Chromosome Single Nucleotide Polymorphisms Research Articles

PSVII-6 Gender prediction in Hanwoo cattle using custom SNP arrays

Abstract Hanwoo is one of the indigenous cattle breeds in South Korea, and genetic evaluation at the national level is conducted using custom Illumina SNP arrays. Accurate gender assignment is essential in genetic evaluation and breeding programs for livestock species. In this study, we described a method for using custom single nucleotide polymorphism (SNP) array data to predict gender of Hanwoo cattle using logistic regression model. We analyzed a set of 958 SNPs, with 947 located on the X chromosome and 11 on the Y chromosome, focusing on heterozygosity rates from the X chromosome and missing rates from Y chromosome SNPs. Using a training dataset comprising 5,000 bulls and 2,005 cows with accurately recorded genders, we built a prediction model. Subsequently, we evaluated the performance of the model on test datasets consisting of 6,657 bulls, 27 steers, and 8,418 cows. The concordance between predicted gender and recorded gender were 99.98%, 100.00% and 99.98% for bulls, steers, and cows, respectively. This result showed better accuracy of gender prediction compared with the GENOMESTUDIO tool that uses only the heterozygosity rate of SNPs in X chromosome in the case of restricted number of SNPs in sex chromosomes. Overall, our findings could be used as an effective method for more precise genetic evaluation by correcting potential gender errors in Hanwoo cattle breeding programs.

A simulative deep learning model of SNP interactions on chromosome 19 for predicting Alzheimer's disease risk and rates of disease progression.

Identifying genetic patterns that contribute to Alzheimer's disease (AD) is important not only for pre-symptomatic risk assessment but also for building personalized therapeutic strategies. We implemented a novel simulative deep learning model to chromosome 19 genetic data from the Alzheimer's Disease Neuroimaging Initiative and the Imaging and Genetic Biomarkers of Alzheimer's Disease datasets. The model quantified the contribution of each single nucleotide polymorphism (SNP) and their epistatic impact on the likelihood of AD using the occlusion method. The top 35 AD-risk SNPs in chromosome 19 were identified, and their ability to predict the rate of AD progression was analyzed. Rs561311966 (APOC1) and rs2229918 (ERCC1/CD3EAP) were recognized as the most powerful factors influencing AD risk. The top 35 chromosome 19 AD-risk SNPs were significant predictors of AD progression. The model successfully estimated the contribution of AD-risk SNPs that account for AD progression at the individual level. This can help in building preventive precision medicine.

Characteristic of Przewalski horses population from Askania-Nova reserve based on genetic markers.

Przewalski horses are considered the last living population of wild horses, however, they are secondarily feral offspring of herds domesticated ~ 5000 years ago by the Botai culture. After Przewalski horses were almost extinct at the beginning of the twentieth century, their population is about 2500 individuals worldwide, with one of the largest breeding centers in Askania-Nova Biosphere Reserve (Ukraine). The research aimed to establish the maternal variation of Przewalski horses population maintained in Askania-Nova Reserve based on mitochondrial DNA hypervariable 1 and hypervariable 2 regions profiling, as well as, analysis of Y chromosome single nucleotide polymorphism unique for Przewalski horses, and coat color markers: MC1R and TBX3. The mtDNA hypervariable regions analysis in 23 Przewalski horses allowed assigning them to three distinctly different haplotypes, showing the greatest similarity to the Equus caballus reference, the Equus przewalskii reference, and to extinct species-Haringtonhippus. The Y chromosome analysis using fluorescently labelled assays differentiated horses in terms of polymorphism (g731821T>C) characteristic of Equus przewalskii. All male individuals presented genotype C characteristics for Przewalski horses. The polymorphisms within the coat color genes indicated only native, wild genotypes. The Y chromosome and coat color analysis denied admixtures of the tested horses with other Equidae.

How Physical and Molecular Anthropology Interplay in the Creation of Biological Profiles of Unidentified Migrants

The skeletal sex and ancestry of unidentified human crania can be inferred both from physical and from molecular features. This paper depicts and discusses the experiences of physical and molecular anthropologists on a set of commingled crania from the largest Mediterranean shipwreck disaster on 18 April 2015, in order to facilitate identification of human crania. Twenty-one disarticulated crania that were recovered from the above-mentioned shipwreck were analyzed to estimate skeletal sex and ancestry, following a physical and a molecular pipeline. The physical analyses applied morphological and metric methods that provided posterior probabilities for the crania to be classified into a sex or ancestral group. The molecular analyses were performed on petrous bones via a shotgun sequencing approach that allowed us to determine the sex of each individual and to retrieve the complete mitochondrial genome, Y chromosome single nucleotide polymorphisms, up to 597573 SNPs across the human genome from each individual. The morphometric sex analyses showed that most crania belonged to male individuals, although some estimations remained uncertain or undetermined. Inconsistent results were obtained for ancestry estimation as well, since morphological methods classified the crania mostly as European/White, in contrast to the most numerous African forms determined by craniometric analyses. This quite agreed with molecular analyses that identified only African males. Overall, undetermined and contrasting results were obtained between disciplines, preventing the creation of reliable and sound biological profiles that could provide guidance on the sex and ancestral group of the victims. Therefore, the times may not be mature for a merger of physical and molecular anthropology. However, future investigations of this research avenue would pave the way to the possible development of novel tools, methods, and wider reference databases that could address the limitations of both disciplines.

Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia.

In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.

The vegetable SNP database: An integrated resource for plant breeders and scientists

Single nucleotide polymorphisms (SNPs) are widely used in genetic research and molecular breeding. To date, the genomes of many vegetable crops have been assembled, and hundreds of core germplasms for each vegetable have been sequenced. However, these data are not currently easily accessible because they are stored on different public databases. Therefore, a vegetable crop SNP database should be developed that hosts SNPs demonstrated to have a high success rate in genotyping for genetic research (herein, “alpha SNPs”). We constructed a database (VegSNPDB, http://www.vegsnpdb.cn/) containing the sequence data of 2032 germplasms from 16 vegetable crop species. VegSNPDB hosts 118,725,944 SNPs of which 4,877,305 were alpha SNPs. SNPs can be searched by chromosome number, position, SNP type, genetic population, or specific individuals, as well as the values of MAF, PIC, and heterozygosity. We hope that VegSNPDB will become an important SNP database for the vegetable research community.

Testing and estimation of X-chromosome SNP effects: Impact of model assumptions.

Interest in analyzing X chromosome single nucleotide polymorphisms (SNPs) is growing and several approaches have been proposed. Prior studies have compared power of different approaches, but bias and interpretation of coefficients have received less attention. We performed simulations to demonstrate the impact of X chromosome model assumptions on effect estimates. We investigated the coefficient biases of SNP and sex effects with commonly used models for X chromosome SNPs, including models with and without assumptions of X chromosome inactivation (XCI), and with and without SNP–sex interaction terms. Sex and SNP coefficient biases were observed when assumptions made about XCI and sex differences in SNP effect in the analysis model were inconsistent with the data‐generating model. However, including a SNP–sex interaction term often eliminated these biases. To illustrate these findings, estimates under different genetic model assumptions are compared and interpreted in a real data example. Models to analyze X chromosome SNPs make assumptions beyond those made in autosomal variant analysis. Assumptions made about X chromosome SNP effects should be stated clearly when reporting and interpreting X chromosome associations. Fitting models with SNP × Sex interaction terms can avoid reliance on assumptions, eliminating coefficient bias even in the absence of sex differences in SNP effect.

Genome-wide Association Mapping for the Identification of SNPs Controlling Lateral Root Plasticity in Selected Rice Germplasms of the Philippines

Lateral root plasticity is a key adaptive mechanism for drought and fluctuating moisture-induced stresses in rice. Thus, understanding the genetic control of lateral root plasticity is important to enhance the climate-resilience and productivity of rice in abiotic stressed-prone environments. Genome-wide association analysis was conducted on a selected panel of traditional rice varieties (TRVs) to find single nucleotide polymorphisms (SNPs) associated with root plasticity traits under different gradients of soil moisture stress. A total of 17 SNPs, which were significantly correlated to root plasticity traits under soil moisture stress conditions, were located in six chromosomes (2, 5, 7, 9, 10, and 12). Additionally, the accessions that showed high plasticity in total lateral root length (TLRL) under severe drought were identified from among the TRVs and assumed to possess the lone SNP associated with the trait found in Chromosome 2. Specifically, the Baksalan Kawalwal accession showed an increase in L-type lateral root length under fluctuating soil moistures (SMF) (+10.31 m) and progressive drought (PDR) (+0.90 m), relative to their continuously waterlogged (CWL) counterparts under rootbox pinboard system. This may suggest the performance of the SNP in controlling the promotion of lateral roots. Furthermore, a possible candidate gene found near the SNP in Chromosome 2 is a member of PYR/PYL/RCAR-like protein family of abscisic acid (ABA) receptors, likely suggesting that plasticity in lateral root development in rice under severe drought could be regulated by ABA. Taken together, these novel root plasticity SNPs and the respective candidate genes on Chromosome 2 have potential use in developing climate-smart rice varieties.

RAI14in the blood featherregulates chicken pigmentation.

A genome-wide association study (GWAS) was performed on a resource family consisting of white and colored chickens for identification of genes related to plumage coloration using the Fixed and random model Circulating Probability Unification (FarmCPU) package. GWAS identified three chromosomal single-nucleotide polymorphisms (SNPs), demonstrating the polygenic basis of plumage phenotypes. Herein, retinoic acid-induced protein 14 (RAI14), a developmentally regulated gene that encodes a protein containing many ankyrin repeats, was identified as a candidate gene involved in plumage color. In this study, mRNA expression profiles of chicken RAI14 were determined, indel (insertion–deletion) variants were identified, and their association was analyzed in white and colored chickens. RA114 mRNA was expressed in all tissues tested (brain, spleen, liver, heart, oviduct, kidney, lung, pituitary gland, ovary, muscle, feather bulb, and skin). A relatively high RAI14 expression in white feather bulb compared to colored feather bulb () indicated a potential association with plumage color. Additionally, statistical analysis revealed that a 4 bp indel genetic variation in RAI14 was associated with plumage phenotypes (). Together, our analysis of the identification of the RAI14 gene will enable us to understand the genetic mechanisms behind chicken pigmentation.

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs.

Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

6q25.1 (TAB2) microdeletion is a risk factor for hypoplastic left heart: a case report that expands the phenotype

IntroductionHypoplastic left heart syndrome (HLHS) is a rare but devastating congenital heart defect (CHD) accounting for 25% of all infant deaths due to a CHD. The etiology of HLHS remains elusive, but there is increasing evidence to support a genetic cause for HLHS; in particular, this syndrome is associated with abnormalities in genes involved in cardiac development. Consistent with the involvement of heritable genes in structural heart abnormalities, family members of HLHS patients have a higher incidence of both left- and right-sided valve abnormalities, including bicuspid aortic valve (BAV).Case presentationWe previously described (Am J Med Genet A 173:1848–1857, 2017) a 4-generation family with a 6q25.1 microdeletion encompassing TAB2, a gene known to play an important role in outflow tract and cardiac valve formation during embryonic development. Affected adult family members have short stature, dysmorphic facial features, and multiple valve dysplasia, including BAV. This follow-up report includes previously unpublished details of the cardiac phenotype of affected family members. It also describes a baby recently born into this family who was diagnosed prenatally with short long bones, intrauterine growth restriction (IUGR), and HLHS. He was the second family member to have HLHS; the first died several decades ago. Postnatal genetic testing confirmed the baby had inherited the familial TAB2 deletion.ConclusionsOur findings suggest TAB2 haploinsufficiency is a risk factor for HLHS and expands the phenotypic spectrum of this microdeletion syndrome. Chromosomal single nucleotide polymorphism (SNP) microarray analysis and molecular testing for a TAB2 loss of function variant should be considered for individuals with HLHS, particularly in those with additional non-cardiac findings such as IUGR, short stature, and/or dysmorphic facial features.

Statistical methods for testing X chromosome variant associations: application to sex-specific characteristics of bipolar disorder

BackgroundBipolar disorder (BD) affects both sexes, but important sex differences exist with respect to its symptoms and comorbidities. For example, rapid cycling (RC) is more prevalent in females, and alcohol use disorder (AUD) is more prevalent in males. We hypothesize that X chromosome variants may be associated with sex-specific characteristics of BD. Few studies have explored the role of the X chromosome in BD, which is complicated by X chromosome inactivation (XCI). This process achieves “dosage compensation” for many X chromosome genes by silencing one of the two copies in females, and most statistical methods either ignore that XCI occurs or falsely assume that one copy is inactivated at all loci. We introduce new statistical methods that do not make these assumptions.MethodsWe investigated this hypothesis in 1001 BD patients from the Genetic Association Information Network (GAIN) and 957 BD patients from the Mayo Clinic Bipolar Disorder Biobank. We examined the association of over 14,000 X chromosome single nucleotide polymorphisms (SNPs) with sex-associated BD traits using two statistical approaches that account for whether a SNP may be undergoing or escaping XCI. In the “XCI-informed approach,” we fit a sex-adjusted logistic regression model assuming additive genetic effects where we coded the SNP either assuming one copy is expressed or two copies are expressed based on prior knowledge about which regions are inactivated. In the “XCI-robust approach,” we fit a logistic regression model with sex, SNP, and SNP-sex interaction effects that is flexible to whether the region is inactivated or escaping XCI.ResultsUsing the “XCI-informed approach,” which considers only the main effect of SNP and does not allow the SNP effect to differ by sex, no significant associations were identified for any of the phenotypes. Using the “XCI-robust approach,” intergenic SNP rs5932307 was associated with BD (P = 8.3 × 10−8), with a stronger effect in females (odds ratio in males (ORM) = 1.13, odds ratio in females for a change of two allele copies (ORW2) = 3.86).ConclusionX chromosome association studies should employ methods which account for its unique biology. Future work is needed to validate the identified associations with BD, to formally assess the performance of both approaches under different true genetic architectures, and to apply these approaches to study sex differences in other conditions.

Using Ancestry-Informative SNPs to Quantify Introgression of European Alleles into North American Red Foxes.

A recent study demonstrated that British red foxes introduced to the mid-Atlantic coastal plain (ACP) of the eastern United States during the late 18th century successfully interbred with indigenous American red foxes despite half a million year's divergence. However, a large disparity in frequency of European mitochondria (27%) versus Y chromosomes (1%) left unclear the magnitude of genetic exchange. We sought to quantify genomic introgression using 35 autosomal and 5 X-chromosome ancestry-informative markers (AIMs) in conjunction with diagnostic Y chromosome single nucleotide polymorphism (Y-SNP) markers to characterize the modern state of red foxes in the eastern United States and to gain insight into the potential role of reproductive barriers. European admixture was highest in the ACP and apparently restricted to the central eastern United States. We estimated only slightly (and nonsignificantly) European ancestry in autosomal than X-chromosome markers. European ancestry from autosomal and X-chromosome markers (36.4%) was higher than the corresponding mitochondrial (mt) DNA estimate (26.4%) in the ACP. Only 1 of 124 males (<1%) in the ACP had European Y chromosomes, which was similar to the neighboring regions, in which 2 of 99 (2%) males carried a European Y chromosome (the same haplotype). Although we could not rule out drift as the cause of low European Y-chromosome frequency, results were also consistent with F1 male infertility. In the future, more extensive genomic sequencing will enable a more thorough investigation of possible barrier genes on the X chromosome as well as throughout the genome.

Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines.

The Estonian Native Horse (ENH) is a medium-size pony found mainly in the western islands of Estonia and is well-adapted to the harsh northern climate and poor pastures. The ancestry of the ENH is debated, including alleged claims about direct descendance from the extinct Tarpan. Here we conducted a detailed analysis of the genetic makeup and relationships of the ENH based on the genotypes of 15 autosomal short tandem repeats (STRs), 18 Y chromosomal single nucleotide polymorphisms (SNPs), mitochondrial D-loop sequence and lateral gait allele in DMRT3. The study encompassed 2890 horses of 61 breeds, including 33 ENHs. We show that the expected and observed genetic diversities of the ENH are among the highest within 52 global breeds, and the highest among 8 related Northern European ponies. The genetically closest breeds to the ENH are the Finn Horse, and the geographically more distant primitive Hucul and Konik. ENH matrilines are diverse and relate to draught and Pontic-Caspian breeds. ENH patrilines relate to draught breeds, and to a unique haplogroup not described before. None of the 33 ENHs carried the “gait” mutation, but the mutation was found in 2 Huculs. The study demonstrates that the ENH is a genetically distinct and diverse breed of ancient origin with no notable pressure of selective breeding.

Genetic Architecture of Southeast-coastal Indian tribal populations: A Y-chromosomal phylogenetic analysis

BackgroundY chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages, haplogroup determinations, and paternity identifications. Since Y chromosome lacks recombination, the haplogroups of this series show a greater extent of diverse genome-specific geographical distributions and these haplogroups have been found to play a major role in forensic investigations and population genetics.Materials and methodsThe present study is aimed at determining the Y chromosomal phylogeny of two southeast coastal Indian tribal populations (Porja and Savara; N = 217), using a set of 15 bi-allelic markers on the non-recombining region of Y chromosome, representing two Austro-Asiatic (AA) language speaking populations.Results and conclusionsThe phylogenetic analysis revealed four paternal haplogroups, viz., H1*-M52, H1a*-M82, O2a*-M95, and R2-M124, with high frequency (84.79%) represented by the Austro-Asiatic-specific haplogroup O2a* (M95), confirming to the fact of O2a* haplogroup being the paternal signature of AA language family of Southeast Asians.

Study of genetic polymorphisms of 7 Y chromosome single nucleotide polymorphism loci among Mongolians from Inner Mongolia Region

To study the genetic polymorphisms of 7 Y chromosome single nucleotide polymorphisms (Y-SNPs) among unrelated Mongolian males from Inner Mongolia Region. Seven Y-SNPs with expected allelic frequencies close to 0.50:0.50 in Mongolian population were selected from databases including HapMap and relevant literature. The Y-SNPs were then analyzed among 95 unrelated male Mongolian DNA samples with ligase detection reaction (LDR) technique. Statistical analysis was carried out with Arlequin 3.5. All of the 7 Y-SNPs had 2 alleles. Seven haplotypes were identified among the 95 samples, with the haplotype diversity (HD) being 0.7990. Except for rs17316007, whose allelic frequencies was 0.832:0.168, each of the remaining Y-SNPs had a allelic frequency close to 0.50:0.50. The gene diversity (GD) for rs17316007 was 0.2825, while those of the remaining Y-SNPs were all greater than 0.4375. Except for rs17316007, the other 6 Y-SNPs showed good diversity and genetic polymorphism, and may be used for individual identification and paternity testing for the Inner Mongolia region.

1202. Multimodal Sequencing of a Clonal Case Cluster of Carbapenem-Resistant Citrobacter Reveals Unexpectedly Rapid Dynamics of KPC3-Containing Plasmids

BackgroundCarbapenem-resistant Enterobacteriaceae (CRE) are a major public health threat. We report four clonally related Citrobacter freundii isolates harboring the blaKPC-3 carbapenemase in April–May 2017 that are nearly identical to a strain from 2014 at the same institution. Despite differing by ≤5 single nucleotide polymorphisms (SNPs), these isolates exhibited dramatic differences in carbapenemase plasmid architecture.MethodsWe sequenced four carbapenem-resistant C. freundii isolates from 2017 and compared them with an ongoing CRE surveillance project at our institution. SNPs were identified from Illumina MiSeq data aligned to a reference genome using the variant caller Pilon. Plasmids were assembled from Illumina and Oxford Nanopore sequencing data using Unicycler.ResultsThe four 2017 isolates differed from one another by 0–5 chromosomal SNPs; two were identical. With one exception, these isolates differed by >38,000 SNPs from 25 C. freundii isolates sequenced from 2013 to 2017 at the same institution for CRE surveillance. The exception was a 2014 isolate that differed by 13–16 SNPs from each 2017 isolate, with 13 SNPs common to all four. Each C. freundii isolate harbored wild-type blaKPC-3. Despite the close relationship among the 2017 cluster, the plasmids harboring the blaKPC-3 genes differed dramatically: the carbapenemase occurred in one of the two different plasmids, with rearrangements between these plasmids across isolates. The related 2014 isolate harbored both plasmids, each with a separate copy of blaKPC-3. No transmission chains were found between any of the affected patients.ConclusionWGS confirmed clonality among four contemporaneous blaKPC-3-containing C. freundii isolates, and marked similarity with a 2014 isolate, within an institution. That only 13–16 SNPs varied between the 2014 and 2017 isolates suggests durable persistence of the blaKPC-3 gene within this lineage in a hospital ecosystem. The plasmids harboring these carbapenemase genes proved remarkably plastic, with plasmid loss and rearrangements occurring on the same time scale as two to three chromosomal point mutations. Combining short and long-read sequencing in a case cluster uniquely revealed unexpectedly rapid dynamics of carbapenemase plasmids, providing critical insight into their manner of spread.Disclosures M. J. Ferraro, SeLux Diagnostics: Scientific Advisor and Shareholder, Consulting fee. D. C. Hooper, SeLux Diagnostics: Scientific Advisor, Consulting fee.

Genomewide association of male reproductive traits in Aksaray Malakli dogs.

Male reproductive parameters are often used for the functional examination and evaluation of predicted genetic values for future aspects. However, these traits are relatively reliable until the measurable effects are expressed on desired traits. Therefore, we aimed to associate the single nucleotide polymorphism (SNP) genotype of the investigated characteristics and reproductive loci. A total of 46 male dogs are divided into three age groups (I ≤3years, n=19; II 4-6years; n=19, and III ≥7years, n=8). The testis, scrotum and body weight, libido sexualis and ejaculation time for each fraction were monitored as functional traits, while the pH, fractional semen volume, motility, concentration, and abnormal and dead spermatozoa rate were recorded as spermatological traits. The Affymetrix Canine 127K SNP genotyping array v2 (Affymetrix Inc., California, USA) was used for SNP genotyping. In the primary results, the scrotal circumference was found to be higher in group II compared to other groups (p<0.05) and the lowest total abnormal spermatozoa rate was found in group I (p<0.05). The normal spermatozoa rate was found to be significantly above the threshold in relation to the SNP in chromosome 17. In conclusion, this study represents an exciting first step towards SNP association with dog semen spermatological parameters. Future studies might be undertaken to evaluate this SNP region for gene-knockout and expression analysis and for fine mapping to validate and/or discover the exact position of the effect region.

Genotyping and phylogenetic placement of Bacillus anthracis isolates from Finland, a country with rare anthrax cases

BackgroundAnthrax, the zoonotic disease caused by the gram-positive bacterium Bacillus anthracis, is nowadays rare in northern parts of Europe including Finland and Scandinavia. Only two minor outbreaks of anthrax in 1988 and in 2004 and one sporadic infection in 2008 have been detected in animals in Finland since the 1970’s. Here, we report on two Finnish B. anthracis strains that were isolated from spleen and liver of a diseased calf related to the outbreak in 1988 (strain HKI4363/88) and from a local scrotum and testicle infection of a bull in 2008 (strain BA2968). These infections occurred in two rural Finnish regions, i.e., Ostrobothnia in western Finland and Päijänne Tavastia in southern Finland, respectively.ResultsThe isolates were genetically characterized by PCR-based methods such as multilocus variable number of tandem repeat analysis (MLVA) and whole genome-sequence analysis (WGS). Phylogenetic comparison of the two strains HKI4363/88 and BA2968 by chromosomal single nucleotide polymorphism (SNP) analysis grouped these organisms within their relatives of the minor canonical A-branch canSNP-group A.Br.003/004 (A.Br.V770) or canonical B-branch B.Br.001/002, respectively. Strain HKI4363/88 clustered relatively closely with other members of the A.Br.003/004 lineage from Europe, South Africa, and South America. In contrast, strain BA2968 clearly constituted a new sublineage within B.Br.001/002 with its closest relative being HYO01 from South Korea.ConclusionsOur results suggest that Finland harbors both unique (autochthonous) and more widely distributed, common clades of B. anthracis. We suspect that members of the common clades such as strains HKI4363/88 have been introduced only recently by anthropogenic activities involving importation of contaminated animal products. On the other hand, autochthonous strains such as isolate BA2968 probably have an older history of their introduction into Finland as evidenced by a high number of single nucleotide variant sites in their genomes.

SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population.

In the present study, 90 autosomal single nucleotide polymorphisms (SNPs) and 34 Y chromosomal SNPs were sequenced simultaneously using HID-Ion AmpliSeq™ Identity Panel on the Ion PGM™ platform for 125 samples in a southern Chinese population. Raw data were analyzed and forensic parameters were calculated. Haplogrouping concordance was also assessed using alternative methods based on Y-SNP haplotypes and Y-STR haplotypes. The results showed that allelic imbalance occurred more frequently with low coverage while several SNPs with high coverage were also observed with poor allelic balance, including rs214955, rs430046, rs7520386, rs876724, rs9171188, rs16981290, and rs2032631. Totally, 21,261 miscalled reads (0.28%) were observed. The rate of allele-specific miscalled reads (ASMRs) was higher than that of allele nonspecific miscalled reads (ANMRs) and associated with genetic diversity of the SNP. The ASMRs of major allele were lower than that of minor allele while there was no difference for ANMRs. The combined discrimination power (CDP) was 1-4.81×10-34 and the combined power of exclusion (CPE) was 0.99989 and 0.99999992 for duo and trio paternity testing, respectively. No significant genetic difference was detected between southern and northern Chinese populations. For haplogroup study, O2 was the predominant haplogroup and 97.01% of samples were assigned consistent haplogoups with Y-SNP and Y-STR haplotypes. In conclusion, the AmpliSeq™ Identity Panel was powerful for individual identification and trio paternity testing. ASMRs were associated with the genetic diversity and allele frequency while neither was related for ANMRs. High concordance of haplogrouping assignment can be obtained with Y-STR and Y-SNP haplotypes.