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.

Abitew, Yosef Amsalu, 2022 (BOKU): Genetic map of Fleckvieh cattle

In this MSc. thesis work, we constructed a genomic map of Fleckvieh cattle using ~39K SNPs and 114228 meiosis events from male parents and 42706 meioses of females. Meiotic recombination is a source of genetic variation as it shuffles genetic material between sister chromatids, breaking down linkage disequilibrium in the process. Studying how recombination varies among individuals and breeds is important to understand how it could respond to selection. We used recombination frequencies between neighbouring markers to construct a genetic map for Fleckvieh cattle. We estimated recombination rates from a total of 4,600,610 crossovers. The average genome wide recombination rate was 1.04 centiMorgan per megabase and 0.92 cM/Mb with a length of 26.05 Morgan and 23.16 Morgan in males and females, respectively. Longer chromosomes showed lower recombination rates and vice versa. A higher number of recombinations was observed in males than females, similar to sheep but unlike many mammals. The genetic map showed a more pronounced recombination rate around the end position of each autosome in males whereas a gradual decline was observed around the same position in females. Using genome wide association study, we identified two previously reported candidate genes (REC8 & RNF212) in chromosome 6 and 10. The strongest signal was found on chromosome 19, near SCO1 gene, not associated with recombination rate so far. Genome wide recombination rate is a highly heritable trait with a 50% chip heritability. This is an estimate higher than previous studies from other breeds.
The genetic map of Fleckvieh cattle emerging from this thesis will be useful for many future research endeavours related to genetic diversity as well as genome wide association.

Ali, Baber, 2021 (APT): The use of prior biological knowledge to account for the ability of the BayesRC model in genomic prediction

BayesRC is an extension of BayesR, in which prior biological information can be used to divide SNPs into different annotation categories. Within each category, SNPs are further categorised into multiple effect classes (null, low, medium, and high) just like BayesR. In this study, we aim to evaluate the ability of BayesRC in predicting five milk production traits (milk yield, fat content, fat yield, protein content, and protein yield) and fertility in a real population of 7483 Holstein bulls. We used three different sources of biological information, namely the Cattle Quantitative Trait Loci database (Cattle QTLdb), the Cattle Genotype-Tissue Expression atlas (cGTEx), and known causal and associated SNPs from INRAE’s updates to EuroG10K SNP chip. We divided this study into two phases, phase 1 comprising Bovine SNP50BeadChip® medium density SNP panel (50K), and phase 2 involving the inclusion of selected sequences from the whole genome sequencing data. We used BayesR as a standard against which to compare the genomic prediction ability of BayesRC. In terms of results, BayesRC tended to perform better than BayesR for low heritability traits.  BayesRC tended to give more weightage to SNPs in enriched SNP lists based on prior biological information, which is certainly the most important feature of this prediction model. BayesRC also highlighted some key QTL regions involving genes like DGAT1, HSF1, MGST1, and GHR. Even though BayesRC did not show significant improvement over BayesR in our study, it still has a potential if used in breeds where marker panels are not well calibrated, and also for traits with very low heritabilities.

Ampofo, Issabelle, 2022 (BOKU): Genetic and Survival Analysis of Survival Time of Local Chicken Ecotypes Naïvely Challenged with Newcastle Disease in Ghana

Newcastle disease (ND) is a global threat to domestic poultry, particularly in Africa and Asia. To investigate the genetic basis of the response of local Ghanaian chicken ecotypes to Newcastle disease virus (NDV), three chicken ecotypes from the forest zone (FO), coastal savanna (CS), and interior savanna (IS) were naively infected with velogenic NDV at 28 days of age. This study focused on genetic analysis and survival analysis of these birds infected with the virus. The data collected included information on the survival time of 1 167 birds. Survival time was calculated as the number of days from NDV exposure to culling time. Survival time was analyzed using a survival model (SM) and a linear model (LM) to estimate genetic parameters. Heritability estimates ranged from 0.12 (LM) to 0.20 (SM) using pedigree information. The heritability estimate for survival time from genomic prediction was slightly higher (0.27). We observed low to moderate genetic correlations between survival time and other disease-resilient traits of interest. Immune-related genes, behaviour-related genes, and growth-related genes were associated with survival time in GWAS analysis. We suggest that the survival of chickens infected with NDV could be improved by selective breeding to produce NDV-resistant chickens in Ghana.

Keywords: survival analysis, survival time, Newcastle disease, survival model, heritability, genomic selection, GWAS, genetic correlation.

Ayres, Lucas, 2022 (NMBU): The accuracy of genomic prediction by singular value decomposition of the genotype matrix

Increasing the order of the genotype matrix by augmenting the number of animals or genetic markers represents a computational challenge for genomic selection. The objective of this study is to evaluate the effect of the number of components in singular value decomposition (SVD) of the genotype matrix on the accuracy of genomic prediction. SVD is a data reduction method that could be useful to save computational time in the prediction of breeding values for genomic selection. Our study combined simulated phenotypes and genetic architectures with real genotypic data from chromosome 1 of Atlantic Salmon. QTL effects were sampled from random normal distributions. We employed principal component ridge regression (PCRR) and principal component-based algorithm for inverting the genomic relationship matrix (PCIG) to obtain predicted breeding values. We used three different heritabilities for the simulated traits. The analysis showed that accuracy increases steeply for the first few principal components until it stabilizes at around 100–200 components and no meaningful gain is obtained with additional components. Accuracies obtained with PCRR using only a fraction of the total number of components were higher than when using genotypes of all SNPs. The peak accuracy varied across replicates when QTL were sampled from a normal distribution. We conclude that SVD, as used in PCRR and PCIG, is a useful tool for genomic selection involving very large genotype matrices because it can save computational effort without compromising the accuracy of genomic prediction.

Babigumira, Brian Martin (WU): 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.

Espinola Alfonso, Roberto Emilio, 2022 (SLU) (with Erling Strandberg and Freddy Fikse): How does a Beef x Dairy Calving Affect the Dairy Cow’s Following Lactation Period?

In dairy x beef breeding, much of the research has focused on the performance of the crossbred calves, yet little focus has been given to the subsequent performance of the cow itself. This study aimed to evaluate the performance of dairy cows for milk yield, fertility, and survival traits after giving birth to crossbred calves, and to compare this to the performance of dairy cows after giving birth to purebred dairy calves. Phenotypic records from 4,980,886 calving events distributed in 4,509 herds from 1997 to 2020 were collected from the Swedish milk recording system from cows of the dairy breeds Swedish Red and Swedish Holstein. A total of 13 performance traits were defined and grouped in three large complexes as follows; cumulative and 305-day milk, fat, and protein yield as milk yield traits; calving to first insemination interval, calving to last insemination interval, first to last insemination interval, calving interval, and number of inseminations as fertility traits; and survival to next calving and last day in milk as survival traits. The data were analyzed for all traits for first and later parities separately using mixed linear models, with a focus on the estimates of sire breed by dam breed combinations. All traits were adjusted for previous milk yield for parities 2-3 based on the expectation that low-yielding cows would more likely be inseminated with beef semen. Overall, milk yield was lower after mating beef x dairy compared to the purebred matings. The largest decrease was about 400 kg for cumulative milk yield when breeding Charolais sires with purebred SR or SH dams. As for fertility traits, for most breed combinations, the effects were not large enough to be significant. Conversely, all sire-dam breed combinations showed significantly lower results for survival traits, suggesting that cows inseminated with beef semen have a lower probability to survive to the next lactation.

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.

Gebeyehu, Samrawit, 2021 (SLU): Genetic mapping on local Swedish chicken breeds

Today, genetic studies are gaining popularity around the world, especially in the developed world. The study of genetic diversity is the basis for genetic protection and future breed improvement. The current study aimed to assess the genetic diversity, genetic relationship, and to identify the genes affecting the plumage colors of eight Swedish chicken breeds. There are about 11 breeds of Swedish chickens in Sweden. The study breeds were Gotlandshöna, Öländsk dvärghöna, Kindahöna, Hedemorahöna, Skånsk blommehöna, Åsbohöna, Ölandhöna, and svarthöna chicken. A total of 83 chickens were genotyped using a 62K SNP chip. The mean observed heterozygosity of the study breeds was 0.40 and the mean inbreeding coefficient (F) of the study breeds calculated from the discrepancy of observed and expected heterozygotes was -0.07. The mean FST of the study breeds was 0.36, which indicated that the Swedish chicken breeds were very diverse. The study breeds formed 3 main clusters in the multi-dimensional scaling (MDS) plot based on their genetic relationship, where most of the breeds were grouped in one of the main groups. Due to population structure, it was not possible to identify potential SNPs involved in plumage color variation. To do GWAS for plumage color variability of Swedish chickens, the sample size must be much larger. The current study on genetic diversity may help to strengthen the genetic conservation program, such as, eliminating inbreeding and conducting additional molecular-based studies. Further research into plumage color variability should be done, by including many more individuals.

Herlino, Astri Olivia, 2013 (SLU): Genomic Analysis of Hydrocephalus in Friesian Horses

Hydrocephalus is an uncommon disorder in horse. However, hydrocephalus is observed more often in the Friesian horse breed than in other breeds. Due to the Friesian horse population has been closed for outside breeding and has a limited genetic pool. It leads to high rate of inbreeding. The general objective of this study is to get better understanding of genetic background of hydrocephalus in Friesian horses, which will be used to develop a DNA-­‐test using genetic markers for hydrocephalus in the Friesian horse breed. Genomic analysis based on case-­‐control study was performed on 20 cases and 47 controls. Data used in this study was provided by Faculty of Veterinary Medicine at Utrecht University, the Netherlands. Population stratification seems to be present between cases and controls because 55.2% of some cases and controls coming from different sires. This population structure was corrected using genomic control method.

Hydrocephalus mutation in Friesian horses was found on chromosome 1:57,760,860-­‐87,079,561 (29.3 Mb region) using genome-­‐wide association study (GWAS). 68 associated SNPs based on genotype frequency differences included the 29 associated SNPs based on allele frequency differences between cases and controls were identified in this region. 85-­‐90% of affected Friesian horses were homozygous  genotypes  of  unfavorable  alleles  for  these  following  SNPs:  BIEC2-­‐ 27351,  BIEC2-­‐27352,  BIEC2-­‐27588,  BIEC2-­‐28874,  BIEC2-­‐28875,  BIEC2-­‐28876, BIEC2-­‐29359, and BIEC2-­‐31514. Haplotype association study was performed on chromosome 1. The result of this study showed that 54 associated haplotype blocks were also identified in the 29.3 Mb region. These haplotype blocks contained all associated SNPs that were found from GWAS. 228 genes were found in this region, but these genes were not the same as identify genes of hydrocephalus in human and other species.

Further  studies  are  necessary  to  be  able  to  develop  a  DNA-­‐test  for hydrocephalus in Friesian horses. These further studies are to validate the identified associations, to narrow down the associated region, to identify causal mutation. Furthermore, this DNA-­‐test can be used in the Friesian horse breeding program to reduce or remove hydrocephalus in the population.

Key words: Friesian horses, genomic analysis, hydrocephalus

Hegedűs, Bernadett, 2021 (WU): Developing and testing mating strategies to increase the gametic variance of the offspring

Gametic variance is the variance of the breeding values of an individual´s gametes. With the increasing possibilities of calculating gametic variance, it represents a new direction in animal breeding that could contribute to increasing genetic gain in recurrent selection. In recent studies selection indices were developed to incorporate gametic variance, therefore it is of interest to create individuals with high gametic variance. This thesis compared four mating strategies relying on quantitative trait loci (QTL) to random mating regarding their effect on offspring gametic variance and genetic gain in a simulation study of 15 generations. The mean gametic variance over 100 replicates was slightly different among the mating strategies for the four investigated selected proportions (0.2, 0.1, 0.05 and 0.02). The mean genetic gain showed some improvement after 15 generations for the selected proportions 0.02 and 0.05. Further research is needed to find mating strategies with higher effects by incorporating linkage in the mating strategies.

Hegedűs, Bernadett, 2022 (SLU): Genomic diversity analysis in the Swedish Landrace Goat

There are four goat breeds present in Sweden. However, no genetic studies were dedicated to investigating the genetic diversity in these breeds. This thesis therefore aims to describe the population structure and the level of inbreeding in the goat breed with the largest population number, the Swedish Landrace goat. Forty-eight (48) samples from eight farms were genotyped with a medium density SNP chip. To study the population structure, a principal coordinate analysis and a Structure analysis were conducted. The level of inbreeding was investigated with three measures; observed heterozygosity, FROH and approximated coancestry. The results show that there is some structuring in the population and this structure is not solely due to the geographic location of these farms. The inbreeding level of the farms is comparable to other European non-island goat populations. A potential pattern of selection was identified on Chromosome 6 with ROH in the region of the Casein genes. Further research is needed to calculate the effective population size and the rate of inbreeding in this breed.

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. 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 (WU): 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.

(de) Kinderen, Maud, 2020 (BOKU): Genotype by Environment interactions of Chickens tested in Ethiopia Two traits analysed: BW in Ethiopia Egg Number and Egg Weight in Oromia 

The African Chicken Genetic Gain (ACGG) project ( aims to achieve an optimization on African smallholder poultry production by introducing commercial dual-purpose breeds into a new African environment. Different breeds may be best suited for different environments of Ethiopia, which is a country with a wide range of Agro-Ecological Zones (AEZ). This study performed genotype environment interaction (GxE) analyses for body weight (BW) of growing male and female chickens, using ACGG data. Hence, research questions of this study were to investigate: 1) If a GxE does take place for BW? 2) Which breed performs best in which environment in terms of predicted BW? Analyses was performed using predicted BW at four different ages (90, 120, 150 and 180 days) of five introduced breeds (Horro, Koekoek, Kuroiler, Sasso-Rhode Island Red (S-RIR) and Sasso) located in five Ethiopian regions (Addis Ababa, Amhara, Oromia, South Region and Tigray) being part of three AEZ (cool humid, cool sub humid and warm semi-arid). 999 females and 989 males were present. GxE was highly significant (p<0.0001) for all analysis combinations. In line with previous research, Sasso was shown to have the highest predicted BW, especially at early age, followed by Kuroiler. Due to the young breeding program of Horro, it was often observed to be the worst performing breed. Best performances were observed in Tigray, Oromia, and Amhara regions, all mainly being part of the cool sub humid AEZ having highest predicted BW. Koekoek and Kuroiler were performing well in Amhara at late age, which can potentially be explained by high precipitation.

Kobiowu, Abdulhadi Akande, 2022 (NMBU): Sequence Analysis and In Vitro Genome Editing of Atlantic Salmon MHC-I-F10 Gene In Atlantic Salmon Macrophage Cell Line TO Cells

During the past few decades, the aquaculture industry has contributed immensely to food security in the face of the continuous growth in the global human population—and farming of Atlantic salmon has significantly contributed to this growth. Consequently, the rapid growth of the industry has led to intensification, which in turn has brought about increased disease incidences; with cardiomyopathy syndrome (CMS), a viral disease caused by piscine myocarditis virus (PMCV), being among the top diseases of economic importance in salmon farming in Norway. There are currently no known effective vaccines against the disease, and several studies have linked resistance against CMS to different variants of the major histocompatibility complex genes. However, no known functional study has pinpointed the mechanisms involved. Therefore, this study explored the sequence distribution and diversity in skin, spleen, heart, gill, liver and head kidney tissues and between infected and uninfected fish for the MHC-I-F10 gene. While no big differences were observed in the MHC-I-F10 gene in the different tissues, some insertions and deletions were only observed in the heart samples. Furthermore, the alignment of clean sequences from these tissues, except the heart, indicated a single nucleotide polymorphism at nt 533, which results in an amino acid change from cysteine to tryptophan. In contrast, the sequences from the heart showed messy chromatograms with double peaks in proximity to the N terminus. Therefore, the heart samples were sequenced with both forward and reverse primers—where the latter returned clean and contrasting results to the former. Moreover, we have developed CRISPR-mediated editing of the MHC gene in the TO cells, a permanent cell line of Atlantic salmon origin, via transfection and electroporation methods and demonstrated the possibility of successful editing of the MHC-I F10 gene in TO cells, which lay the foundation for further functional studies of this gene related to PMCV infection. The editing efficiency was low, which might have emanated from many factors. The most significant one is the short duration set aside for these studies, which has influenced the overall results. However, the foundation laid for editing the MHC-I-F10 gene in this study can serve as a component of a toolbox for future functional genetics and immunological studies in Atlantic salmon.

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 (WU)

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.

Nalpadan, Avon Augustin, 2022 (NMBU): Developing Cas9 expressing MDBK cell lines for GeCKO screening against bovine diseasesPhoto of Avon Augustin Nalpadan in the lab

Recent developments in CRISPR/Cas9 technology have opened several possibilities for gene editing in various model organisms. However, seldom research has been done in applying this research in developing suitable tools for gene editing in large production animals against viral diseases. The objective of this project was to develop Cas9 integrated Madin-Darby Bovine Kidney (MDBK) cell lines for a genome wide CRISPR/Cas9 knockout screening against Bovine Viral Diarrhea Virus (BVDV) and Bovine Coronavirus (BCoV). Two-step vector was used for the screening. LentiCas9-Blast was transduced into MDBK cells for generating Cas9 integrated cell lines. Stable cell lines were then selected using blasticidin scelection, followed by expanding homogenous cell lines from single cell clones obtained through serial dilutions. The lines were then grouped based on Cas9 gene expression (using RT-qPCR) and protein levels (using Western blotting). ADAM 10 gene was then cloned into lentiGuide-Puro and was then transduced into the grouped cell lines and selected using Puromycin. The lines were then sequenced to confirm the genome editing. The major result involved the successful development of multiple Cas9 integrated cell lines with varied Cas9 expression, ready for the subsequent genome wide screening. Additionally, CRISPR editing efficiencies of cell lines were also correlated with their Cas9 gene expression to obtain a few optimal cell lines ready to perform GeCKO screening.

Keywords: BVDV, BCoV, CRISPR/Cas9, MDBK cell lines, Transduction, GeCKO screening

Nyamiel, Agnes, 2022 (APT): Study of genetic variability of milk lactose content in French dairy cattle

Lactose is the most abundant bovine milk solid, it can be accurately predicted from mid-infrared spectra routinely collected in dairy cattle, and genetic links between milk lactose content (LC) and other traits, such as milk persistency, udder health, and fertility have been previously described. The present study aimed to characterize the genetic determinism of LC and its potential in performance prediction and selection. Specifically, to estimate the heritability of lactose content during the first two lactations and to study the genetic links between LC and dairy performance.

For the present study, we used a total of 1,761,670 milk test-day records (TDR) collected on 145,537 Montbéliarde cows originating from 2,315 commercial herds in Eastern France’s Franche-Comté region. Test-day information was the following: herd, cow Identity (Id) and date of test, lactose content (LC), protein content (PC), fat content (FC), as predicted from mid-infrared spectra; milk yield (MY), fat yield (FY), protein yield (PY), beta-hydroxybutyrate (BHB), acetone (ACET), somatic cell count (SCC), and somatic cell score (log-transformed (SCC). We computed 305-day milk yield (TOTMY), protein yield (TOTPY), and fat yield (TOTFY), and relative and absolute persistency of milk yield (PERS_MY1 PERS_MY2), protein yield (PERS_PY1; PERS_PY2), and fat yield (PERS_FY1; PERS_FY2). Lactation LC was defined for first (LC1st lact) and second lactation (LC2nd lact). LC was also defined for the first 100 days in milk (DIM) (LC1_100 and LC2_100). Additional traits were recovered from the national database: fertility (FERT), udder development (UD), and milking speed (MS). Heritabilities of LC were estimated through single-trait lactation animal models, single-trait test-day repeatability animal models, and a test-day random regression model (RRM) using a second order Legendre polynomials with heterogeneous residual variances. The genetic and permanent environmental correlations were computed using a bivariate lactation model and a bivariate RRM. Lactation curves of LC increased from the onset of lactation to the peak of lactation (50 days in milk) and then decreased, mirroring the typical milk yield curve. The heritability of LC in the first lactation (0.60 and 0.72) was higher than the heritability in the second lactation (0.50 and 0.59). The heritabilities estimated at lactation level (0.50 to 0.72) were higher than those estimated at test-day level (0.46 and 0.47). Also, LC had lower heritabilities at the start of lactation and higher values towards the end of lactation when computed with the random regression model. We noted higher repeatabilities for LC in the first lactation (0.57 and 0.60) when we computed with the test-day repeatability model and higher repeatabilities towards the end of lactation when we used an RRM. Genetically, LC in the milk of Montbéliarde cows is less variable (genetic coefficient of variation (Cvgen) =  1.9%) than other milk components. Genetic correlations between LC in first and second lactations were strong (0.97). They were weak between LC and other traits studied, e.g., MY, -0.21; FERT, -0.07, SCS, -0.18, BHB, – 0.14, and persistencies, 0.12 to 0.20. Milk LC is highly heritable but with limited variability making its inclusion into the breeding goal in overall French dairy production systems limited. In the near future, the same analysis could be conducted in other large French breeds, such as Holstein and Normande, to assess the interest of using LC as a predictor of other traits. Also, the use of genomic information to characterize genes associated with this trait would be relevant.

Keywords: Lactose content, persistency, Montbéliarde cows, genetic parameters, lactation model, repeatability model, random regression model.

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 (WU): 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.

Rasheduzzaman, Mohammad, 2022 (APT): Role of Kif1c in Health and Disease: Function in Myelination

KIF1C is a motor protein which uses microtubules as a rail to transport various cargoes in the cells. Mutations in KIF1C are responsible for neurodegenerative diseases, namely hereditary spastic paraplegia type 58 (HSP58/SPAX2) in human and progressive ataxia in Charolais cattle. A transgenic knock-out (KO) mouse line mimicking the bovine progressive ataxia confirmed the defect in myelin maintenance and the potential involvement of oligodendrocytes in the pathology. However, the function of KIF1C in myelination remains to be proved, as well as the cargoes of KIF1C in the oligodendrocytes, the myelinating cells of the central nervous system. Due to unavailability of suitable commercial antibodies against KIF1C protein, a transgenic mouse line (TAG) was created by inserting the V5-tag before the N-terminal motor domain of KIF1C protein. In this study, we showed by histopathological analyzes and by electron microscopy that none of the hallmarks of KIF1C loss-of-function in the central nervous system could be found in tagged mice, so the insertion of the V5-tag has no impact on myelin integrity. By in-situ analysis and immunofluorescence, we sought to determine the pattern of expression of KIF1C mRNA and protein in the brain. With the same techniques and with RT-qPCR, we also analyzed the expression of a major myelin protein, MBP, and highlighted a possible effect of the V5-tag insertion on KIF1C function in the transport of Mbp mRNAs. However, it had no effect on myelination, suggesting that most of the function of KIF1C is retained. Then, to better understand the function of KIF1C, we performed an analysis from the transcriptome of WT and KO mice’s cerebellum, aged 2 weeks, during myelination. Nervous system development and function was the top physiological system associated with DEGs, suggesting that KIF1C loss-of-function may not only have an impact on myelination, but also maybe during brain development. Finally, as soon as the immunofluorescence conditions are optimized to study KIF1C expression on tissue sections, we will be able to use the TAG mouse line to identify KIF1C cargoes, and understand its role during brain development and myelination.
Keywords: Kif1c, Mbp, Myelination, Ataxia, DEG, Mouse

Saha, Atal, 2011 (WU): Parentage analysis in Nile tilapia with two types of DNA-markers

Molecular pedigree is an effective tool to assure correct parentage in a selective fish breeding program. Although microsatellites are commonly used for this purpose, SNPs are getting more common because of their higher abundance and low cost. The objective of the present study is to re-construct the family pedigree of the selected Nile tilapia individuals using microsatellite and SNP markers and to estimate the best marker type for these studies. The main results suggested SNPs as very promising tool in parentage analyses.

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.

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.

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.

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.

Tusingwiire, Tomasi, 2022 (APT): Interest to implement differential weighting among markers in genomic evaluation in French dairy cattle

The current single-step genomic evaluation of dairy cattle used in France gives equal prior effect variances (PrV) to all markers considered in the evaluation, but this assumption is biologically incorrect. Some single nucleotide polymorphisms (SNPs) that have a strong LD with causal mutations may explain a higher genetic variance than others. Therefore, the aim of this internship was (1) to test different strategies to identify and classify candidate markers according to their expected importance in the genetic determinism of the evaluated traits and (2) to evaluate the impact of increasing the weight given to these markers in the evaluation model (Single Step) in terms of accuracy and bias. We hypothesized that including and increasing the weight of these candidate SNPs that are in high LD with causal mutations would improve genomic prediction accuracy while reducing prediction bias.
The breeds studied were Abondance and Montbéliarde French dairy cattle breeds. There were 215,620 animals in the Abondance pedigree file, of which 7,338 were genotyped, and 4,173,934 animals in the Montbéliarde pedigree file, of which 179,310 were genotyped. The traits analysed were milk yield (MY) and protein content (PC). There were 3,866 animals in the training population and 3,456 animals in the validation population for Abondance, while there were 8,4313 animals in the training population and 93,883 animals in the validation population for Montbéliarde. The total number of MY performances was 442,309 for Abondance, and 8,859,756 for Montbéliarde. The number of PC performances for Abondance and Montbéliarde was 442,260 and 8,858,901, respectively. The HSSGBLUP program was used to implement a hybrid single-step model that considers random effects of marker genotypes for genotyped animals and random effects of breeding values for non-genotyped animals. This model combines pedigree information, genomic information, and performances to estimate SNP effects and GEBV for each animal in the pedigree. The following scenarios were considered: (1) evaluation with only the basic SNPs with all SNPs having the same prior effect variance (PrV); (2) evaluation of basic SNPs plus candidate SNPs with all SNPs having the same PrV; and (3) evaluation of basic SNPs plus candidate SNPs with the PrV of candidate SNPs being increased. The number of markers considered in various basic scenarios included 1000, 10000, 20000, 30000, and about 40000 markers sampled from the 43570 markers after removing markers with a minor allele frequency (MAF) of less than 0.005 and some candidate markers found on the 50K Beadchip®. The proportion of total genetic variance given to the candidate SNPs ranged from 3% to 99%. The accuracy of genomic prediction was quantified as the correlation between the predicted genomic estimated breeding values (GEBV) of the validation and its corresponding yield deviations (YD) or daughter yield deviations (DYD). To determine prediction bias, the regression coefficients (slopes) of the validation population’s YD/DYD on the GEBV were calculated, and slopes of approximately 1 indicated zero bias. The accuracy increased when the candidate SNPs were added to basic markers with all the SNPs having the same PrV, though the increase was more pronounced in the scenario with 1000 basic SNPs. In general, increasing the PrV of candidate SNPs reduced prediction bias but did not improve prediction accuracy. In both breeds, the prediction accuracy of GEBV for PC was higher than that of MY.
The accuracy of prediction of GEBV was higher in Montbéliarde than in Abondance for both traits. More research should be done using alternative methods to investigate if increasing the prior effect variance of candidate SNPs would increase prediction accuracy and reduce bias, or to focus on less heritable traits, such as reproductive traits.

Key words: single step genomic Best Linear Unbiased Prediction, prior effect variance, genomic prediction, genomic estimated breeding values, Single nucleotide polymorphisms

Utida Reznik, Gabriela, 2022 (APT): Identification and Functional Characterization of Small Insertions/Deletions in the Bovine Genome

Small insertions/deletions (indels) represent close to 10% of the smaller genetic variation in bovine genome. Such variation can result in highly deleterious consequences to proteins when there is a frameshift or when start and stop codons are lost or gained. Splicing alteration can also be caused by indels as well as impacts in gene expression regulation. Despite the importance of this type of polymorphism, indels have been far less characterized than Single Nucleotide Polymorphisms (SNPs). By exploring properties of total bovine indels and analyzing additional data sources from tissue gene expression, genotyping, QTL regions and ATAC-seq we aim to partially elucidate the magnitude of potential functional impacts resulted from indels, their role across tissues, their impact to economically interesting traits and gene regulation mechanisms. We were able to establish that possible hotspots in chromosomes are expected for indels and that this class of variation affects almost all bovine transcripts and genes. Highly deleterious variants are mostly represented by frameshift variants that account for 1.1% of all indels and are located in 58% of all bovine genes. 517 indels related to potential disruptive outcomes affecting valuable phenotypic traits were identified. Association analysis of muscle tissue resulted in 769 expression QTL (eQTL) indels modulating gene expression of 367 genes. One cis-eQTL was reported as well as eQTL indels controlling multiple gene expressions and genes regulated by multiple indels. We also established that detection of coding indels in animals is likely affected by selective pressure.

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.

Worede, Zinabu Gebremariam, 2010 (BOKU): Characterization of the global Brown Swiss cattle population structure

The global Brown Swiss population was studied to estimate population genetic parameters, measure genetic variation and identify most influential animals. The population was found to have 3.30 mean equivalent complete generations. The mean inbreeding coefficient was 0.77% for the pedigree population. There was, in most cases, periodic and generational increase of mean inbreeding coefficient. Results showed that there was 0.40% increase in inbreeding by equivalent complete generations. Increase in average generation per period was also noted from the study. The pedigree population had 1.1% mean average relatedness. Effective population size for the equivalent complete generations was a mere 125.97, which could be considered as a small size considering the number of individuals in the population under study. There was big variation between average generation intervals for the four parental pathways. The highest average generation interval was seen in the sire-son path way, having a value of 8.73. The average generation interval for the whole population, which was 6.53, was also high. The pedigree population had 0.55% mean coancestry between its individuals. The French Brown Swiss subpopulation had the highest mean coancestry among its individuals. The French and the Austrian subpopulations had the highest mean coancestry between their subpopulations. The Italian subpopulation had the highest equivalent complete generation. The lowest genetic distance was recorded between the Italian and the US subpopulation, implying they had the highest genetic similarity. Most of the genetically influential individuals were sires. The highest contributing founder was a sire with 3.22% contribution. The highest contributing dam had 1.75% contribution. The effective number of founders and effective number of ancestors were 141 and 88, respectively.

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: 10.05.2023