scholarly journals Testing a Local Inbreeding Hypothesis as a Cause of Observed Antler Characteristics in Managed Populations of White-Tailed Deer

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 116 ◽  
Author(s):  
Stephen L. Webb ◽  
Randy W. DeYoung ◽  
Stephen Demarais ◽  
Bronson K. Strickland ◽  
Kenneth L. Gee
Keyword(s):  
Odocoileus Virginianus ◽  
Genetic Relatedness ◽  
Microsatellite Data ◽  
Genome Wide ◽  
Internal Relatedness ◽  
Close Inbreeding

The increased use of antler restrictions by state game agencies has led to a focus on antlers by the hunting public, particularly the potential for an association between genetics and antler characteristics. We analyzed microsatellite data from 1231 male white-tailed deer (Odocoileus virginianus) from three states (Oklahoma, Mississippi, and Texas) within USA to determine if genetic relatedness, internal relatedness (IR), homozygosity weighted by locus (HL), or correlations among uniting gametes (Fis) influenced total antler points, antler score, non-typical points or antler malformations. Within each location, deer in the lower and upper quartile intervals for number of antler points and score were unrelated (95% CI included 0 or was <0) and relatively heterozygous for four measures of inbreeding. Antler score and points were positively influenced by age but negatively influenced by IR and HL, except for antler score in Mississippi. Relatedness, HL, IR and Fis did not differ between groups of deer with and without antler malformations. Perceived differences in antler quality do not appear to be affected by heterozygosity or a result of close inbreeding because we found deer were unrelated and measures of inbreeding and genome-wide heterozygosity were not correlated with antler characteristics.

scholarly journals Endocrine Fertility Parameters—Genomic Background and Their Genetic Relationship to Boar Taint in German Landrace and Large White

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 231
Author(s):  
Ines Brinke ◽  
Christine Große-Brinkhaus ◽  
Katharina Roth ◽  
Maren Julia Pröll-Cornelissen ◽  
Sebastian Klein ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Young Male ◽  
Boar Taint ◽  
Genetic Progress ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Different Origins ◽  
Fertility Traits

The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h2) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h2 differed between the breeds except for follicle-stimulating hormone (FSH) (h2: 0.28–0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (rg) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on Sus Scrofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, rg partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes.

scholarly journals Author Correction: Testing the key assumption of heritability estimates based on genome-wide genetic relatedness

2019 ◽  
Vol 64 (6) ◽  
pp. 597-598
Author(s):  
Dalton Conley ◽  
Mark L. Siegal ◽  
Benjamin W. Domingue ◽  
Kathleen Mullan Harris ◽  
Matthew B. McQueen ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Genome Wide ◽  
Heritability Estimates

scholarly journals The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans

2018 ◽  
Author(s):  
Dayana A. Delgado ◽  
Chenan Zhang ◽  
Kathryn Demanelis ◽  
Lin S. Chen ◽  
Jianjun Gao ◽  
...  
Keyword(s):  
Telomere Length ◽  
Genetic Relatedness ◽  
Meta Analysis ◽  
Telomere Maintenance ◽  
Leukocyte Telomere Length ◽  
Relative Pair ◽  
Identity By Descent ◽  
Novel Approach ◽  
Genome Wide ◽  
Heritable Trait

ABSTRACTLeukocyte telomere length (LTL) is a heritable trait with two potential sources of heritability (h2): inherited variation in non-telomeric regions (e.g., SNPs that influence telomere maintenance) and variability in the lengths of telomeres in gametes that produce offspring zygotes (i.e., “direct” inheritance). Prior studies of LTL h2have not attempted to disentangle these two sources. Here, we use a novel approach for detecting the direct inheritance of telomeres by studying the association between identity-by-descent (IBD) sharing at chromosome ends and phenotypic similarity in LTL. We measured genome-wide SNPs and LTL for a sample of 5,069 Bangladeshi adults with substantial relatedness. For each of the 7,254 relative pairs identified, we used SNPs near the telomeres to estimate the number of chromosome ends shared IBD, a proxy for the number of telomeres shared IBD (Tshared). We then estimated the association between Tsharedand the squared pairwise difference in LTL ((ΔLTL)2) within various classes of relatives (siblings, avuncular, cousins, and distant), adjusting for overall genetic relatedness (ϕ). The association between Tsharedand (ΔLTL)2was inverse among all relative pair types. In a meta-analysis including all relative pairs (ϕ >0.05), the association between Tsharedand (ΔLTL)2(P=0.002) was stronger than the association between ϕ and (ΔLTL)2(P=0.45). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h2despite telomere “reprogramming” during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h2attributable to direction transmission.

scholarly journals Correction: Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
Author(s):  
Christopher M. Seabury ◽  
Eric K. Bhattarai ◽  
Jeremy F. Taylor ◽  
Ganesh G. Viswanathan ◽  
Susan M. Cooper ◽  
...  
Keyword(s):  
Odocoileus Virginianus ◽  
Conservation Genomics ◽  
Comparative Analyses ◽  
Genome Wide

scholarly journals Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data

2018 ◽  
Vol 82 (4) ◽  
pp. 216-226 ◽  
Author(s):  
Chee Wei Yew ◽  
Mohd Zahirul Hoque ◽  
Jacqueline Pugh-Kitingan ◽  
Alexander Minsong ◽  
Christopher Lok Yung Voo ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Ethnic Groups ◽  
Genetic Relatedness ◽  
Snp Data ◽  
Genome Wide

scholarly journals The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Liam Shaw ◽  
Andre L. R. Ribeiro ◽  
Adam P. Levine ◽  
Nikolas Pontikos ◽  
Francois Balloux ◽  
...  
Keyword(s):  
Genetic Similarity ◽  
Genetic Relatedness ◽  
Dominant Factor ◽  
Shared Environment ◽  
Ashkenazi Jewish ◽  
Nucleotide Polymorphisms ◽  
Host Genetics ◽  
Microbiome Composition ◽  
Genome Wide ◽  
Host Genetic

ABSTRACT The human microbiome is affected by multiple factors, including the environment and host genetics. In this study, we analyzed the salivary microbiomes of an extended family of Ashkenazi Jewish individuals living in several cities and investigated associations with both shared household and host genetic similarities. We found that environmental effects dominated over genetic effects. While there was weak evidence of geographical structuring at the level of cities, we observed a large and significant effect of shared household on microbiome composition, supporting the role of the immediate shared environment in dictating the presence or absence of taxa. This effect was also seen when including adults who had grown up in the same household but moved out prior to the time of sampling, suggesting that the establishment of the salivary microbiome earlier in life may affect its long-term composition. We found weak associations between host genetic relatedness and microbiome dissimilarity when using family pedigrees as proxies for genetic similarity. However, this association disappeared when using more-accurate measures of kinship based on genome-wide genetic markers, indicating that the environment rather than host genetics is the dominant factor affecting the composition of the salivary microbiome in closely related individuals. Our results support the concept that there is a consistent core microbiome conserved across global scales but that small-scale effects due to a shared living environment significantly affect microbial community composition. IMPORTANCE Previous research shows that the salivary microbiomes of relatives are more similar than those of nonrelatives, but it remains difficult to distinguish the effects of relatedness and shared household environment. Furthermore, pedigree measures may not accurately measure host genetic similarity. In this study, we include genetic relatedness based on genome-wide single nucleotide polymorphisms (SNPs) (rather than pedigree measures) and shared environment in the same analysis. We quantify the relative importance of these factors by studying the salivary microbiomes in members of a large extended Ashkenazi Jewish family living in different locations. We find that host genetics plays no significant role and that the dominant factor is the shared environment at the household level. We also find that this effect appears to persist in individuals who have moved out of the parental household, suggesting that aspects of salivary microbiome composition established during upbringing can persist over a time scale of years. IMPORTANCE Previous research shows that the salivary microbiomes of relatives are more similar than those of nonrelatives, but it remains difficult to distinguish the effects of relatedness and shared household environment. Furthermore, pedigree measures may not accurately measure host genetic similarity. In this study, we include genetic relatedness based on genome-wide single nucleotide polymorphisms (SNPs) (rather than pedigree measures) and shared environment in the same analysis. We quantify the relative importance of these factors by studying the salivary microbiomes in members of a large extended Ashkenazi Jewish family living in different locations. We find that host genetics plays no significant role and that the dominant factor is the shared environment at the household level. We also find that this effect appears to persist in individuals who have moved out of the parental household, suggesting that aspects of salivary microbiome composition established during upbringing can persist over a time scale of years.

scholarly journals Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions

2020 ◽  
Vol 60 (4) ◽  
pp. 976-990 ◽  
Author(s):  
Gitanjali E Gnanadesikan ◽  
Brian Hare ◽  
Noah Snyder-Mackler ◽  
Josep Call ◽  
Juliane Kaminski ◽  
...  
Keyword(s):  
Nervous System ◽  
Noncoding Rna ◽  
Genome Wide Association Study ◽  
Genetic Relatedness ◽  
Phenotypic Diversity ◽  
Nervous System Development ◽  
Genome Wide ◽  
Dog Cognition ◽  
Breed Differences ◽  
Vesicle Exocytosis

Synopsis Given their remarkable phenotypic diversity, dogs present a unique opportunity for investigating the genetic bases of cognitive and behavioral traits. Our previous work demonstrated that genetic relatedness among breeds accounts for a substantial portion of variation in dog cognition. Here, we investigated the genetic architecture of breed differences in cognition, seeking to identify genes that contribute to variation in cognitive phenotypes. To do so, we combined cognitive data from the citizen science project Dognition.com with published breed-average genetic polymorphism data, resulting in a dataset of 1654 individuals with cognitive phenotypes representing 49 breeds. We conducted a breed-average genome-wide association study to identify specific polymorphisms associated with breed differences in inhibitory control, communication, memory, and physical reasoning. We found five single nucleotide polymorphisms (SNPs) that reached genome-wide significance after Bonferroni correction, located in EML1, OR52E2, HS3ST5, a U6 spliceosomal RNA, and a long noncoding RNA. When we combined results across multiple SNPs within the same gene, we identified 188 genes implicated in breed differences in cognition. This gene set included more genes than expected by chance that were (1) differentially expressed in brain tissue and (2) involved in nervous system functions including peripheral nervous system development, Wnt signaling, presynapse assembly, and synaptic vesicle exocytosis. These results advance our understanding of the genetic underpinnings of complex cognitive phenotypes and identify specific genetic variants for further research.

Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 557-567 ◽  
Author(s):  
Daryl J. Somers ◽  
Travis Banks ◽  
Ron DePauw ◽  
Stephen Fox ◽  
John Clarke ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Simple Sequence Repeats ◽  
Linkage Disequilibrium Analysis ◽  
Microsatellite Data ◽  
Significance Level ◽  
Genome Wide ◽  
Simple Sequence ◽  
Genome Wide Linkage Disequilibrium

Bread wheat and durum wheat were examined for linkage disequilibrium (LD) using microsatellite markers distributed across the genome. The allele database consisted of 189 bread wheat accessions genotyped at 370 loci and 93 durum wheat accessions genotyped at 245 loci. A significance level of p < 0.001 was set for all comparisons. The bread and durum wheat collections showed that 47.9% and 14.0% of all locus pairs were in LD, respectively. LD was more prevalent between loci on the same chromosome compared with loci on independent chromosomes and was highest between adjacent loci. Only a small fraction (bread wheat, 0.9%; durum wheat, 3.2%) of the locus pairs in LD showed R2 values > 0.2. The LD between adjacent locus pairs extended (R2 > 0.2) approximately 2–3 cM, on average, but some regions of the bread and durum wheat genomes showed high levels of LD (R2 = 0.7 and 1.0, respectively) extending 41.2 and 25.5 cM, respectively. The wheat collections were clustered by similarity into subpopulations using unlinked microsatellite data and the software Structure. Analysis within subpopulations showed 14- to 16-fold fewer locus pairs in LD, higher R2 values for those pairs in LD, and LD extending further along the chromosome. The data suggest that LD mapping of wheat can be performed with simple sequence repeats to a resolution of <5 cM.

scholarly journals Genomic relatedness and diversity of Swedish native cattle breeds

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Maulik Upadhyay ◽  
Susanne Eriksson ◽  
Sofia Mikko ◽  
Erling Strandberg ◽  
Hans Stålhammar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Demographic History ◽  
Genomic Diversity ◽  
Founder Population ◽  
Southern Sweden ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Native Cattle

Abstract Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. Results We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. Conclusions This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

scholarly journals Recombination, variance in genetic relatedness, and selection against introgressed DNA

2019 ◽  
Author(s):  
Carl Veller ◽  
Nathaniel B. Edelman ◽  
Pavitra Muralidhar ◽  
Martin A. Nowak
Keyword(s):  
Gene Flow ◽  
Genetic Relatedness ◽  
Hybrid Vigor ◽  
Recombination Rates ◽  
Deleterious Alleles ◽  
Genome Wide ◽  
Average Proportion ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Hybrid Cross

AbstractThe genomic proportion that two relatives share identically by descent—their genetic relatedness—can vary depending on the patterns of recombination and segregation in their pedigree. Here, we calculate the precise connection between genome-wide genetic shuffling and variance in genetic relatedness. For the relationships of grandparent-grandoffspring and siblings, the variance in genetic relatedness is a simple decreasing function of , the average proportion of locus pairs that recombine in gametogenesis. These formulations explain several recent observations about variance in genetic relatedness. They further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling F2-based tests for various kinds of selection, such as Dobzhansky-Muller incompatibilities and hybrid vigor. Our calculations also allow us to characterize how recombination affects the rate at which selection eliminates deleterious introgressed DNA after hybridization—by modulating the variance of introgressed ancestry across individuals. Species with low aggregate recombination rates, like Drosophila, purge introgressed DNA more rapidly and more completely than species with high aggregate recombination rates, like humans. These conclusions also hold for different genomic regions. Within the genomes of several species, positive correlations have been observed between local recombination rate and introgressed ancestry. Our results imply that these correlations can be driven more by recombination’s effect on the purging of deleterious introgressed alleles than its effect in unlinking neutral introgressed alleles from deleterious alleles. In general, our results demonstrate that the aggregate recombination process—as quantified by and analogs—acts as a variable barrier to gene flow between species.

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