl2 was quantified in early life stages in NEAC. Both genes were expressed from late gastrula with 8 somites until the larval size of 10-15 mm body length, indicating functional significance during early cod development. Ubiquitous expression of Pan I and Sypl2 was revealed in various tissues in adult NEAC and NCC. Phylogenetic and syntenic analysis confirmed the high degree of evolutionary conservation of pantophysin, synaptophysin and synaptophysin-like genes in various vertebrates, including Atlantic cod.

Das, Amit, 2011 (NMBU): Screening of blood and mucus parameters towards breeding for resistance to salmon louse(Lepeophtheirus salmonis) in Atlantic Salmon

Indications of additive genetic difference in lice resistance in Atlantic salmon (Salmo salar) have led us to hypothesize that biomarkers of resistance are present in the plasma and/or mucus of fish. High throughput Fourier Transform Infrared (FT-IR) profiling of plasma and mucus together with screening of the selected blood parameters (with the help of i-STAT blood gas analyzer) were coupled with multivariate statistical analysis to investigate the differences between two groups (susceptible (S) and Resistant (R)) of Atlantic salmon that shown different in their susceptibility to sea lice. The assignment was based on the sea lice challenge test results of their full-sibs. With respect to lice count, S and R groups of Atlantic salmon were different in both sessile and motile stages of lice, indicating genetic background for this trait. Most of the measured blood parameters by i-STAT did not show significant differences between the S and R groups of Atlantic salmon, indicating that they were expressed at constitutive levels. Further studies are still required and metabolomics approach may be more useful at higher level of lice infection to detect the variation in metabolites.

Demissie, Direba Hunde, 2012 (BOKU): Survival, Reproductive and Productive Performance of Pure Jersey Cattle at Adea Berga Dairy Research Center in the Central Highlands of Ethiopia

The data for this study was obtained from long-term records of pure Jersey breed that has been kept since 1986.
The results of likelihood ratio test using proportional hazard model showed that the effect of calving year, parity and milk yield on disposal risk were significant (P<0.01) where as the relative risk of age at first calving was moderate (P<0.05), However calving season didn’t have significant effect. The relative disposal risk of parity one is 3.33 times higher compared to parity three (reference class) and the risk of disposal is gradually decreasing after fourth parity. Cows with extremely low milk production (less than 2 standard deviations below average) had a 6.98 times higher disposal risk than average cows. Similarly cows with extremely high milk production (greater than 2 standard deviations above average) had a 3.31 times higher disposal risk than average cows. Very late age at calving cows ( greater than two standard deviation) had 1.87 times higher disposal risk than average cows (+- one standard deviation) and also they had double disposal risk than early matured cows (less than one standard deviation). The estimated genetic variance and heritability for herd life of current study were 0.26 and 0.18 respectively. The relative breeding value of the herd life ranged from 63.01 to 149.49 with a maximum observed reliability of 70 percent.

François, Liesbeth (APT):

In animal populations, the genetic diversity is the amount of variance in the genetic material that is present in that population. It is an importance indicator to look at the viability and level of endangerment for extinction of those populations. In this work we examined the possibilities of using genomic information for the estimation of genetic variability in livestock populations. The focus lay on the estimation of the effective population size using linkage disequilibrium between unlinked loci. Using the information of four sheep breeds, this method gave promising results but there were some issues for the construction of the genotyped population. The size of the genotyped population needs to be larger than sixty in these breeds to avoid bias on the estimation. Furthermore it is important that the individuals are representative of the population. Further research is necessary to examine whether these suggestions are sufficient to aleviate the problem. Additionally, we look deeper into the possibility of using genomic in-
formation for conservation purposes, using the information of six chicken breeds. We found that using sampling strategies combined with different diversity coefficients, can give an answer to the two possible sampling objectives. They were able to create samples that were representative of the population or conserved the maximal amount of diversity possible. However further research is needed to compare the results in populations where pedigree information is available.

Garcia, Ignacio P., 2012 (SLU): Production objectives and selection criterions of three endemic ruminant breeds in The Gambia and Senegal

Livestock plays a major role in the livelihood of poor rural communities, being the source of tangible and intangible benefits. The objective of this study was to analyse the production objectives and selection criteria for cattle (N’Dama) and small ruminants (Djallonké sheep
and West African Dwarf goat) in The Gambia and Senegal. A Participatory Rural Appraisal (PRA) survey was conducted in 18 villages in both countries. A total of 412 livestock owners and contract herders participated in the survey. The results showed that benefits such as manure production, income, savings and insurance, were the most important reasons for keeping ruminants. Furthermore, cows were important for milk sale and domestic milk consumption, and bulls were kept for draught. Intangible benefits, such as ceremonial and dowry were some of the main reasons for keeping small ruminants. In The Gambia body size was the most important selection criterion for all species. Trypanosomiasis resistance was essential when selecting cattle. Other important selection criterion traits were milk yield in cows, growth in bulls, and fertility and disease resistance in goats. In Senegal, cattle selection was based mainly on morphological characteristics, i.e. body size, conformation and growth. Trypanosomiasis resistance in cattle was rated lower than in The Gambia. In both countries, body size, fertility and growth were the main traits when selecting small ruminants. Generally, most of the farmer’s production objectives were in harmony with the selection criteria. However, a number of differences were noted. In The Gambia sheep were selected for milk yield, but this was not an essential production objective. In addition, milk yield was an important selection criterion for cows but not for bulls. Inbreeding was the least important selection criterion in both countries. This divergence in production objectives with selection criteria, and the negative effects of inbreeding need to be addressed in breeding programmes in order to conserve, improve and sustainably utilise these three endemic ruminant species.

Herlino, Astri Olivia, 2013 (SLU): Genomic Analysis of Hydrocephalus in Friesian Horses
Karakas, Bahriye, 2011 (SLU): Impact of a maternal high-fat diet on mouse placental epigenetic programming.

To assess how nutrient intakes of mouse mothers during pregnancy influence placental and fetal growth, we fed pregnant mother with a high-fat diet (HFD) and collect fetus and placentas in the middle of fetal period and at term.

Material and methods:
We studied gene expression by RT-qPCR and DNA methylation by LUMA to understand the molecular mechanisms of placental epigenetic programming in the labyrinth layer of the placenta, where nutrient exchanges take place.

Food intake of the mother was adjusted for caloric intake during gestation. Fetal and placental weights were affected by the diet and sex of the fetus. At term, there was a diet effect on placental gene expression of Dnmt3l, coding for a Dnmt cofactor important for regulating DNA methylation. However, the expression of three other epigenetic enzymes Suv39h1, Suv39h2 and Jarid 1c, did not change either between the diets nor between the sexes at the two stages 15.5 and 18.5 days. No differences in global DNA methylation was observed between diet or sex at the two stages.

These findings suggest that a HFD intake during pregnancy has an impact on fetal and placental growth and gene expression. Such an effect could have long term consequences for the offspring’s risk of metabolic syndrome by altering programming in utero.

Keywords: Epigenetic, high-fat diet, placenta, DOHaD, Sexual dimorphism

Khaw, Hooi Ling, 2009 (WUR): Genetic analysis of Nile tilapia (Oreochromis niloticus) selection line reared in two input environments in Egypt

Ascertaining the appropriate selection environment for Nile tilapia (Oreochromis niloticus) in Africa is a critical issue. Two data sets derived from two selection lines originating from a common base population were analysed in this study. The lines were selected in two different input environments, here named ‘low input’ and ‘high input’. Both data sets were combined and jointly analyzed to estimate the phenotypic and genetic parameters, with a special focus on the examination of genotype by environmental interaction. The data sets included a total of 7640 animals with phenotypic information from three discrete generations. Four different models (in terms of fixed effects) were fitted in univariate (harvest weight) and bivariate (harvest weight in each input line treated as two different traits) animal models to estimate variance and covariance components. The heritabilities estimated from the four different models by univariate analyses ranged from 0.15 to 0.41 (all with standard errors of 0.04). The genetic correlations between harvest weights expressed in the two environments, obtained from the bivariate analyses, ranged from 0.74 to 0.84 (with standard error in the range 0.15 to 0.36). We concluded that there was no significant evidence for genotype by environmental interaction for these two particular input environments.

Kocho Ketema, Tsedeke, 2011 (SLU): Sequence Analysis of a Porcine Normalized Full-length cDNA Library

The pig is besides an important livestock species also a model organism for human biomedical research. Knowledge of the porcine genome is essential for improving product quality, animal welfare and also the biomedical research. This is accomplished through investigating the transcribed regions of the genome by collecting, sequencing and analyzing transcribed sequences (mRNA) converted into a complimentary DNA (cDNA) providing a complete sets of expressed genes. Therefore, the objective of this study was to sequence and analyze 10,000 porcine normalized full-length cDNA clones. Total RNA was extracted from 11 tissues of a fetal clone of pig and a normalized full-length cDNA library was constructed by a commercial company. The cDNA clones were cultured in 384-well plates and sequenced using Sanger sequencing method. The sequence similarity search was performed using Basic Local Alignment Search Tool (BLAST) against the porcine genome, porcine cDNA, human
cDNA and mouse cDNA databases. Combining sequences from this study and the dataset generated earlier, a total of 13,989 sequences of at least 50 bps or more were generated from an overall of 19,968 cDNA clones processed. From the overall clone sequences, a total of 12,220 sequences provided hit in one or more of the pig, human or mouse databases. Blasting against the pig genome provided larger hits of 10,857. On the other hand, the pig cDNA database has provided total hits of 6,597. The human and mouse cDNA provided a total hits of 4,786 and 2,801, respectively, that enable comparative analyses to identify the homologous pig genes. Only 52 sequences have the same start-site with their respective pig transcripts and the majority of sequences shown variation. A total of 3,164 genes were identified from the library. A large-scale collection and characterization of the normalized cDNA library using direct sequencing on 384-well plates provides a valuable tool for understanding and investigation of the pig genome.

Li, Fuyong, 2012 (WUR)

The symbiotic rumen microorganisms are essential for the digestion of plant fibers and have been reported to affect production and health traits in ruminants. Here, we explored the associations between rumen microbiome, feed efficiency, and host genetics using cutting-edge omics approaches. Firstly, experimental and bioinformatics pipelines were developed to estimate compositional and functional profiles of rumen microbiome using both metagenomics and metatranscriptomics. Secondly, linkages between feed efficiency of beef cattle and rumen microbiome were successfully revealed. Although microbial community structures of efficient and inefficient beef cattle did not show obvious difference, they had distinguishable microbial functional profiles, and inefficient cattle had higher and more diverse activities than those of efficient cattle. Thirdly, we observed that beef cattle from different breeds had distinguishable rumen microbial composition and metabolic functions. Host additive genetics affected the rumen microbial community structure and the relative abundance of ~ 34% of microbial taxa. Moreover, 19 SNPs located on 12 bovine chromosomes were detected to be associated with 14 rumen microbial taxa. This highlights the potential to manipulate and obtain a desirable rumen microbial community using genetic selection and breeding.

Mao, Xiaowei, 2012 (BOKU): Detection of selection signatures using whole genome sequence from Bos Taurus beef and dairy breeds

Bos Taurus beef and dairy breeds have been extensively and successfully bred for human consumption such as traits of daily gain, milk yield, protein content, etc. This strong artificial selection has led to significant phenotypic changes in morphology, physiology and even behavior. Deeper understanding of evolutionary history of these two main lines of cattle breeds can help explain the different biological backgrounds shaping phenotypic diversity. In recent years, selection signatures detection has been carried on, mainly using single nucleotide polymorphisms (SNP) data. In our study here, individual full sequence data from four Bos Taurus breeds were analyzed to call SNPs and then locate the regions with differences in linkage disequilibrium patterns, to finally identify possible causative regions and pinpoint candidate genes which could be responsible for beef and dairy breed specialization. In total 9,610,809 SNPs were reported and around half of them were confirmed in the official SNP database. A handful of genes were found as candidate genes related to differences in beef and dairy production traits. One remarkable gene that we found is PLAG1, which has been repeatedly shown in association studies before, and that it is related to growth and carcass merit in beef traits. However, some well known genes related to beef and dairy production, such as DGAT1, were not detected with our approach.

Phuthaworn, Chontida, 2011 (BOKU): Genome-wide association study of health traits in Fleckvieh cattle

Many health traits in cattle display low heritability and conventional genetic improvements often yield unsatisfying selection responses. In this study, single-SNP and multiple-SNP GWAS analyses were conducted to find SNPs associated with longevity, fertility and cystic ovaries in Fleckvieh cattle. ~2000 unrelated progeny tested bulls were recorded for longevity, fertility and cystic ovaries as daughter yield deviations and genotyped with Illumina 54K bovine SNPChip. Bonferroni correction and false discovery rate (FDR) for multiple testing were applied to adjust the significance threshold in the single-SNP analyses, and the elastic net method (lambda = 0.05 and 1000-fold cross validation) was used in the multiple-SNP analyses. Bonferroni correction resulted in 4 significant SNPs for longevity and 9 SNPs for fertility, while 270 and 726 SNPs were significant for longevity and fertility respectively with FDR correction. 143 SNPs for longevity and 183 SNPs for fertility were detected using the multiple-SNP analyses, and no SNPs were significant for cystic ovaries neither in the single-SNP nor multiple-SNP analyses. The associated SNPs identified in this study indicated possibilities in applying genomic selection for longevity and fertility in Fleckvieh cattle.

Rafati, Nima, 2011 (SLU): Transcriptome analysis of Atlantic Herring (Clupea harengus) using Next Generation Sequencing (NGS)

The Atlantic herring is one of the most abundant fish species in the Northern hemisphere especially in the Northeast Atlantic. Many studies have tried to characterize herring populations and these efforts can be combined with massively parallel sequencing technologies to develop genetic resources. In this study we used mRNA sequencing data to study transcriptome. Studying stranscriptome have been mainly dependent on a reference genome and developed tools are not applicable for non-model organisms for which the reference genome is missing. In this study we present a de novo transcriptome assembly by using different strategies and one specific transcriptome assembler, Trinity. The RNA was collected from muscle of a male spring spawning herring. After trimming low quality nucleotides and possible contaminations, the assembly resulted in 131,788 contigs with a total size of 40 million nucleotides. The transcriptome generated by Trinity was compared with other assemblies including SOAPdenovo, Inchworm, SSPACE, and CAP3. The results showed that Trinity developed a more reliable assembly. We validated almost 47% of all contigs by comparison to available databases such as nr and other vertebrate transcripts. Also, we quantified the relative expression of transcripts. Furthermore, we preformed indepth studies of two genes. We identified two copies of Glucose 6-phosphate isomerase (GPI) on draft genome assembly. Our results showed that the sampled fish was heterozygous at the GPIb locus. Among the alpha actin isoforms, we identified the alpha actin b transcript (ACTA1b) in fast muscle corresponding to spring spawning herring fish characteristics.

Rafati, Nima, 2010 (WUR): Whole genome assembly of Culicoides obsoletus: the causing agent of insect-bite hypersensitivity (IBH) in horses

IBH is an allergic skin disease in horses that reduces the welfare and the commercial value of the horses. Immunological studies have shown some responsible allergen for this reaction in horses. The next step is to detect the identified responsible genes for these allergens. The main objectives of this study are whole genome assembly of the prepared fragments by Illumina technology and assembly validation. The genome was assembled with de novo assembly software, SOAPdenovo. Assembly was validated by comparison to other software like CLC-Bio and ABySS and using some visualizing software such as Tablet. Moreover, we compared our result with two other evolutionary closed insects including A. gambiae and C. quinquefasciatus.

Shrestha, Merina, 2012 (NMBU): Genetic Basis for Inherited Eye Diseases in Dogs : A Case Study of Pigmentary Chorioretinopathy in Chinese Crested Dogs

A novel inherited retinal disease, pigmentary chorioretinopathy, has been observed in one of the oldest purebred breed, Chinese crested. Two forms of progressive retinal atrophy (PRA), Progressive rod con degeneration (prcd) and one other form with unknown genetic basis, has already been observed in the breed. This novel retinopathy showed clinical features of progressive nature with bilateral degeneration, migration of lesions from tapetal to non-tapetal and central area in fundus and end stage leading to blindness. A distinct feature of primary defect in retinal pigment epithelium differentiates this disease from PRA. A genome-wide association study with 170K Illumina CanineHD SNP chip was performed using 19 cases and 21 controls. After correcting for population stratification, applying a combined approach of Mixed model and Structured association in R (GenABEL package), an association analysis using 14 cases and 21 controls resulted in a stronge association with two SNPs (P-raw: 4.59e-06 and 5.74e-06) located around 300 kb apart, on chromosome 8. After further analysis in Ensembl (CanFam 2.0), we found that one of the SNPs was located in an intronic sequence of the gene MDGA2 (MAM domain containing glycosylphosphatidylinostitol anchor 2 – 371.42 kb) and the other was located downstream to this gene. MDGA2 is a member of the immunoglobulin superfamily class (IgCAM) and is involved in cell adhesion, migration and recruitment to inflammatory sites. Sequencing of the coding region of MDGA2 revealed a non-synonymous mutation that caused an amino acid shift from “threonine” to “serine”. The sequence analysis was inconclusive; hence more individuals need to be sequenced for a definite conclusion. Also, a manual gene annotation of MDGA2 is required for a mutation to be concluded as not causative. Hence, additional studies need to be performed to unravel the genetic basis of the disease which will guide us to the possible preventing strategy in near future.

Stjelja, Suzana, 2012 (SLU): Gene expression, phylogenetic and syntenic analyses of pantophysin (Pan I) and synaptophysin-like2 (Sypl2) genes in Atlantic cod (Gadus morhua L.)

The pantophysin (Pan I) locus reveals differences between Norwegian coastal cod (NCC) and Northeast Arctic cod (NEAC) populations that are highly significant, temporally stable and larger than for any other genetic marker. However, the biochemical basis for selection and the functional role of pantophysin in fishes are unknown. The observed polymorphism might be related to different expression levels and/or function of Pan I genotypes.
Since pantophysin expression in fish has not yet been investigated, this study provides the first characterization of the Pan I and synaptophysin-like2 (Sypl2) spatio-temporal expression patterns in Atlantic cod. Using quantitative PCR analysis, expression of Pan I and Sypl2 was quantified in early life stages in NEAC. Both genes were expressed from late gastrula with 8 somites until the larval size of 10-15 mm body length, indicating functional significance during early cod development. Ubiquitous expression of Pan I and Sypl2 was revealed in various tissues in adult NEAC and NCC. Phylogenetic and syntenic analysis confirmed the high degree of evolutionary conservation of pantophysin, synaptophysin and synaptophysin-like genes in various vertebrates, including Atlantic cod.

Shumbusho, Felicien, 2010 (BOKU): Fine Mapping of Quantitative Trait Loci for Pig Meat Quality Traits

Meat quality improvement is a major concern for pig industry. Several research programs have identified QTL for pork quality as an attempt to use them in Marker or Gene Assisted Selection. Yet, their application has been limited by the large QTL interval generated by linkage analysis. In this study, we performed genome-wide association study (GWAS) to map SNPs associated with pork quality traits such as water-holding capacity (WHC), colour measures, ultimate pH (pH24) measures, androstenone and skatole content in French Large White pigs genotyped with 60K chip. A total of 54 SNPs were significantly detected (P-value < 10-4) for 13 quality traits: 5 SNPs for WHC, 20 SNPs for colour measures, 18 SNPs for pH24 measures, 3 SNPs for androstenone and 8 SNPs for skatole content. We followed up with Linkage Disequilibrium and Linkage Analysis (LDLA) method to comfort association results and studied LD and haplotype blocks in most important regions. LDLA gave less and sharp peaks compared to GWAS but not necessary in same positions. LD and haplotype blocks results suggest more SNPs could be linked to one QTL. These results confirm that quality QTL segregate in Large White pigs and SNPs, haplotypes detected should be used in MAS programs.

Tadel Gebre, Kahsa, 2009 (SLU): Estimates of economic values for important traits of two indigenous sheep breeds of Ethiopia

A bio-economic model was adapted to estimate economic values for important traits of two Ethiopian indigenous sheep breed. To do so, a meat sheep herd for fattening lambs and rearing young replacement sheep was simulated. Traits included in the analysis were: daily gain (fattening trait), live weight of ewes, length of productive life, lambing interval, litter size, stillbirths and lamb survival (functional traits). To avoid double counting, the economic value for each trait was derived while keeping all other traits constant. Economic values were obtained per ewe place, year, and genetic standard deviation. For the Menz breed, economic values in EUR per genetic standard deviation were 0.63 (daily gain), -0.77 (mature ewe live weight), -0.97 (length of productive life), 1.57 (lambing interval), 0.98 (litter size), 0.41 (stillbirths) and 2.20 (lamb survival). Economic values (in EUR) of 1.35 (daily gain), -1.26 (mature ewe live weight), -1.15 (length of productive life), 1.98 (lambing interval), 3.67 (litter size), 0.56 (stillbirth) and 3.25 (lamb survival) were derived for the Horro breed. Negative economic values for length of productive life and mature ewe live weight were estimated for both breeds. After setting the economic values of length of productive life and mature ewe live weight to zero, the economic values (in %) for the ratio of the trait complexes fattening: functional traits were 11:89 and 12.5:87.5 for Menz and Horro, respectively. Economic values for litter size, lambing interval and lamb survival traits were sensitive to changes in price for breeding rams in both breeds.

Viluma, Agnese, 2012 (NMBU): Polymorphism in myostatin gene and athletic performance in Nordic horse breeds

Athletic performance including working ability, riding, racing and endurance has played a leading role in horse breeding possibly since their domestication. Even though traits of athletic performance are considered as complex and dependant on environment, management and training, it has been shown that heritability of some performance traits can be considerably high. Skeletal muscle system seems to be a key factor to exceptional athletic performance and numerous studies in other species (dogs, humans, sheep, cattle etc.) have shown that polymorphisms in MSTN gene can be responsible for phenotypic changes in muscle tissues. Several studies focusing on horse MSTN gene region have been made and some significant associations discovered in Thoroughbred populations. The main objective of this study is to estimate the allele frequencies of the g.66493737 SNP, which is the strongest associated SNP with the optimim race distance, and some additional SNPs (two in a promoter region and one downstream the gene) in MSTN gene of Nordic horse breeds and correlate them with performance trait data to create a deeper understanding of the gene’s influence on performance ability in horses.

Welderufael, Berihu, 2009 (NMBU): Casein gene haplotypes in Norwegian dairy goats

In the goat species caseins (αs1, β, αs2, and к), nearly 80% of the milk proteins, are encoded by single copy genes (CSN1S1, CSN2, CSN1S2 and CSN3) clustered on about 250-kb segment of chromosome 6. Such genes have high tendency to be co-regulated as well as inherited together as haplotypes. The aim of the study was to assess the linkage disequilibrium (LD) within and among the casein genes, to construct haplotypes for each casein gene thereby to compare with previously constructed casein haplotypes in the Norwegian dairy goats. Thirty seven SNP genotypes of 463 Norwegian dairy bucks were collected from the literature and imported to the PHASE and Haploview programs to construct the haplotypes and assess the LD within and among the casein genes. A total of 18 haplotypes; six for CSN1S1, four for CSN2, three for CSN1S2, and five for CSN3 had a frequency of higher than 0.01. It was not observed much variation in the haplotypes of the two samples of the Norwegian dairy bucks. Among the 27 haplotypes collected from the literature 18 of them (the most frequent) were confirmed in the current study with almost the same frequencies. Out of these shared haplotypes only four were significantly different in their frequencies from the previous findings. Although recombination among the casein genes is essential in shaping the haplotype variability, strong LD was found in the chromosomal segment containing the caseins, resulting in almost similar distribution of haplotypes with the previous findings in the population. The fact that only a few haplotypes occur with a high frequency in the breeding samples may indicate that selection has strongly favored LD to reduce the casein haplotype variability. This strong LD makes the SNPs to be inherited together as haplotypes because recombination during meiosis separates them only seldom as evident by the association of the deletion to the specific haplotype of gene CSN1S1 in both studies.

Younis, Shady, 2011 (BOKU): Molecular Characterization of ZC3H11A Functions and Expression Patterns During Embryonic Development

The previous discovery of a single nucleotide substitution in intron 3 of the insulin-like growth factor 2 (IGF2) gene in pigs revealed a novel mechanism for regulation of muscle growth. This mutation disrupts binding of a transcription factor, ZBED6. This domesticated DNA transposon is located within the first intron of ZC3H11A gene, which encodes a poorly characterized zinc finger binding protein. In this project, we attempted to characterize the expression patterns and biological function of ZC3H11A. We hypothesized that ZC3H11A may play a role in RNA splicing and muscle development. ZC3H11A was silenced in mouse myoblast cell lines using RNA interference. At 48 h post-transfection, total RNA was isolated and the expression levels of genes associated with myogenesis (MYOGENIN, PAX7 and SRF) and IGF2 regulation (ZBED6 and BAHD1) were quantified by real-time PCR. Effects of gene silencing on cell proliferation and differentiation were also assessed. The alternative splicing of various genes was evaluated in ZC3H11A-silenced cells. Whole mount mouse embryo and placenta samples were prepared for immunohistochemistry (IHC) at embryonic days 7.5, 8.5, 10.5, 12.5 and 13.5 to visualize the expression pattern of ZC3H11A during mouse embryo development. Results showed that silencing ZC3H11A was associated with a down-regulation of MYOGENIN, PAX7 and BAHD1 mRNA (p < 0.05). As silencing of ZC3H11A targets the transcript containing ZBED6, ZBED6 mRNA was also down-regulated (p < 0.001). When ZBED6 was knocked down in C2C12 cells using siRNA, IGF2 mRNA was up-regulated (P<0.001) more than 2-fold. No aberrant RNA splicing was detected in ZC3H11A-silenced cells. Immunohistochemical staining revealed a nuclear localization for the ZC3H11A protein. The ZC3H11A protein was restricted to certain tissues during embryo development, particularly cartilage and muscle. ZC3H11A appears to be a factor important for mammalian development. Because of the integration of ZBED6 into the first intron of the ZC3H11A gene and use of a common promoter for transcription, it is difficult to elucidate the underlying mechanisms regarding regulation and function of these two unique genes.

Key words: ZC3H11A, splicing machinery, myogenesis, ZBED6.

Last updated: 04.09.2020