Pleomorphic adenoma gene1 in reproduction and implication for embryonic survival in cattle: a review

The pleomorphic adenoma gene1 (PLAG1) encodes a DNA-binding, C2H2 zinc-finger protein which acts as a transcription factor that regulates the expression of diverse genes across different organs and tissues; hence, the name pleomorphic. Rearrangements of the PLAG1 gene, and/or overexpression, are associated with benign tumors and cancers in a variety of tissues. This is best described for pleomorphic adenoma of the salivary glands in humans. The most notable expression of PLAG1 occurs during embryonic and fetal development, with lesser expression after birth. Evidence has accumulated of a role for PLAG1 protein in normal early embryonic development and placentation in mammals. PLAG1 protein influences the expression of the ike growth factor 2 (IGF2) gene and production of IGF2 protein. IGF2 is an important mitogen in ovarian follicles/oocytes, embryos, and fetuses. The PLAG1-IGF2 axis, therefore, provides one pathway whereby PLAG1 protein can influence embryonic survival and pregnancy. PLAG1 also influences over 1,000 other genes in embryos including those associated with ribosomal assembly and proteins. Brahman (Bos indicus) heifers homozygous for the PLAG1 variant, rs109815800 (G > T), show greater fertility than contemporary heifers with either one, or no copy, of the variant. Greater fertility in heifers homozygous for rs109815800 could be the result of early puberty and/or greater embryonic survival. The present review first looks at the broader roles of the PLAG1 gene and PLAG1 protein and then focuses on the emerging role of PLAG1/PLAG1 in embryonic development and pregnancy. A deeper understanding of factors which influence embryonic development is required for the next transformational increase in embryonic survival and successful pregnancy for both in vivo and in vitro derived embryos in cattle.

Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

Background

Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs).

Results

The most significant SNP (rs133012258, P_GC = 1.34 × 10^-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length.

Conclusions

This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus).

Tracking the emergence of a new breed using 49,034 SNP in sheep

Domestic animals are unique in that they have been organised into managed populations called breeds. The strength of genetic divergence between breeds may vary dependent on the age of the breed, the scenario under which it emerged and the strength of reproductive isolation it has from other breeds. In this study, we investigated the Gulf Coast Native breed of sheep to determine if it contains lines of animals that are sufficiently divergent to be considered separate breeds. Allele sharing and principal component analysis (PCA) using nearly 50,000 SNP loci revealed a clear genetic division that corresponded with membership of either the Florida or Louisiana Native lines. Subsequent analysis aimed to determine if the strength of the divergence exceeded that found between recognised breed pairs. Genotypes from 14 breeds sampled from Europe and Asia were used to obtain estimates of pair-wise population divergence measured as F(ST). The divergence separating the Florida and Louisiana Native (F(ST) = 6.2%) was approximately 50% higher than the average divergence separating breeds developed within the same region of Europe (F(ST) = 4.2%). This strongly indicated that the two Gulf Coast Native lines are sufficiently different to be considered separate breeds. PCA using small SNP sets successfully distinguished between the Florida and Louisiana Native animals, suggesting that allele frequency differences have accumulated across the genome. This is consistent with a population history involving geographic separation and genetic drift. Suggestive evidence was detected for divergence at the poll locus on sheep chromosome 10; however drift at neutral markers has been the largest contributor to the genetic separation observed. These results document the emergence of populations that can be considered separate breeds, with practical consequences for bio-conservation priorities, animal registration and the establishment of separate breed societies.

Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection

Genomic structure in a global collection of domesticated sheep reveals a history of artificial selection for horn loss and traits relating to pigmentation, reproduction, and body size.

Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species.

During the process of domestication, mankind recruited animals from the wild into a captive environment, changing their morphology, behaviour, and genetics. In the case of sheep, domestication and subsequent selection by their animal handlers over thousands of years has produced a spectrum of breeds specialised for the production of wool, milk, and meat. We sought to use this population history to search for the genes that directly underpin phenotypic variation. We collected DNA from 2,819 sheep, belonging to 74 breeds sampled from around the world, and assessed the genotype of each animal at nearly 50,000 locations across the genome. Our results show that sheep breeds have maintained high levels of genetic diversity, in contrast to other domestic animals such as dogs. We also show that particular regions of the genome contain strong evidence for accelerated change in response to artificial selection. The most prominent example was identified in response to breeding for the absence of horns, a trait now common across many modern breeds. Furthermore, we demonstrate that other genomic regions under selection in sheep contain genes controlling pigmentation, reproduction, and body size.

Molecular genetic approaches for identifying the basis of variation in resistance to tick infestation in cattle

In recent years there has been renewed interest in the adaptation of cattle to challenging environments, largely driven by advances in genomic methods. The current interest in tick resistance is understandable given the major production and welfare implications of tick infestation in tropical and subtropical zones where around 70% of beef cattle are located. Heritability for tick burden in cattle has been shown to range about 0.30, which is sufficient to result in the success of some programs of selection for tick resistance in cattle. Gene-expression studies strongly indicate that both immune and non-immune mechanisms are associated with tick resistance in cattle. Recent quantitative-trait mapping studies have identified chromosome segments and single nucleotide polymorphisms associated with tick burden, but no causal variant has been identified so far. Most of the genetic markers identified for tick burden explain a relatively small proportion of the variance, which is typical of markers for quantitative traits. This leads to the conclusion that panels of multiple markers for tick resistance rather than a single marker will most likely be developed, possibly involving specific panels for zebu or taurine breeds, which could be used for future selection and breeding programs in cattle.

Effect of SNP origin on analyses of genetic diversity in cattle

The methods of single nucleotide polymorphism (SNP) identification can lead to ascertainment bias, which will affect population genetic analyses based on those data. In livestock species, the methods of SNP identification through genome sequencing are likely to suffer from this ascertainment bias. In the present study, a subset of data from the Bovine HapMap Project was re-analysed to quantify the effects of ascertainment bias on a range of common analyses and statistics. Data from 189 animals of the zebu breeds Brahman, Nelore and Gir, taurine beef Angus, Limousin and Hereford and taurine dairy Holstein, Jersey and Brown Swiss were analysed. There were 141 SNPs each of Angus, Brahman and Holstein origin, giving a total of 423 SNPs organised in 141 triplets. Each triplet consisted of one SNP of each breed, separated on average by 0.75 Mb within each triplet and where triplets were separated by 14.96 Mb to ensure that each triplet was unaffected by linkage disequilibrium. The minor allele frequency distribution, estimates of the F-statistic, FST, the partitioning of variance and population substructure were relatively unaffected by breed of origin of the SNPs. Estimates of heterozygosity were significantly affected by breed of origin of the SNPs. The clustering of animals of closely related breeds varied in the principal component analyses (PCA). However, in the PCA the effect of breed of origin of 141 SNPs was similar to the effect of using different panels of 141 SNPs of all three breeds, so the differences found in the PCA may not be all due to bias by the origin of the SNPs. Based on these results, analyses that depend on FST, including signatures of selection, gene flow and effective population size are unlikely to be strongly affected by SNP origin. Analyses that partition genetic variance and some analyses of population substructure will also be largely unaffected. However, analyses that are dependent on locus heterozygosity, which can be used for studying population bottlenecks, or those that study selection using extended haplotype homozygosity may be significantly affected by breed of origin of the SNPs.

A genome-wide association study of tick burden and milk composition in cattle

To study the genetic basis of tick burden and milk production and their interrelationship, we collected a sample of 1961 cattle with multiple tick counts from northern Australia of which 973 had dairy production data in the Australian Dairy Herd Information Service database. We calculated heritabilities, genetic and phenotypic correlations for these traits and showed a negative relationship between tick counts and milk and milk component yield. Tests of polymorphisms of four genes associated with milk yield, ABCG2, DGAT1, GHR and PRLR, showed no statistically significant effect on tick burden but highly significant associations to milk component yield in these data and we confirmed separate effects for GHR and PRLR on bovine chromosome 20. To begin to identify some of the molecular genetic bases for these traits, we genotyped a sample of 189 of these cattle for 7397 single nucleotide polymorphisms in a genome-wide association study. Although the allele effects for adjusted milk fat and protein yield were highly correlated (r = 0.66), the correlations of allele effects of these milk component yields and tick burden were small (|r| ≤ 0.10). These results agree in general with the phenotypic correlations between tick counts and milk component yield and suggest that selection on markers for tick burden or milk component yield may have no undesirable effect on the other trait.