Eesti piimaveisetõugude iseloomustamine geneetiliste markerite alustel

There are three dairy cattle breeds in Estonia that differ in their demographic history, phenotypic characteristics and current census sizes. The aim of the study was to characterize these breeds on the basis of genetic markers and compare the results with those for other Baltic and Nordic dairy breeds in order to explore the current status and uniqueness of Estonian dairy cattle genetic resources. The Estonian dairy cattle breeds, Estonian Holstein, Estonian Red and Estonian Native, were characterized using different types of genetic marker in order to measure genetic diversity within and among the breeds. Besides the markers used in routine genotyping of cattle in Estonia, also ISAG/FAO recommended markers were included and therefore the data could be used for comparing Estonian cattle populations in a wider setting, and exploring their current status and uniqueness in the European context. The results showed that the Estonian dairy cattle breeds are genetically variable and the level of variation within Estonian Red, Estonian Native and Estonian Holstein is relatively similar. It can be concluded that inbreeding, causing loss of heterozygosity in a small population, was not established to be at a high level (computed from marker data, the intra-breed inbreeding estimates did not differ from zero) in Estonian Holstein, Estonian Red or Estonian Native cattle. However, comparing Estonian Holstein with Estonian Red, the allelic richness and total number of unique alleles was higher in Estonian Red. It was demonstrated by constructing a tree and network based on genetic relationships between the Baltic and Nordic cattle breeds (36) that the Estonian dairy breeds were distinct from each other, falling into different genetic clusters – the Estonian Holstein fell into the Black-and-White breed group (9), the Estonian Red into the European/Baltic Red group (21), and the Estonian Native Cattle into the group of wide Nordic breeds, clustering closely with Western Finncattle. According to the microsatellite based allele-sharing distances among individuals, the genetic uniqueness of Estonian Native cattle was not confirmed in the Nordic-Baltic context. Due to prolonged gene flow from Western Finncattle, the genepool of the Estonian Native overlaps with that of Western Finncattle and that diminishes its genetic value among North European cattle breeds for conservation in terms of breed uniqueness. Despite that, the Estonian Native cattle are important in the Estonian context due to their genetic distinctiveness from the two Estonian breeds, their degree of endangerment, the cultural-historical value of the breed and from an environment management perspective.Eestis kasvatatakse kolme piimaveise tõugu, mis erinevad üksteisest välimiku, jõudluse, populatsioonimahu ja tõu ajaloolis-demograafilise kujunemise poolest. Uuringu eesmärgiks oli iseloomustada tõuge geneetiliste markerite alusel, võrrelda eesti maa-, eesti punast ning holsteini tõugu piimaveiseid teiste Balti- ja Põhjamaades levinud (piima)veisetõugudega ning selgitada välja Eesti veisetõugude geneetiliste ressursside seisund ja erisused. Eesti veisetõugude iseloomustamiseks ja tõu sisese ning tõugudevahelise muutlikkuse hindamiseks ja tõugude omavaheliseks võrdlemiseks kasutati erinevaid markeritüüpe. DNA markeritest kuuluvad 25 kasutatud mikrosatelliidi lookust ISAG/FAO töörühma poolt geneetilise mitmekesisuse uuringute läbiviimiseks 30 hetkel standardse ja soovitusliku markeri hulka. Lisaks mikrosatelliitidele määrati valitud loomadel kõik käesoleval ajal Eesti veiste rutiinseks geneetiliseks identifitseerimiseks kasutatavad markerid. Kasutatud mikrosatelliitide valik võimaldab võrrelda Eesti tõuge suurema arvu tõugudega ja hinnata nende geneetilist unikaalsust laiemas, Euroopa kontekstis. Uurimistulemused näitasid, et Eesti tõud on geneetiliselt erinevad ning hoolimata erinevast populatsioonimahust on tõugudesisene variatsioon eesti punases, eesti maatõus ja eesti holsteini tõus sarnane. Mõnevõrra vaesem oli eesti holsteini tõug alleelirikkuse poolest võrreldes eesti punase tõuga. Markerite põhjal leitud inbriidingu ehk sisearetuse määr ei erinenud ühelgi tõul statistiliselt oluliselt nullist. Suurema arvu, kokku 36 Põhja- ja Baltimaade tõugude suguluse uuringus eristusid Eesti tõud üksteisest grupeerudes erinevatesse geneetilistesse klastritesse. Eesti punane tõug grupeerus Baltimaade punaste tõugude (6 tõugu), eesti holstein mustakirjude tõugude (9) ning eesti maatõug suurde mitmekesisesse tõugude gruppi (21), mis jaotus omakorda mitmesse Põhjamaade tõugude alamgruppi. NJ (neighbor-joining) dendrogrammil moodustas eesti maatõug koos läänesoome tõuga ülejäänud tõugudest statistiliselt oluliselt erineva geneetilise klastri. Mikrosatelliitide analüüs näitas, et eesti maatõug on olulisel määral geneetiliselt segunenud läänesoome tõuga. Ohustatud tõu staatuses eesti maatõu geneetiline lähedus läänesoome tõuga vähendab eesti maatõu säilitamise tähtsust laiemas, Põhjamaade vanade tõugude geneetilise unikaalsuse kontekstis. Siiski on eesti maatõug oluline geneetilist mitmekesisust suurendav komponent Eesti veisetõugude hulgas, sealhulgas ka kultuurilis-ajaloolise aspekti poolest ning omab säilitamise tähtsust tõu ohustatuse tõttu.The publication of this dissertation is granted by Eesti Maaülikool and by the Graduate School in Biomedicine and Biotechnology

The results of a survey on the genetic diversity of Estonian dairy cattle breeds

The Estonian dairy cattle breeds: Estonian Holstein, Estonian Red and Estonian Native, have been characterized using different types of genetic markers in order to measure genetic diversity within and between the breeds. In addition to the routine markers commonly used in the genotyping of cattle in Estonia, ISAG/FAO recommended markers were also included and therefore the data could be used to compare Estonian cattle populations in a wider context, and exploring their current status and uniqueness in the European context. The results showed that the Estonian dairy cattle breeds are genetically variable and the level of variation within the Estonian Red, Estonian Native and Estonian Holstein breeds is relatively similar. It can be concluded that inbreeding, causing loss of heterozygosity in a small population, was not found to be at a high level in these breeds. The within-breed diversity estimates, based on the DNA microsatellite data, were at the same level as those reported for other modern dairy breeds. It was demonstrated, by constructing a tree and net-work based on genetic relationships between the Baltic and Nordic cattle breeds, that the Estonian dairy cattle breeds are distinct from each other, and fall into different genetic clusters – the Estonian Holstein is in the Black-and-White breed group, the Estonian Red is in the European/Baltic Red group, and the Estonian Native Cattle is in the group of wider Nordic breeds, clustering closely with Western Finncattle

The dynamics of hereditary scrapie resistance in Estonian sheep breeds

A total of 2,411 sheep from the Estonian Whitehead (N = 1301) and Estonian Blackhead (N = 1110) breeds were genotyped for markers of scrapie risk in the period 2005–2017. Sanger sequencing was used to identify nucleotide substitutions in the PRNP gene at codons 136, 141, 154 and 171 to determine corresponding amino acids in prion protein. Sheep were divided into 13 groups according to their birth year to assess the temporal changes on the genetic profile of the studied population. Seven different alleles and 16 different genotypes (12 for Estonian Blackhead and 16 for Estonian Whitehead) were identified. In the birth year group 2007 (two years after the introduction of a scrapie eradication programme) a statistically significant change in the allele ALRR frequencies was found. The selective breeding for allele ALRR (the scrapie resistant marker) increased in frequency from 0.40 to 0.70 during the period 2006–2017. Significant declines in allele frequencies ALRQ (0.40–0.20) and ALRH (0.13–0.03) were found. The frequency of the most susceptible to scrapie allele (VLRQ) was low (< 0.03), and the decrease of the frequency during the program was insignificant. Both sheep breeds showed statistically significant changes in allele, genotype and risk group frequencies between the birth year groups before the introduction of the scrapie eradication programme and at its end. The effect on genetic profile in terms of changed allele frequencies was statistically more significant in the Estonian Whitehead sheep (p < 0.001) than in the Estonian Blackhead sheep (p < 0.05)

Maareformid Eestis

http://tartu.ester.ee/record=b1044265~S1*es

Microsatellite, blood group and transferrin protein diversity of Estonian dairy cattle breeds

This study investigates genetic diversity within and among three Estonian dairy cattle breeds (Estonian Native, Estonian Red and Estonian Holstein). A total of 36 markers (25 microsatellites, 10 blood group systems and transferrin protein) were investigated and the within-breed diversity was quantified by expected heterozygosity, number of private alleles and mean allelic richness. The population structure was studied by computing the inbreeding coefficients, breed differentiation and relationships were investigated with random drift-based measures and a factorial correspondence analysis. In addition, a neighbour-joining tree was drawn summarising allele sharing distances for 195 individuals of the Estonian breeds, Western Finncattle, and Danish Jersey. The Estonian breeds displayed generally similar levels of within-population diversity. Depending on the set of markers used 6.2 or 4.3% of the total genetic variation can be explained by differences among the breeds. Construction of the tree for individuals revealed a distinctive pattern of grouping for Estonian Holstein, Estonian Red and Danish Jersey, but Estonian Native and Western Finncattle appeared on the same branches. This indicates that the gene pool of Estonian Native largely overlaps with that of Western Finncattle. However, our genetic marker analysis shows that the three Estonian breeds are genetically differentiated, suggesting that the current gene pool of Estonian dairy cattle is diverse.v2010o

Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data

The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017–2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5–37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires

Milk protein genotypes and milk coagulation properties of Estonian Native cattle

The genetic variation of ás1-, â- and ê-caseins and b-lactoglobulin was determined and their effects on the rennet coagulation properties were examined using 335 milk samples from 118 Estonian Native (EN) cows. We found 16 aggregate casein genotypes (ás1-, â-, ê-caseins), of which four . namely, BB A2A2 AA (21.2%), BB A1A2 AB (16.9%), BB A1A2 AA (14.4%), and BB A2A2 AB (10.2%) occurred among nearly two-thirds of the analysed cows. Aggregate casein genotype had a significant overall effect on rennet coagulation parameters. Better rennet coagulation properties were found for aggregate casein genotypes CC A2A2 AB and BC A1A2 BB, among frequent genotypes for BB A1A2 AB. Of the cattle breeds raised in Estonia, milk from EN had the best coagulation properties and highest frequency of favourable ê-Cn B allele.vo

North European Cattle Diversity (N-EURO-CAD)

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Genetic diversity of Estonian horse breeds and their genetic affinity to northern European and some Asian breeds

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