Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda

Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis could not identify heterozygous SNPs present on the denser chip. Conversely, data from the denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a ROH. Using this options ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as dependent on pedigree depth. In the analysis of inbreeding depression a significant influence of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10, 17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are known to be directly associated with spermatogenesis, energy levels in spermatozoa and osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do affect estimates of autozygosity from ROH, ROH distributions (number and size) enables precise estimation of autozygosity at individual and population levels in cattle and genomic autozygosity does have influence on bull semen quality.“Runs Of Homozygosity” (ROH) nov su pristup utvrđivanja inbridinga kod diploidnih organizama i smatraju se pouzdanijim i više dostupnim od rodovnika, no nedostaju jedinstveni standardi za njihovu uporabu. U ovoj disertaciji ROH su analizirani kod pet pasmina goveda (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer i Tyrol Grey). Utjecaj gustoće genomske informacije (SNP chipa) i utjecaj genotipskih pogrešaka na detekciju ROH-ova istražen je na pasminama Brown Swiss, Pinzgauer i Tyrol Grey. SNP chip manje gustoće sustavno je precjenjivao broj ROH-ova <4 Mb, što je uzrokovalo i precjenjivanje inbridinga. Gušći SNP chip podcjenjivao je velike segmente osim u slučaju kada se dozvoljavao određen broj heterozigotnih genotipova. Koristeći ova saznanja procijenjen je ROH inbriding (FROH) za populacije Brown Swiss, Fleckvieh, Norwegian Red i Tyrol Grey, te je uspoređen s koeficijentima inbridinga iz rodovnika (FPED). Za sve četiri populacije vrijednosti FROH > 8 Mb i FROH > 16 Mb bile su slične vrijednosti FPED dok su FROH > 1 Mb i FROH > 2 Mb vrijednosti inbridinga bile mnogo veće od FPED. Pearsonovi korelacijski koeficijenti između FROH i FPED bili su rasponu od 0.50 do 0.72, a vrijednost je ovisila o dubini rodovnika. Kod analize inbriding depresije uočen je značajan utjecaj FPED, FROH2 - 4 Mb i FROH > 2 Mb na ukupan broj spermatozoida kod bikova Fleckvieh pasmine. Detekcija autozigotnih regija koje utječu na ovo svojstvo otkrila je regije na kromosomima 7, 10, 17, 20, 22 i 27 u kojima je pronađen 41 gen od kojih je pet izglednih kandidata, jer su povezani sa spermatogenezom, razinom energije spermatozoida i osmotskom ravnotežom spermatozoida i sjemene tekućine. Sve navedeno dovodi sljedećih zaključaka; greške genotipizacije i gustoća SNP chipa imaju utjecaj na identifikaciju ROH-ova; ROH metodom procijenjena autozigotnost predstavlja dobar pokazatelj stupnja inbridinga; autozigotnost genoma je povezana s plodnošću bikova

Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda

Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis could not identify heterozygous SNPs present on the denser chip. Conversely, data from the denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a ROH. Using this options ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as dependent on pedigree depth. In the analysis of inbreeding depression a significant influence of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10, 17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are known to be directly associated with spermatogenesis, energy levels in spermatozoa and osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do affect estimates of autozygosity from ROH, ROH distributions (number and size) enables precise estimation of autozygosity at individual and population levels in cattle and genomic autozygosity does have influence on bull semen quality.“Runs Of Homozygosity” (ROH) nov su pristup utvrđivanja inbridinga kod diploidnih organizama i smatraju se pouzdanijim i više dostupnim od rodovnika, no nedostaju jedinstveni standardi za njihovu uporabu. U ovoj disertaciji ROH su analizirani kod pet pasmina goveda (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer i Tyrol Grey). Utjecaj gustoće genomske informacije (SNP chipa) i utjecaj genotipskih pogrešaka na detekciju ROH-ova istražen je na pasminama Brown Swiss, Pinzgauer i Tyrol Grey. SNP chip manje gustoće sustavno je precjenjivao broj ROH-ova <4 Mb, što je uzrokovalo i precjenjivanje inbridinga. Gušći SNP chip podcjenjivao je velike segmente osim u slučaju kada se dozvoljavao određen broj heterozigotnih genotipova. Koristeći ova saznanja procijenjen je ROH inbriding (FROH) za populacije Brown Swiss, Fleckvieh, Norwegian Red i Tyrol Grey, te je uspoređen s koeficijentima inbridinga iz rodovnika (FPED). Za sve četiri populacije vrijednosti FROH > 8 Mb i FROH > 16 Mb bile su slične vrijednosti FPED dok su FROH > 1 Mb i FROH > 2 Mb vrijednosti inbridinga bile mnogo veće od FPED. Pearsonovi korelacijski koeficijenti između FROH i FPED bili su rasponu od 0.50 do 0.72, a vrijednost je ovisila o dubini rodovnika. Kod analize inbriding depresije uočen je značajan utjecaj FPED, FROH2 - 4 Mb i FROH > 2 Mb na ukupan broj spermatozoida kod bikova Fleckvieh pasmine. Detekcija autozigotnih regija koje utječu na ovo svojstvo otkrila je regije na kromosomima 7, 10, 17, 20, 22 i 27 u kojima je pronađen 41 gen od kojih je pet izglednih kandidata, jer su povezani sa spermatogenezom, razinom energije spermatozoida i osmotskom ravnotežom spermatozoida i sjemene tekućine. Sve navedeno dovodi sljedećih zaključaka; greške genotipizacije i gustoća SNP chipa imaju utjecaj na identifikaciju ROH-ova; ROH metodom procijenjena autozigotnost predstavlja dobar pokazatelj stupnja inbridinga; autozigotnost genoma je povezana s plodnošću bikova

Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda

Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis could not identify heterozygous SNPs present on the denser chip. Conversely, data from the denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a ROH. Using this options ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as dependent on pedigree depth. In the analysis of inbreeding depression a significant influence of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10, 17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are known to be directly associated with spermatogenesis, energy levels in spermatozoa and osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do affect estimates of autozygosity from ROH, ROH distributions (number and size) enables precise estimation of autozygosity at individual and population levels in cattle and genomic autozygosity does have influence on bull semen quality.“Runs Of Homozygosity” (ROH) nov su pristup utvrđivanja inbridinga kod diploidnih organizama i smatraju se pouzdanijim i više dostupnim od rodovnika, no nedostaju jedinstveni standardi za njihovu uporabu. U ovoj disertaciji ROH su analizirani kod pet pasmina goveda (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer i Tyrol Grey). Utjecaj gustoće genomske informacije (SNP chipa) i utjecaj genotipskih pogrešaka na detekciju ROH-ova istražen je na pasminama Brown Swiss, Pinzgauer i Tyrol Grey. SNP chip manje gustoće sustavno je precjenjivao broj ROH-ova <4 Mb, što je uzrokovalo i precjenjivanje inbridinga. Gušći SNP chip podcjenjivao je velike segmente osim u slučaju kada se dozvoljavao određen broj heterozigotnih genotipova. Koristeći ova saznanja procijenjen je ROH inbriding (FROH) za populacije Brown Swiss, Fleckvieh, Norwegian Red i Tyrol Grey, te je uspoređen s koeficijentima inbridinga iz rodovnika (FPED). Za sve četiri populacije vrijednosti FROH > 8 Mb i FROH > 16 Mb bile su slične vrijednosti FPED dok su FROH > 1 Mb i FROH > 2 Mb vrijednosti inbridinga bile mnogo veće od FPED. Pearsonovi korelacijski koeficijenti između FROH i FPED bili su rasponu od 0.50 do 0.72, a vrijednost je ovisila o dubini rodovnika. Kod analize inbriding depresije uočen je značajan utjecaj FPED, FROH2 - 4 Mb i FROH > 2 Mb na ukupan broj spermatozoida kod bikova Fleckvieh pasmine. Detekcija autozigotnih regija koje utječu na ovo svojstvo otkrila je regije na kromosomima 7, 10, 17, 20, 22 i 27 u kojima je pronađen 41 gen od kojih je pet izglednih kandidata, jer su povezani sa spermatogenezom, razinom energije spermatozoida i osmotskom ravnotežom spermatozoida i sjemene tekućine. Sve navedeno dovodi sljedećih zaključaka; greške genotipizacije i gustoća SNP chipa imaju utjecaj na identifikaciju ROH-ova; ROH metodom procijenjena autozigotnost predstavlja dobar pokazatelj stupnja inbridinga; autozigotnost genoma je povezana s plodnošću bikova

Hipokalcijemija nakon "completion" tireoidektomije zbog papilarnog karcinoma štitnjače

Surgical management of papillary thyroid carcinoma (PTC) includes total thyroidectomy and lobectomy. After lobectomy, a reoperation called completion thyroidectomy is occasionally required. Postoperative hypocalcemia is the most common complication associated with thyroid surgery. Our main goal was to determine if there is a significant difference between the incidence rate of postoperative hypocalcemia in patients who underwent total thyroidectomy for PTC compared with patients who underwent completion thyroidectomy for PTC. Apart from that, we analyzed the following potential predictive factors for the occurrence of hypocalcemia: sex, age, size of tumor, side of tumor, maximum diameter of individual lobe, occult metastasis, and operating surgeon. The study involved 340 patients who underwent surgery for PTC at the Department of ENT and Head and Neck Surgery, Zagreb University Hospital Centre, between February 25, 2013 and January 3, 2016. Postoperative hypocalcemia incidence rates were higher in the total thyroidectomy group than in the completion thyroidectomy group (37.8% and 29.0%, respectively). However, these differences were not statistically significant. Every analyzed potential predictive factor was proven not to have any correlation with postoperative hypocalcemia. This study demonstrated that there was no significant difference between postoperative hypocalcemia rates in patients who underwent completion thyroidectomy compared with patients who underwent total thyroidectomy for PTC.Kirurška terapija papilarnog karcinoma štitnjače obuhvaća totalnu tireoidektomiju i lobektomiju. Katkad je nakon lobektomije potrebno napraviti reoperaciju koja se naziva „completion“ tireoidektomija. Postoperativna hipokalcijemija najčešća je komplikacija povezana s kirurgijom štitnjače. Cilj našeg rada bio je utvrditi postoji li značajna razlika u učestalosti postoperativne hipokalcijemije kod pacijenata koji su bili podvrgnuti totalnoj tireoidektomiji zbog papilarnog karcinoma štitnjače i pacijenata kod kojih je rađena „completion“ tireoidektomija zbog papilarnog karcinoma štitnjače. Osim toga analizirali smo sljedeće potencijalne prediktivne faktore za pojavu hipokalcijemije: spol, dob, veličina tumora, strana tumora, maksimalni promjer pojedinačnog režnja, okultne metastaze i kirurg. U istraživanje je bilo uključeno 340 pacijenata operiranih zbog papilarnog karcinoma štitnjače na Klinici za bolesti uha, grla i nosa i kirurgiju glave i vrata, KBC Zagreb, u razdoblju od 25. veljače 2013. do 3. siječnja 2016. Učestalost hipokalcijemije nakon totalne tirodektomije bila je veća, 37, 8% u usporedbi s 29% nakon „completion“ tireoidektomije. Unatoč tome, ta razlika nije bila statistički značajna. Nijedan od analiziranih faktora nije doveden u korelaciju s postoperativnom hipokalcijemijom. Naše je istraživanje pokazalo da ne postoji značajna razlika u učestalosti postoperativne hipokalcijemije između pacijenata podvrgnutih „completion“ tireoidektomiji i pacijenata podvrgnutih totalnoj tireoidektomiji zbog papilarnog karcinoma štitnjače

Variance Estimation of Maternal Lineage Effect on Milk Traits in Croatian Holstein Cattle

The effect of maternal lineage (ML) on milk production traits: milk, fat and protein yield (MY, FY, and PY), fat and protein content (FC and PC) was evaluated in the Croatian Holstein cattle. Data included 102,961 records for 46,696 cows calved from January 2000 to July 2015 taken from the Central database of the Croatian Agricultural Agency. Pedigree file consisted of 77,398 animals. Variance components were estimated by REML method using VCE-6 program. Statistical model included parity, region, and calving season as fixed class effects, while age at first calving was fitted as quadratic regression. Random effects were: interaction herd-year, permanent environment, maternal lineage, and direct additive genetic effect. Identification of ML was based on the pedigree information. The contribution of ML to the phenotypic variance was 2% for FC and PC and 3% for MY, FY, and PY. The estimates of ML for milk traits were within the range of other studies

The Impact of Cytoplasmic Inheritance on Sperm Quality in Fleckvieh Bulls

Detrimental impact of certain mitogenome mutations on sperm quality traits, and consequently on male fertility is well documented in humans. With a quantitative genetic mixed model, we analysed the impact of cytoplasmic effects, maternal lineages treated as random effect, on sperm quality traits in 554 Austrian Fleckvieh bulls. We have observed that 2% of the phenotypic variance for transformed total number of spermatozoa is due to cytoplasmic (maternal lineage) effects. Regarding percent of viable live spermatozoa, no cytoplasmic effects were detected. However, the observed effects still need to be further evaluated from three perspectives, the analysis of the mitogenome polymorphism effects and the impact of the mitogenome effects on the realised fertility as well as on the whole production economically

The Impact of Cytoplasmic Inheritance on Sperm Quality in Fleckvieh Bulls

Detrimental impact of certain mitogenome mutations on sperm quality traits, and consequently on male fertility is well documented in humans. With a quantitative genetic mixed model, we analysed the impact of cytoplasmic effects, maternal lineages treated as random effect, on sperm quality traits in 554 Austrian Fleckvieh bulls. We have observed that 2% of the phenotypic variance for transformed total number of spermatozoa is due to cytoplasmic (maternal lineage) effects. Regarding percent of viable live spermatozoa, no cytoplasmic effects were detected. However, the observed effects still need to be further evaluated from three perspectives, the analysis of the mitogenome polymorphism effects and the impact of the mitogenome effects on the realised fertility as well as on the whole production economically

GENOMIC BACKGROUND OF ENTROPION IN FLECKVIEH CATTLE

Runs of homozygosity (ROH) and genome wide association study (GWAS) were used to identify genomic regions of entropion in Austrian Fleckvieh cattle. Entropion is an eye disorder where the eye lids turn inward, causing inflammations, cornea damage or even blindness if left untreated. A total of 196 bulls genotyped by BovineSNP50 BeadChip were analysed, nine of which had the disorder confirmed by a veterinarian, ten were unconfirmed and 177 were healthy control animals. Runs of homozygosity analysis highlighted regions on seven chromosomes where the proportion of animals in ROH significantly (p<0.001) differed between cases and controls. None of the 19 genes identified in these regions showed any connection to entropion or eye development. The GWAS study using only cases and controls had a mild peak directly on top of the ITGA9 gene. This gene was previously identified in mice affecting cornea and eye lid development, therefore we consider it being a candidate to influence entropion also in cattle

EFFECT OF SEASON ON VARIATION IN SOMATIC CELL COUNT IN MILK

Broj somatskih stanica u mlijeku pokazatelj je higijenske kvalitete mlijeka i opći indikator zdravlja vimena. Njihov povećan broj je pouzdan znak poremećaja zdravlja krava ili higijensko-sanitarnih uvjeta proizvodnje. U cilju povećanja proizvodnje mlijeka te s obzirom na čitav niz čimbenika koji mogu utjecati na variranje broja somatskih stanica vrlo je važno poznavanje njihovog utjecaja u našim proizvodnim uvjetima. U ovom radu su prikazani rezultati analiza broja somatskih stanica od 395.299 uzoraka mlijeka u razdoblju od 2000. do 2008. godine. Testiran je utjecaj sezone (godišnje doba) na broj somatskih stanica u mlijeku. Rezultati istraživanja pokazuju značajno variranje broja somatskih stanica tijekom razdoblja 2000.-2008. godine. S izuzetkom 2003. i 2004. godine može se uočiti trend postepenog smanjenja broja somatskih stanica, koji je najvjerojatnije posljedica donošenja zakonskih propisa koji uređuju to područje (Pravilnika o kakvoći svježeg sirovog mlijeka i Uredbe o ciljnoj cijeni svježeg sirovog mlijeka) odnosno utjecaja broja somatskih stanica na formiranje otkupne cijene mlijeka. Nadalje, utvrđeno je da sezona (godišnje doba) ima značajnog utjecaja na variranje broja somatskih stanica u mlijeku. U našim klimatskim uvjetima povećan broj somatskih stanica uočen je u ljetnim i jesenskim mjesecima, a niži u proljetnim i zimskim mjesecima što je najvjerojatnije posljedica visokih temperatura i vlage u tim razdobljima godine.The number of somatic cells in milk is an indicator of hygienic quality of milk and a general indicator of udder health. The increase in their number is a reliable sign of impaired health or cow health and sanitary conditions of production. In order to increase milk production and with regard to a number of factors that can affect the variation of somatic cells is very important to know their impact in terms of our production conditions. This paper presents the results of the analysis of somatic cell count of 395,299 milk samples in the period from 2000 – 2008. It was tested the effect of season on the number of somatic cells in milk. The study results show a significant variation of somatic cells during period 2000th-2008th year. With the exception of the year 2003 and 2004 the trend can be seen a gradual reduction in the number of somatic cells, which is probably the result of the adoption of legislation governing this area (Ordinance on the quality of fresh raw milk and the Regulation on the target price of the fresh raw milk) and the impact of somatic cells in the formation of the price of milk. Furthermore, it was found that the season has a significant effect on the variation of the number of somatic cells in milk. In our climatic conditions, increased number of somatic cells was observed in the summer and autumn and lower in the spring and winter, it is most likely a result of high temperatures and humidity in those periods of the year