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The history of people’s movements and interactions shapes both genetic and linguistic variation. Genes and languages are transmitted separately and their distributions reflect different aspects of human history, but some demographic processes can cause them to be similarly distributed. In particular, forms of societal organization, including movements in and out of a community, may have shaped the transmission of both genes and languages. If children were more likely to learn their mother’s language than their father’s when their parents were from populations that spoke different languages or dialects, then language variation might show a closer association with maternally transmitted genetic markers than autosomal ones; this association could be further reinforced if children reside with predominantly maternal kin. We analyze the worldwide relationship between linguistic and genomic variation, leveraging the sex-biased transmission of X chromosomes to assess whether language has tended to be preferentially transmitted along the male or female line. In addition, we measure the effects of postmarital residence with female kin, matrilineal descent, and endogamy on the covariation of mitochondrial DNA and languages, using mtDNA because genomic data were available for very few populations with these ethnographic traits. We find that while there is little evidence for a consistent or widespread sex bias in the transmission of language, such biased transmission may have occurred locally in several parts of the world and might have been influenced by population-level ethnographic characteristics, such as female-based descent or residence patterns. Our results highlight the complex relationships between genes, language, ethnography, and geography. [ABSTRACT FROM AUTHOR]

Record-breaking heat waves over the past 20 years have led to a global increase in heat-related deaths, including heatstroke. Heat-related illnesses occur when the body cannot adapt to the elevated temperatures in the environment, leading to various symptoms. In severe situations, such as heatstroke, the body temperature can rise above 40°C, leading to significant injury to body systems, with particular susceptibility of the central nervous system (CNS). Neuroimaging studies conducted months or years after a heatstroke have revealed cellular damage in the cerebellum and other brain regions, including the hippocampus, midbrain, and thalamus, with the potential for long-term neurological complications in survivors of a heatstroke. This mini review aimed to describe the mechanisms and pathways underlying the development of brain injury induced by heatstroke and identify diagnostic imaging tools and biomarkers for injury to the CNS due to a heatstroke. [ABSTRACT FROM AUTHOR]

Osteoarthritis (OA) is one of the most prevalent musculoskeletal disorders and a primary cause of pain and disability among the elderly population. Research on the relationship between metalloproteins (MPs) and OA is limited, and causality remains unclear. Our objective is to utilize Mendelian randomization (MR) to explore the possible causal relationship between MPs and OA. The data on MPs were derived from a Genome-Wide Association Study (GWAS) analysis involving 3301 samples. The GWAS data for OA were obtained from an analysis involving 462,933 European individuals. In this study, a variety of two-sample Mendelian randomization methods (two-sample MR) to evaluate the causal effect of MPs on OA, including inverse variance weighted method (IVW), MR-Egger method, weighted median method (WM), simple mode, weight mode, and Wald ratio. The primary MR analysis using the IVW method reveals a significant negative correlation between Metallothionein-1F (MT-1F), zinc finger protein 134 (ZNF134), calcium/calmodulin-dependent protein kinase type 1D (CAMK1D), and EF-hand calcium-binding domain-containing protein 14 (EFCAB14) with the occurrence of osteoarthritis (OA) (p value < 0.05). However, no causal relationship was observed in the opposite direction between these MPs and OA. Notably, even in combined models accounting for confounding factors, the negative association between these four MPs and OA remained significant. Sensitivity analysis demonstrated no evidence of horizontal pleiotropy or heterogeneity, and leave-one-out analysis confirmed the robustness of the results. In this study, we have established a conspicuous association between four distinct MPs and OA. This discovery augments our understanding of potential avenues for the diagnosis and treatment of this condition. Key Points • The MR method was employed to assess the relationship between MPs and OA. • A total of four types of MPs have demonstrated inhibitory effects on the occurrence of OA. [ABSTRACT FROM AUTHOR]

Introduction: Previous observational studies have found an increased risk of frailty in patients with stroke. However, evidence of a causal relationship between stroke and frailty is scarce. The aim of this study was to investigate the potential causal relationship between stroke and frailty index (FI). Methods: Pooled data on stroke and debility were obtained from genome-wide association studies (GWAS).The MEGASTROKE Consortium provided data on stroke (N = 40,585), ischemic stroke (IS,N = 34,217), large-vessel atherosclerotic stroke (LAS,N = 4373), and cardioembolic stroke (CES,N = 7 193).Summary statistics for the FI were obtained from the most recent GWAS meta-analysis of UK BioBank participants and Swedish TwinGene participants of European ancestry (N = 175,226).Two-sample Mendelian randomization (MR) analyses were performed by inverse variance weighting (IVW), weighted median, MR-Egger regression, Simple mode, and Weighted mode, and heterogeneity and horizontal multiplicity of results were assessed using Cochran's Q test and MR-Egger regression intercept term test. Results: The results of the current MR study showed a significant correlation between stroke gene prediction and FI (odds ratio 1.104, 95% confidence interval 1.064 − 1.144, P < 0.001). In terms of stroke subtypes, IS (odds ratio 1.081, 95% confidence interval 1.044 − 1.120, P < 0.001) and LAS (odds ratio 1.037, 95% confidence interval 1.012 − 1.062, P = 0.005). There was no causal relationship between gene-predicted CES and FI. Horizontal multidimensionality was not found in the intercept test for MR Egger regression (P > 0.05), nor in the heterogeneity test (P > 0.05). Conclusions: This study provides evidence for a causal relationship between stroke and FI and offers new insights into the genetic study of FI. [ABSTRACT FROM AUTHOR]

The horseshoe bats of the Rhinolophus ferrumequinum group form a well‐defined lineage within the Afro‐Palaearctic clade of the genus Rhinolophus. The group currently comprises four species widely distributed across the Palaearctic and Afrotropic regions: R. bocharicus (Central Asia), R. clivosus (from northern Africa and the Levant through Arabian Peninsula and eastern Africa to southern Africa), R. ferrumequinum (from western Europe and northern Africa through the Balkans and Middle East to Central Asia and India) and R. nippon (southern and central China, Korea, and Japan). The broad ranges and geographical variations within these species have led to the proposal of numerous subspecies. The phylogenetic relationships and intraspecific variation of the R. ferrumequinum group were investigated using a genetic approach. One mitochondrial marker and five nuclear markers were sequenced and supplemented with available sequences for all four species of the group. Our study revealed five major lineages within the R. ferrumequinum group, resulting in the recognition of four currently known species and identification of a new species. The prior name available for this lineage/species is R. acrotis. The relationships between the lineages varied depending on the chosen marker, leaving the interspecific relations within the ferrumequinum group unresolved. In addition, the results indicated that R. clivosus experienced historic introgression from northern Africa and the Levant, resulting in replacement of its mtDNA by that of R. ferrumequinum. Together, this study introduces a new Rhinolophus species, which increases the number of species in the ferrumequinum group to five. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease. [ABSTRACT FROM AUTHOR]

Hybridization between native and introduced species is one of the most important reasons underlying the impact on biodiversity exerted by biological invasions and also one of the hardest to be detected. The East-Asian sika deer Cervus nippon has been introduced to several European countries, where it is known to generate fertile offspring with the congeneric native red deer C. elaphus, threatening its local populations with genetic pollution. Most studies on hybrid populations have been carried out in northern and eastern Europe, whereas introductions of this deer and their effects are still poorly known in Southern countries. In this study, we updated the distribution of sika deer in Italy, where the species has been present since at least 25 years ago, but where no formal assessment has ever been conducted. We confirm the occurrence of sika deer genes in formerly pure red-deer populations in central Italy by means of genetic analyses. Further range expansion of invasive sika deer and red × sika deer hybrids is likely to lead to further hybridisations and introgression, with implications for the genetic integrity of native red deer populations. [ABSTRACT FROM AUTHOR]

The aim of this research work was to find historical varieties that existed in this area before phylloxera and to identify them on the basis of historical written sources and genetic analyses. At the beginning of the 19th century, around 300 grape varieties were cultivated in Styria. Between 2020 and 2022, old vineyards were monitored at 115 locations in Styria (between the Mura and Sava rivers) in Slovenia. The directly collected samples (340 grapevine accessions) were determined by molecular analysis with 24 SSR markers. A total of 66 different genotypes were detected. After comparison with the available databases, 29 historical varieties and 37 unknown historical genotypes were identified. Several parameters were calculated to evaluate the usefulness of the selected loci in this work, and a dendrogram representing the genetic similarities between the origins was created using the neighbor-joining method to investigate possible ancestry relationships in the sample set. The most common historical varieties were 'Belina' ('Heunisch weiss'), 'Vrbovec' ('Tantovina Eihenblaetrige'), 'Ranfol' ('Ranfol beli'), and 'Pelesovna' ('Vulpea'). Varieties from the current variety list were also frequently found, such as 'Frankinja' ('Blaufraenkisch') and 'Žametovka' ('Kavčina črna'). In a few locations, one of the most important red varieties from the beginning of the 20th century was also found in this area (alongside 'Frankinja' and 'Žametovka'), i.e., 'Vranek' ('Zimmettraube balu'). At that time, this variety was planted in multi-variety vineyards and was preserved, but its importance in single-variety vineyards quickly declined due to female flower. In addition, genetic analyses have shown that 37 unknown historical genotypes have been found in this area. These genotypes need to be described ampelographically and technologically evaluated in the future. Most of the vegetative offsprings of these genotypes have already been transferred to the Meranova gene bank, where they can be accurately described ampelographically under the same pedoclimatic conditions. [ABSTRACT FROM AUTHOR]

Objective: To explore the bidirectional causal relationship between Ankylosing Spondylitis (AS) and Osteoarthritis (OA) at the genetic level within the European ancestry. Methods: We implemented a series of quality control steps to select instrumental variables (IVs) related to the exposure. We conducted two-sample Mendelian randomization (MR) using the inverse-variance weighted method as the primary approach. We adjusted significance levels using Bonferroni correction, assessed heterogeneity using Cochrane's Q test. Sensitivity analysis was conducted through leave-one-out method. Additionally, externaldatasets and relaxed IV selection criteria were employed, and multivariate MR analyses were performed for validation purposes. Finally, Bayesian colocalization (COLOC) analysis identified common genes, validating the MR results. Results: Theinvestigation focusedonthe correlationbetweenOAandAS inknee, hip, and hand joints.MR results revealed that individuals with AS exhibit a decreased risk of knee OA (OR = 0.9882, 95% CI: 0.9804-0.9962) but no significant increase in the risk of hip OA (OR = 0.9901, 95% CI: 0.9786-1.0018). Conversely, AS emerged as a risk factor for hand OA (OR = 1.0026, 95% CI: 1.0015-1.0036). In reverse-direction MR analysis, OA did not significantly influence the occurrence of AS. Importantly, minimal heterogeneity was observed in ourMRanalysis results (p>0.05), andthe robustnessof these findingswas confirmed through sensitivity analysis andmultivariateMR analysis. COLOC analysis identified four colocalized variants for AS and handOA (rs74707996, rs75240935, rs181468789, and rs748670681). Conclusion: In European population, individuals with AS have a relatively lower risk of knee OA, whereas AS serves as a risk factor for hand OA. However, no significant causal relationship was found between AS and hip OA. Additionally, it offers novel insights into genetic research on AS and OA. [ABSTRACT FROM AUTHOR]

Introduction: Fatty‐acid oxidation disorders (FAODs) are recessive genetic diseases. Materials and methods: We report here clinical and paraclinical data from a retrospective study of 44 adults with muscular FAODs from six French reference centers for neuromuscular or metabolic diseases. Results: The study cohort consisted of 44 adult patients: 14 with carnitine palmitoyl transferase 2 deficiency (32%), nine with multiple acyl‐CoA deficiency (20%), 13 with very long‐chain acyl‐CoA dehydrogenase deficiency (30%), three with long‐chain 3‐hydroxyacyl‐CoA dehydrogenase deficiency (7%), and five with short‐chain acyl‐CoA dehydrogenase deficiency (11%). Disease onset occurred during childhood in the majority of patients (59%), with a mean age at onset of 15 years (range = 0.5–35) and a mean of 12.6 years (range = 0–58) from disease onset to diagnosis. The principal symptoms were acute muscle manifestations (rhabdomyolysis, exercise intolerance, myalgia), sometimes associated with permanent muscle weakness. Episodes of rhabdomyolysis were frequent (84%), with a mean creatinine kinase level of 68,958 U/L (range = 660–300,000). General metabolic complications were observed in 58% of patients, respiratory manifestations in 18% of cases, and cardiological manifestations in 9% of cases. Fasting acylcarnitine profile was used to orient genetic explorations in 65% of cases. After a mean follow‐up of 10 years, 33% of patients were asymptomatic and 56% continued to display symptoms after exercise. The frequency of rhabdomyolysis decreased after diagnosis in 64% of cases. Conclusion: A standardized register would complete this cohort description of muscular forms of FAODs with exhaustive data, making it possible to assess the efficacy of therapeutic protocols in real‐life conditions and during the long‐term follow‐up of patients. [ABSTRACT FROM AUTHOR]

The aim of this study is to evaluate changes in variance components for dairy cows under heat stress conditions using a random regression model. The daily milk yield and pedigree records used in the research were obtained from a dairy farm in Sanliurfa, Türkiye. The records were from Holstein dairy cows registered between 2017 and 2019 at the farm. A total of 690 lactations from 690 healthy dairy cows were used in the study and the total number of cow-days was 207,003. In order to evaluate heat stress on animals meteorological data were used and collected from a public weather station located 15.04 km away from the farm. In the study, variance components were separately estimated for the comfort period (CP) and the heat stress period (HSP) using a random regression test-day model and six-knot linear spline function was used. In the study, it was observed that heat stress resulted in an increase in additive genetic, permanent environmental, and consequently, phenotypic variance. During the lactation period, the average heritability was determined to be 0.13±0.007 for CP, while it was found to be 0.18±0.010 for HSP. According to the findings obtained from the study, it was concluded that the time periods for selection should coincide with the peak milk yield under heat stress conditions, while for the period without heat stress, it should be around the 120th day of lactation. These results indicate that climatic factors such as temperature and humidity should be included in the models used for genetic parameter and breeding value estimation. Thus, it may be possible to identify dairy cattle that are genetically more tolerant to hot conditions. In this way, more successful outcomes can be achieved in selection studies.

Abstract Familial chylomicronemia syndrome (FCS) is an autosomal recessive disorder, characterized by alterations in the catabolism of chylomicrons and by increased levels of plasma triglycerides. It has been shown that about 60-90% of FCS patients have biallelic mutations in the LPL gene and the remaining patients have mutations in genes encoding proteins closely related to LPL function. The objective of this manuscript is to illustrate the different clinical scenarios of FCS presentation, and to guide practitioners on the usefulness of genetic tests in each of them. To this end, several published papers about recommendations for the diagnosis of FCS are discussed briefly, in addition to the presentation of several hypothetical cases, highlighting different clinical presentations and possible associated genetic findings. These cases illustrate the multiplicity of potential aspects of family history, clinical manifestations, biochemical parameters, and patterns of genetic variants found in genomic analyses of FCS.

The aim of this study is to evaluate changes in variance components for dairy cows under heat stress conditions using a random regression model. The daily milk yield and pedigree records used in the research were obtained from a dairy farm in Sanliurfa, Türkiye. The records were from Holstein dairy cows registered between 2017 and 2019 at the farm. A total of 690 lactations from 690 healthy dairy cows were used in the study and the total number of cow-days was 207,003. In order to evaluate heat stress on animals meteorological data were used and collected from a public weather station located 15.04 km away from the farm. In the study, variance components were separately estimated for the comfort period (CP) and the heat stress period (HSP) using a random regression test-day model and six-knot linear spline function was used. In the study, it was observed that heat stress resulted in an increase in additive genetic, permanent environmental, and consequently, phenotypic variance. During the lactation period, the average heritability was determined to be 0.13±0.007 for CP, while it was found to be 0.18±0.010 for HSP. According to the findings obtained from the study, it was concluded that the time periods for selection should coincide with the peak milk yield under heat stress conditions, while for the period without heat stress, it should be around the 120th day of lactation. These results indicate that climatic factors such as temperature and humidity should be included in the models used for genetic parameter and breeding value estimation. Thus, it may be possible to identify dairy cattle that are genetically more tolerant to hot conditions. In this way, more successful outcomes can be achieved in selection studies. [ABSTRACT FROM AUTHOR]

INTRODUCTION: Idiopathic hypogonadotropic hypogonadism (IHH) is classified into two groups-Kalman syndrome and normosmic IHH (nIHH). Half of all cases can be explained by mutations in >50 genes. Targeted gene panel testing with nexrt generation sequencing (NGS) is required for patients without typical phenotypic findings. The aim was to determine the genetic etiologies of patients with IHH using NGS, including 54 IHH-associated genes, and to present protein homology modeling and protein stability analyzes of the detected variations. METHODS: Clinical and demographic data of 16 patients (eight female), aged between 11.6-17.8 years, from different families were assessed. All patients were followed up for a diagnosis of nIHH, had normal cranial imaging, were without anterior pituitary hormone deficiency other than gonadotropins, had no sex chromosome anomaly, had no additional disease, and underwent genetic analysis with NGS between the years 2008-2021. Rare variants were classified according to the variant interpretation framework of the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology. Changes in protein structure caused by variations were modeled using RoseTTAFold and changes in protein stability resulting from variation were analyzed. RESULTS: Half of the 16 had no detectable variation. Three (18.75%) had a homozygous (pathogenic) variant in the GNRHR gene, one (6.25%) had a compound heterozygous [likely pathogenic-variants of uncertain significance (VUS)] variant in PROK2 and four (25%) each had a heterozygous (VUS) variant in HESX1, FGF8, FLRT3 and DMXL2. Protein models showed that variants interpreted as VUS according to ACMG could account for the clinical IHH. DISCUSSION AND CONCLUSION: The frequency of variation detection was similar to the literature. Modelling showed that the variant in five different genes, interpreted as VUS according to ACMG, could explain the clinical IHH.

Seed coat colour in adzuki bean is an important quality trait and closely associated with anthocyanin metabolism pathways. To further understand the inheritance of seed coat colour pattern, the inheritance between multiple seed coat colours and ivory seed were analysed using F 1:2, F 2:3 and F 3:4 populations derived from five bi-parental crosses. The differences between ivory and red mottle on ivory are controlled by a single recessive R locus and RI locus, respectively. Green, light brown and golden are all dominant to red and governed by two loci. The B (brown) locus shows dominant epistasis over T locus. The R (red) locus was recessive epistasis to B (black), T (light brown), G (golden), GR (green) and RI (red mottle on ivory) loci. The new insight into the strong recessive epistasis of the R locus will be important for gene mapping and cloning, candidate gene functional validation and quality improvement in adzuki bean. [ABSTRACT FROM AUTHOR]

Hereditary myotonia (HM) is characterized by delayed muscle relaxation after contraction as a result of a mutation in the CLCN1 gene. We describe here a complex CLCN1 variant in a mixed-breed dog with clinical and electromyographic signs of HM. Blood samples from the myotonic dog, as well as from his male littermate and parents, were analyzed via amplification of the 23 exons encoding CLCN1. After sequencing the CLCN1 gene, a complex variant was found in exon 6 c.[705T>G; 708del; 712_732del], resulting in a premature stop codon in exon 7 and a protein that was 717 amino acids shorter than the normal CLC protein. The myotonic dog was identified as homozygous recessive for the complex CLCN1 variant; its parents were heterozygous, and its male littermate was homozygous wild-type. Knowledge of the CLCN1 mutations responsible for the development of hereditary myotonia allows greater clarification of this condition. [ABSTRACT FROM AUTHOR]

Objective: Idiopathic hypogonadotropic hypogonadism (IHH) is classified into two groups-Kalman syndrome and normosmic IHH (nIHH). Half of all cases can be explained by mutations in >50 genes. Targeted gene panel testing with nexrt generation sequencing (NGS) is required for patients without typical phenotypic findings. The aim was to determine the genetic etiologies of patients with IHH using NGS, including 54 IHH-associated genes, and to present protein homology modeling and protein stability analyzes of the detected variations. Methods: Clinical and demographic data of 16 patients (eight female), aged between 11.6-17.8 years, from different families were assessed. All patients were followed up for a diagnosis of nIHH, had normal cranial imaging, were without anterior pituitary hormone deficiency other than gonadotropins, had no sex chromosome anomaly, had no additional disease, and underwent genetic analysis with NGS between the years 2008-2021. Rare variants were classified according to the variant interpretation framework of the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology. Changes in protein structure caused by variations were modeled using Rose TTA Fold and changes in protein stability resulting from variation were analyzed. Results: Half of the 16 had no detectable variation. Three (18.75%) had a homozygous (pathogenic) variant in the GNRHR gene, one (6.25%) had a compound heterozygous [likely pathogenic-variants of uncertain significance (VUS)] variant in PROK2 and four (25%) each had a heterozygous (VUS) variant in HESX1, FGF8, FLRT3 and DMXL2. Protein models showed that variants interpreted as VUS according to ACMG could account for the clinical IHH. Conclusion: The frequency of variation detection was similar to the literature. Modelling showed that the variant in five different genes, interpreted as VUS according to ACMG, could explain the clinical IHH. [ABSTRACT FROM AUTHOR]

Phenotypic sex-based differences exist for many complex traits. In other cases, phenotypes may be similar, but underlying biology may vary. Thus, sex-aware genetic analyses are becoming increasingly important for understanding the mechanisms driving these differences. To this end, we provide a guide outlining the current best practices for testing various models of sex-dependent genetic effects in complex traits and disease conditions, noting that this is an evolving field. Insights from sex-aware analyses will not only teach us about the biology of complex traits but also aid in achieving the goals of precision medicine and health equity for all. Sex-associated characteristics influence human health in many ways. This primer reviews best practices for testing various models of sex-related genetic effects in complex traits and diseases. Such analyses not only improve our understanding of biology but can also, when done properly, further precision medicine and health equity goals. [ABSTRACT FROM AUTHOR]

ABSTRACT: Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.

The aim of this research work was to find historical varieties that existed in this area before phylloxera and to identify them on the basis of historical written sources and genetic analyses. At the beginning of the 19th century, around 300 grape varieties were cultivated in Styria. Between 2020 and 2022, old vineyards were monitored at 115 locations in Styria (between the Mura and Sava rivers) in Slovenia. The directly collected samples (340 grapevine accessions) were determined by molecular analysis with 24 SSR markers. A total of 66 different genotypes were detected. After comparison with the available databases, 29 historical varieties and 37 unknown historical genotypes were identified. Several parameters were calculated to evaluate the usefulness of the selected loci in this work, and a dendrogram representing the genetic similarities between the origins was created using the neighbor-joining method to investigate possible ancestry relationships in the sample set. The most common historical varieties were ‘Belina’ (‘Heunisch weiss’), ‘Vrbovec’ (‘Tantovina Eihenblaetrige’), ‘Ranfol’ (‘Ranfol beli’), and ‘Pelesovna’ (‘Vulpea’). Varieties from the current variety list were also frequently found, such as ‘Frankinja’ (‘Blaufraenkisch’) and ‘Žametovka’ (‘Kavčina črna’). In a few locations, one of the most important red varieties from the beginning of the 20th century was also found in this area (alongside ‘Frankinja’ and ‘Žametovka’), i.e., ‘Vranek’ (‘Zimmettraube balu’). At that time, this variety was planted in multi-variety vineyards and was preserved, but its importance in single-variety vineyards quickly declined due to female flower. In addition, genetic analyses have shown that 37 unknown historical genotypes have been found in this area. These genotypes need to be described ampelographically and technologically evaluated in the future. Most of the vegetative offsprings of these genotypes have already been transferred to the Meranova gene bank, where they can be accurately described ampelographically under the same pedoclimatic conditions.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a valuable agronomic and industrial promising crop with high adaptation potentials considered as understudied species and is not attributed the interest it deserves. This investigation reports for the first time the transferability of barley nuclear microsatellites to pearl millet genome. This allowed the inference of the considerable potential of transferability of the nuclear simple sequence repeats (nSSRs) mapped from Hordeum vulgare L. genome to P. glaucum species. Out of the 42 tested SSRs, ten were found to be transferable, giving a transferability rate of 23.8%. These latter markers enabled the molecular characterization of the nine barley and nine pearl millet autochthonous landraces and revealed high levels of polymorphism and discriminatory powers. All the microsatellites were proved to be highly informative with an average polymorphic information content value of 0.74. The gene diversity index revealed a high level of diversity encompassed in both germplams with a mean H e value of 0.80. At the species level, comparable amounts of genetic variability were detected for H. vulgare and P. glaucum landraces. Furthermore, the set of ten transferable nSSRs exhibited high ability in revealing the genetic structure, differentiation and phylogenetic relationships among the studied germplasms. The new available nSSRs present an additional informative and discriminant set of molecular markers which will be useful in further genetic studies concerning the multipurpose species P. glaucum L. such as molecular fingerprinting, genetic purity assessment, genome mapping, marker-assisted breeding and conservation programs.

NIMA-related kinase 1(NEK1) gene was related to amyotrophic lateral sclerosis (ALS). However, genetic spectrum and clinical characteristics of ALS patients with NEK1 variants was largely unknown. We conducted genetic analysis on 1587 Chinese ALS patients and used software to predict the pathogenicity of NEK1 missense variant. We searched the literatures in PubMed, Embase, and Web of Science. In our ALS cohort, 42 ALS patients (2.6%) carried NEK1 variants, including 10 novel loss-of-function (LoF) variant carriers and 32 missense variant carriers. 90% of the NEK1 LoF variant carriers had upper limbs onset. The median survival time of LoF variant carriers tend to be shorter than that of probably pathogenic variant carriers (23.80 vs. 42.77 months). In 16 related studies, 167 different NEK1 variants, including 62 LoF and 105 missense variants, were found in 237 reported ALS patients. It was found that the survival time of LoF variant carriers was significantly shorter than that of missense variant carriers. Our study expanded the genotype and phenotype spectrum of ALS patients with NEK1 variants. [ABSTRACT FROM AUTHOR]

Background: Psoriasis is observationally associated with a higher risk of nonalcoholic fatty liver disease (NAFLD); however, the causal relationship between the two diseases remains unclear. Objective: We hypothesized that individuals with NAFLD or elevated liver fat content have higher risk of psoriasis and that NAFLD is a causal risk factor for psoriasis. We tested this using a Mendelian randomization approach. Methods: We included 108,835 individuals from the Danish general population, including 1,277 individuals with psoriasis and 802 individuals with NAFLD according to ICD codes. To estimate liver fat content, a subset of the participants (N = 7,416) also had a CT scan performed. First, we tested whether a diagnosis of NAFLD or elevated liver fat content was observationally associated with risk of psoriasis. Subsequently, we used the genetic variants PNPLA3 and TM6SF2, both strongly associated with NAFLD and high liver fat content, to test whether NAFLD was causally associated with increased risk of psoriasis. Results: Observationally, individuals with vs. without a diagnosis of NAFLD had higher risk of psoriasis with an odds ratio of 2.03 (95% confidence interval 1.28- 3.21). The risk of psoriasis increased in a stepwise manner with increasing liver fat content with an odds ratio of 5.00 (2.63-9.46) in individuals in the highest quartile of liver fat content compared to individuals in the lowest quartile. In genetic analyses, PNPLA3 and TM6SF2 were both associated with increased risk of NAFLD but not with increased risk of psoriasis. Conclusion: Observationally, a diagnosis of NAFLD or elevated liver fat content was associated with higher risk of psoriasis. However, using genetic variants as a proxy for NAFLD, we did not find evidence of a causal relationship between NAFLD and psoriasis. Thus, the observational association between NAFLD and psoriasis is presumably a result of shared confounding factors or reverse causation. [ABSTRACT FROM AUTHOR]

Objective: Observational studies have shown the association between iron status and osteoarthritis (OA). However, due to difficulties of determining sequential temporality, their causal association is still elusive. Based on the summary data of genome-wide association studies (GWASs) of a large-scale population, this study explored the genetic causal association between iron status and OA. Methods: First, we took a series of quality control steps to select eligible instrumental SNPs which were strongly associated with exposure. The genetic causal association between iron status and OA was analyzed using the two-sample Mendelian randomization (MR). Inverse-variance weighted (IVW), MR-Egger, weighted median, simple mode, and weighted mode methods were used for analysis. The results were mainly based on IVW (random effects), followed by sensitivity analysis. IVW and MR-Egger were used for heterogeneity testing. MR-Egger was also used for pleiotropy testing. Leave-one-SNP-out analysis was used to identify single nucleotide polymorphisms (SNPs) with potential impact. Maximum likelihood, penalized weighted median, and IVW (fixed effects) were performed to further validate the reliability of results. Results: IVW results showed that transferrin saturation had a positive causal association with knee osteoarthritis (KOA), hip osteoarthritis (HOA) and KOA or HOA (p < 0.05, OR > 1), and there was a negative causal association between transferrin and HOA and KOA or HOA (p < 0.05, OR < 1). The results of heterogeneity test showed that our IVW analysis results were basically free of heterogeneity (p > 0.05). The results of the pleiotropy test showed that there was no pleiotropy in our IVW analysis (p > 0.05). The analysis results of maximum likelihood, penalized weighted median and IVW (fixed effects) were consistent with our IVW results. No genetic causal association was found between serum iron and ferritin and OA. Conclusions: This study provides evidence of the causal association between iron status and OA, which provides novel insights to the genetic research of OA. [ABSTRACT FROM AUTHOR]

BackgroundPsoriasis is observationally associated with a higher risk of non-alcoholic fatty liver disease (NAFLD); however, the causal relationship between the two diseases remains unclear.ObjectiveWe hypothesized that individuals with NAFLD or elevated liver fat content have higher risk of psoriasis and that NAFLD is a causal risk factor for psoriasis. We tested this using a Mendelian randomization approach.MethodsWe included 108,835 individuals from the Danish general population, including 1,277 individuals with psoriasis and 802 individuals with NAFLD according to ICD codes. To estimate liver fat content, a subset of the participants (N = 7,416) also had a CT scan performed. First, we tested whether a diagnosis of NAFLD or elevated liver fat content was observationally associated with risk of psoriasis. Subsequently, we used the genetic variants PNPLA3 and TM6SF2, both strongly associated with NAFLD and high liver fat content, to test whether NAFLD was causally associated with increased risk of psoriasis.ResultsObservationally, individuals with vs. without a diagnosis of NAFLD had higher risk of psoriasis with an odds ratio of 2.03 (95% confidence interval 1.28-3.21). The risk of psoriasis increased in a stepwise manner with increasing liver fat content with an odds ratio of 5.00 (2.63-9.46) in individuals in the highest quartile of liver fat content compared to individuals in the lowest quartile. In genetic analyses, PNPLA3 and TM6SF2 were both associated with increased risk of NAFLD but not with increased risk of psoriasis.ConclusionObservationally, a diagnosis of NAFLD or elevated liver fat content was associated with higher risk of psoriasis. However, using genetic variants as a proxy for NAFLD, we did not find evidence of a causal relationship between NAFLD and psoriasis. Thus, the observational association between NAFLD and psoriasis is presumably a result of shared confounding factors or reverse causation.

This paper attempts to review the methods and experiences in preserving and restoring grayling stocks in water bodies, which this species currently inhabits or previously inhabited. The study includes a retrospective analysis of the status of grayling populations in their natural conditions as well as a review of current ecological and anthropogenic factors negatively impacting the survival and reproduction of the European grayling in Carpathians. The review includes both foreign and Ukrainian experiences in the creation of broodstocks, which could be used to restore grayling populations in Ukrainian waters in the future. We discuss the use of molecular methods for controlling and maintaining the optimal state of European grayling broodstocks at fish hatcheries as well as their application in supporting river restocking efforts to restore ichthyosis is also discussed. We highlight the state and contemporary problems for the existence of the European grayling in Ukraine. The review presents fundamental approaches using aquaculture and molecular methods that can be employed to address ongoing tasks and challenges in grayling stock recovery. [ABSTRACT FROM AUTHOR]

OBJECTIVE: Our primary objective was to identify discrete and syndromic cases of Pectus excavatum (PE) and Pectus carinatum (PC). We also intended to highlight the significance of further genetic exploration in clinically suspected syndromic cases of PC and PE. Pectus excavatum (PE) and Pectus carinatum (PC) are the most common morphological chest wall deformities. Although various hypotheses have been put forth, the pathogenesis of both entities is largely unknown. Clinicians often refer such cases for further genetic evaluation to exclude an associated underlying connective tissue disorder or a syndrome. Additionally, a detailed anamnesis with focused family history and thorough dysmorphological physical examination was done. PE and PC are considered isolated abnormalities if there is the absence of features of other syndromes, eliminating the need for further genetic evaluations. It is believed that the pattern of inheritance of these non-syndromic isolated PE and PC cases with positive family history could be multifactorial in nature. The recurrence risk of such isolated cases is thought to be low. Further diagnostic studies are indicated as PE and PC could be a part of a syndrome. Among the many syndromes, the most common monogenic syndromes associated with PE and PC are Marfan's and Noonan's. PATIENTS AND METHODS: After obtaining the consent, we compiled a database of the patients who presented with chest wall deformities during the period 2017-2019. We selected 70 cases with PC and PE deformities to identify the discrete and syndromic PC and PE cases. During the study, we perused the cytogenetic and/or molecular analyses, that had been conducted to confirm the clinically suspected syndromic cases. We also scrutinized for the presence of PC and PE cases that are associated with the rare syndrome (s). RESULTS: Various genetic abnormalities were identified in 28 (40%) of the 70 cases that had been diagnosed with chest wall abnormalities. Along with PE and PC, other thoracic wall abnormalities were also identified, such as the broad chest, bell-shaped thorax, and elongated or enlarged thorax. One case of a rare genetic disorder of Morquio syndrome associated with PC was also identified. Novel (previously unpublished) genomic variants are reported here. CONCLUSIONS: It is important to delve deeper when encountering cases of PE and PC by conducting a further genetic exploration of such cases to identify syndromic associations that cause other structural and functional disorders, diagnosis of which might be missed during the early developmental period. Early identification of such disorders may help us correcting the defects, slowing the progression of disease processes, and preparing better to deal with the potential outcome. [ABSTRACT FROM AUTHOR]

Uveal melanoma (UM) is the most frequently found primary intraocular tumor, although it accounts for only 5% of all melanomas. Despite novel systemic therapies, patient survival has remained poor. Indeed, almost half of UM patients develop metastases from micro-metastases which were undetectable at diagnosis. Genetic analysis is crucial for metastatic risk prediction, as well as for patient management and follow-up. Several prognostic parameters have been explored, including tumor location, basal dimension and thickness, histopathologic cell type, vascular mimicry patterns, and infiltrating lymphocytes. Herein, the Authors review the available literature concerning cytogenetic prognostic markers and biochemical pathways correlated to UM metastasis development. [ABSTRACT FROM AUTHOR]

The mouse bile duct tapeworm Hymenolepis microstoma, is a potentially zoonotic species with a wide variety of reported definitive hosts of rodent genera. In the present study the occurrence of H. microstoma in free-living small mammals in selected areas of Slovakia and the retrospective analysis of epidemiological data published in Slovakia were performed. Hymenolepis microstoma was detected in two animal species, the common shrew (Sorex araneus) and the European hamster (Cricetus cricetus) of 186 small mammals examined from two ecosystems, urban and natural ecosystem of national park. No mention about the presence of this parasite in Slovakia in the past was found following a bibliographical search. Partial sequences of the nuclear paramyosin gene showed the shrew isolate placed in a subclade together with H. microstoma from Portugal, with high bootstrap value for its differentiation from the sister species Hymenolepis nana. Similarly, the analysis of the nuclear ribosomal ITS region placed the hamster isolate in the cluster composed of H. microstoma from Australia, Spain and Portugal. The Slovak isolate was the most distinctive sample among available H. microstoma, differing in 1.4 – 1.9% of nucleotides from the remaining isolates. The difference (seven of 17 nucleotide positions) was partially due to indel polymorphisms associated with two and five nucleotides. To our knowledge, these are the first reports of H. microstoma in Central Europe and also the first record of infection in the common shrew. A recently indicated zoonotic potential of H. microstoma along with a possibility of its direct transmission between animals and/or humans without the need of intermediate hosts pose a public health concern in contaminated areas of Slovakia. The use of molecular techniques may substantially facilitate more thorough understanding of the epidemiological situation of H. microstoma and related tapeworms in various ecosystems of the country.

Uveal melanoma (UM) is the most frequently found primary intraocular tumor, although it accounts for only 5% of all melanomas. Despite novel systemic therapies, patient survival has remained poor. Indeed, almost half of UM patients develop metastases from micro-metastases which were undetectable at diagnosis. Genetic analysis is crucial for metastatic risk prediction, as well as for patient management and follow-up. Several prognostic parameters have been explored, including tumor location, basal dimension and thickness, histopathologic cell type, vascular mimicry patterns, and infiltrating lymphocytes. Herein, the Authors review the available literature concerning cytogenetic prognostic markers and biochemical pathways correlated to UM metastasis development.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a valuable agronomic and industrial promising crop with high adaptation potentials considered as understudied species and is not attributed the interest it deserves. This investigation reports for the first time the transfer- ability of barley nuclear microsatellites to pearl millet genome. This allowed the inference of the considerable potential of transferability of the nuclear simple sequence repeats (nSSRs) mapped from Hordeum vulgare L. genome to P. glaucum species. Out of the 42 tested SSRs, ten were found to be transferable, giving a transferability rate of 23.8%. These latter markers enabled the molecular characterization of the nine barley and nine pearl millet autochthonous landraces and revealed high levels of poly- morphism and discriminatory powers. All the microsatellites were proved to be highly informative with an average poly- morphic information content value of 0.74. The gene diversity index revealed a high level of diversity encompassed in both germplams with a mean He value of 0.80. At the species level, comparable amounts of genetic variability were detected for H. vulgare and P. glaucum landraces. Furthermore, the set of ten transferable nSSRs exhibited high ability in revealing the genetic structure, differentiation and phylogenetic relation- ships among the studied germplasms. The new available nSSRs present an additional informative and discriminant set of molecular markers which will be useful in further genetic studies concerning the multipurpose species P. glaucum L. such as molecular fingerprinting, genetic purity assessment, genome mapping, marker-assisted breeding and conservation programs. [ABSTRACT FROM AUTHOR]

Purpose: Bilateral childhood cataracts can be caused by a metabolic disease, constitute a part of a syndrome, run in families, be sporadic or iatrogenic. The amount of work-up needed to establish a cause is discussed and the aim of the present study was to evaluate causes of bilateral childhood cataract. Methods: Chart review of 211 Danish children with bilateral cataracts. Information on work-up was retrieved with special focus on general health, metabolic screening, evaluation for congenital infections and genetic testing. Results: Cataract was seen in combination with systemic disease in 40.8%, 29.4% had hereditary cataracts, 27.0% had isolated cataract, in 1.4% it was associated with ocular malformations and 1.4% had been born prematurely without any other sequelae than the cataract. A genetic cause could be demonstrated in 74 children. Conclusion: Systemic comorbidities are very common in children with cataract and are not always known prior to the diagnosis of cataract. Genetic evaluation, especially targeted analyses, provided a molecular genetic diagnosis in a large proportion of those tested but it also failed to provide a molecular genetic diagnosis in some patients with a family history suggesting autosomal dominant inheritance. Most importantly, in some patients, genetic work-up provided a diagnosis in patients where it had therapeutic consequences and where the systemic disease would have caused irreversible damage, had it not been treated timely. Given the high prevalence of systemic disease, it seems advisable to co-manage children with bilateral cataracts with a pediatrician and to include genetic evaluation as part of the work-up. [ABSTRACT FROM AUTHOR]

Guava (Psidium guajava L., Myrtaceae) is a Neotropical fruit that is widely consumed around the world. However, its evolutionary history and domestication process are unknown. Here we examine available ecological, taxonomic, genetic, archeological, and historical evidence about guava. Guava needs full sunlight, warm temperatures, and well-distributed rainfall throughout the year to grow, but tolerates drought. Zoochory and anthropochory are the main forms of dispersal. Guava’s phylogenetic relationships with other species of the genus Psidium are unclear. A group of six species that share several morphological characteristics are tentatively accepted as the Psidium guajava complex. DNA analyses are limited to the characterization of crop genetic diversity within localities and do not account for possible evolutionary and domestication scenarios. A significant amount of archeological information exists, with a greater number and older records in South America than in Mesoamerica, where there are also numerous historical records. From this information, we propose that: (1) the guava ancestor may have originated during the Middle or Late Miocene, and the savannas and semi-deciduous forests of South America formed during the Late Pleistocene would have been the most appropriate ecosystems for its growth, (2) the megafauna were important dispersers for guava, (3) dispersal by humans during the Holocene expanded guava’s geographic range, including to the southwestern Amazonian lowlands, (4) where its domestication may have started, and (5) with the European conquest of the Neotropics, accompanied by their domestic animals, new contact routes between previously remote guava populations were established. These proposals could direct future research on the evolutionary and domestication process of guava.

The ability to use genome-wide association studies (GWAS) for genetic discovery depends upon our ability to distinguish true causative from false positive association signals. Population structure (PS) has been shown to cause false positive signals in GWAS. PS correction is routinely used for analysis of human GWAS results, and it has been assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been carefully investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Rather than treat PS as a confounding variable, we examined it as a response variable. Surprisingly, we found that PS had a minimal impact on datasets measuring responses in ≤20 strains; and had surprisingly little impact on most datasets characterizing 21 – 40 inbred strains. Moreover, we show that true positive association signals arising from haplotype blocks, SNPs or indels, which were experimentally demonstrated to be causative for trait differences, would be rejected if PS correction were applied to them. Our results indicate because of the special conditions created by GWAS (the use of inbred strains, small sample sizes) PS assessment results should be carefully evaluated in conjunction with other criteria, when murine GWAS results are evaluated.

Guava (Psidium guajava L., Myrtaceae) is a Neotropical fruit that is widely consumed around the world. However, its evolutionary history and domestication process are unknown. Here we examine available ecological, taxonomic, genetic, archeological, and historical evidence about guava. Guava needs full sunlight, warm temperatures, and well-distributed rainfall throughout the year to grow, but tolerates drought. Zoochory and anthropochory are the main forms of dispersal. Guava's phylogenetic relationships with other species of the genus Psidium are unclear. A group of six species that share several morphological characteristics are tentatively accepted as the Psidium guajava complex. DNA analyses are limited to the characterization of crop genetic diversity within localities and do not account for possible evolutionary and domestication scenarios. A significant amount of archeological information exists, with a greater number and older records in South America than in Mesoamerica, where there are also numerous historical records. From this information, we propose that: (1) the guava ancestor may have originated during the Middle or Late Miocene, and the savannas and semi-deciduous forests of South America formed during the Late Pleistocene would have been the most appropriate ecosystems for its growth, (2) the megafauna were important dispersers for guava, (3) dispersal by humans during the Holocene expanded guava's geographic range, including to the southwestern Amazonian lowlands, (4) where its domestication may have started, and (5) with the European conquest of the Neotropics, accompanied by their domestic animals, new contact routes between previously remote guava populations were established. These proposals could direct future research on the evolutionary and domestication process of guava. [ABSTRACT FROM AUTHOR]

The ability to use genome-wide association studies (GWAS) for genetic discovery depends upon our ability to distinguish true causative from false positive association signals. Population structure (PS) has been shown to cause false positive signals in GWAS. PS correction is routinely used for analysis of human GWAS results, and it has been assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been carefully investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Rather than treat PS as a confounding variable, we examined it as a response variable. Surprisingly, we found that PS had a minimal impact on datasets measuring responses in ≤20 strains; and had surprisingly little impact on most datasets characterizing 21 – 40 inbred strains. Moreover, we show that true positive association signals arising from haplotype blocks, SNPs or indels, which were experimentally demonstrated to be causative for trait differences, would be rejected if PS correction were applied to them. Our results indicate because of the special conditions created by GWAS (the use of inbred strains, small sample sizes) PS assessment results should be carefully evaluated in conjunction with other criteria, when murine GWAS results are evaluated. [ABSTRACT FROM AUTHOR]

In northern Australia, wild dog populations potentially interact with domestic dogs from remote communities, which would create opportunities for disease transmission at the wild–domestic interface. An example is rabies, in the event of an incursion into northern Australia. However, the likelihood of such wild–domestic interactions is ambiguous. Hybridisation analyses based on 23 microsatellite DNA markers were performed on canine‐origin scats collected in bushland areas around remote Indigenous communities in the Northern Peninsula Area, Queensland. Sufficient DNA was extracted from 6 of 41 scats to assess the percentage of dingo purity. These scats most likely originated from two 'pure' domestic dogs (0% dingo purity), one hybrid (20% dingo purity) and three 'pure' dingoes (92%–98% dingo purity). The two domestic dog samples were collected in the vicinity of communities. The location of two of the dingo‐origin samples provides genetic evidence that dingoes are present in areas close to the communities. The availability of anthropogenic food resources likely creates opportunities for interactions with domestic dogs in the region. The hybrid sample demonstrates the occurrence of antecedent contacts between both populations by means of mating and supports the likelihood of a spatio‐temporal overlap at the wild–domestic interface. This represents the first genetic survey involving a wild dog population of equatorial northern Queensland, with evidence of dingo purity. Our results have implications for potential disease transmission within a priority area for biosecurity in northern Australia. [ABSTRACT FROM AUTHOR]

Coronaviruses are the well-known cause of severe respiratory, enteric and systemic infections in a wide range of hosts including man, mammals, fish, and avian. The scientific interest on coronaviruses increased after the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) outbreaks in 2002-2003 followed by Middle East Respiratory Syndrome CoV (MERS-CoV). This decade’s first CoV, named 2019-nCoV, emerged from Wuhan, China, and declared as ‘Public Health Emergency of International Concern’ on January 30th, 2020 by the World Health Organization (WHO). As on February 4, 2020, 425 deaths reported in China only and one death outside China (Philippines). In a short span of time, the virus spread has been noted in 24 countries. The zoonotic transmission (animal-to-human) is suspected as the route of disease origin. The genetic analyses predict bats as the most probable source of 2019-nCoV though further investigations needed to confirm the origin of the novel virus. The ongoing nCoV outbreak highlights the hidden wild animal reservoir of the deadly viruses and possible threat of spillover zoonoses as well. The successful virus isolation attempts have made doors open for developing better diagnostics and effective vaccines helping in combating the spread of the virus to newer areas.

We created a suite of packages to enable analysis of extremely large genomic data sets (potentially millions of individuals and millions of molecular markers) within the R environment. The package offers: a matrix-like interface for .bed files (PLINK’s binary format for genotype data), a novel class of linked arrays that allows linking data stored in multiple files to form a single array accessible from the R computing environment, methods for parallel computing capabilities that can carry out computations on very large data sets without loading the entire data into memory and a basic set of methods for statistical genetic analyses. The package is accessible through CRAN and GitHub. In this note, we describe the classes and methods implemented in each of the packages that make the suite and illustrate the use of the packages using data from the UK Biobank.

Abstract Background Autosomal recessive congenital ichthyosis (ARCI) is a rare genetically heterogeneous cutaneous disease predominantly characterized by erythroderma, generalized abnormal scaling of the whole body and a collodion membrane at birth. Numerous causative genes have been demonstrated to be responsible for ARCI including PNPLA1 which can cause ARCI type 10. The objectives of this study are to describe clinical features of three ARCI patients from two Chinese unrelated families and to identify the underlying causative mutations. Methods Genomic DNA was extracted from peripheral venous blood obtained from the two Chinese ARCI families in Shandong province. Subsequently, targeted regions sequencing (TRS) followed by Sanger sequencing was conducted to identify and validate the likely pathogenic mutations of the ARCI families. Results Genetic analyses revealed four novel PNPLA1 variants that are predicted to be probably to lead to ARCI in three patients of two families. Patient 1 in one family was in compound heterozygous status for c.604delC/p.Arg202Glyfs*27 and c.820dupC/p.Arg274Profs*15, whereas c.738_742delinsCCCACAGATCCTGC/ p.Gly247_Tyr248delinsProGlnIleLeuHis, and c.816dupC/p.Arg274Profs*15 were found in patient 2 and 3 of the other family. In addition, these variants cosegregate in the two pedigrees and are all within highly conserved regions of the PNPLA1 protein, which indicate that the four mutations are likely pathogenic. Conclusion Our findings not only broaden the mutational spectrum of PNPLA1, but also contribute to establishing genotype–phenotype correlations for different forms of ARCI.

Aromia bungii (Faldermann) (Coleoptera: Cerambycidae) is an invasive pest, damaging Rosaceae trees (particularly Prunus) in Japan and Europe. The establishment of this beetle in Japan was first detected in 2012, and subsequently, it has rapidly expanded its distribution. Currently, Japanese populations of A. bungii are widely distributed in six non-contiguous regions. In this study, we compared the nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 of the populations in these six regions in Japan to examine whether multiple introductions or human-mediated long-distance dispersal have contributed to the non-contiguous distribution of A. bungii. Seven haplotypes were detected from Japanese populations, and one of these was identical to a sequence deposited from China. One to two haplotypes were detected in each region, suggesting a genetic bottleneck. Detected haplotypes differed between introduced regions, although two regions shared a single haplotype. These results suggest that multiple independent introductions of A. bungii have contributed to its non-contiguous distribution in Japan. Quarantine measures for wood-packing materials in trade need to be strengthened to prevent the establishment of further populations of A. bungii.

Abstract Background Pulmonary arterial hypertension (PAH) is a progressive and fatal disorder associated with high pulmonary artery pressure. Genetic testing enables early diagnosis and offers an opportunity for family screening. To identify genetic mutations and help make a precise diagnosis, we performed genetic testing in 191 probands with PAH and tried to analyze the genotype-phenotype correlation. Methods Initially, PAH samples (n = 119) were submitted to BMPR2 screening using Sanger sequencing. Later, we developed a PAH panel test to identify causal mutations in 13 genes related to PAH and tried to call BMPR2 copy number variations (CNVs) with the panel data. Multiplex ligation-dependent probe amplification (MLPA) was used to search for CNVs in BMPR2, ACVRL1 and ENG. Notably, EIF2AK4 gene was also involved in the panel, which allowed to distinguish pulmonary veno-occlusive disease (PVOD)/pulmonary capillary hemangiomatosis (PCH) patients from idiopathic PAH (IPAH). Characteristics of patients were compared using t test for continuous variables. Results Pathogenic BMPR2 mutations were detected most frequently in 32 (17.9%) IPAH and 5 (41.7%) heritable PAH (HPAH) patients by sequencing, and 12 BMPR2 CNVs called from the panel data were all successfully confirmed by MLPA analysis. In addition, homozygous or compound heterozygous EIF2AK4 mutations were identified in 6 patients, who should be corrected to a diagnosis of PVOD/PCH. Genotype-phenotype correlation analysis revealed that PAH patients with BMPR2 mutations were younger at diagnosis (27.2y vs. 31.6y, p = 0.0003) and exhibited more severe pulmonary hemodynamic impairment and a worse cardiac index compared with those without BMPR2 mutations. Conclusions The panel assay represented a highly valuable tool in PAH genetic testing, not only for the detection of small sequence alterations, but also for an indication of BMPR2 CNVs, which had implications for the specific samples to perform further MLPA assay. Analyses of PAH causal genes have a great help to clinical diagnosis and deep implications in disease treatment.

BACKGROUND Evolution and spread of resistance to glyphosate in kochia [Bassia scoparia (L.) A.J. Scott] is a major challenge for the sustainability of glyphosate‐resistant crop technology in this region. Dicamba offers a viable option to manage glyphosate‐resistant kochia. However, the recent and rapid evolution of dicamba resistance in glyphosate‐resistant kochia populations in Kansas (KS), and other states in the USA is a threat to the management of this weed. Our previous research suggests that two distinct mechanisms confer dicamba resistance in KS (KSUR) and NE (CSUR) kochia. CSUR kochia is dicamba‐resistant due to a double mutation in an auxin and dicamba coreceptor gene (Aux/IAA16), and CSUR kochia plants show reduced dicamba translocation. However, the mechanism of dicamba resistance in KSUR is not known. The objective of this research was to determine if dicamba resistance in KSUR is due to a different mechanism and therefore evolved independently from CSUR by measuring whether the resistance traits are chromosomally linked. RESULTS: The F1 and F2 progenies from KSUR × CSUR were generated. Single dicamba rate tests were conducted using the F1 and F2 progeny. The results indicate that two different genes confer dicamba resistance in KSUR and CSUR; importantly, these two genes are not linked. CONCLUSION: This research provides evidence that different populations of kochia have independently evolved resistance to dicamba by different mechanisms, and we confirmed that the genes conferring resistance to the same herbicide in different populations are not chromosomally linked. [ABSTRACT FROM AUTHOR]

Abstract Objective The study aimed to investigate the suitability of DNA extracted from saliva for high throughput molecular genotyping and DNA methylation platforms by comparing its performance with that of DNA extracted from blood. The genome-wide methylation profile, using the Infinium HumanMethylation450 Beadchip array® (Illumina, San Diego, CA), was measured for 20 DNA samples. Common genetic variation was measured, using the Infinium HumanCore Beadchip® (Illumina, San Diego, CA) for 4 samples (matching samples from 2 people). Results DNA from blood and saliva returned genotyping call rates and reproducibility frequencies of > 99%. High-quality DNA methylation data was obtained from both saliva and blood DNA, with average detection p-values for each sample ranging from 0.001 to 0.006. Slightly higher global DNA methylation levels were observed in whole blood DNA than saliva DNA. Correlations between individuals for each sample type were generally greater than correlations between two sample types from the same individual (Pearson’s correlation, r = 0.9696 in 10 pairs of matched blood and saliva derived DNA, r = 0.9702 between saliva samples, and r = 0.9769 between blood derived DNA). Saliva yields DNA of sufficient quantity and quality to compare favourably with blood as a source of DNA for genetic and epigenetic research purposes.

A novel papillomavirus (PV) associated with hyperplastic nodules scattered over the muco-cutaneous border of the oral cavity of a dead, wild, subadult northern sea otter Enhydra lutris kenyoni (NSO) in 2004 in Homer, Alaska, USA, was genetically characterized. Primers for the amplification of 2 large overlapping DNA fragments that contained the complete genome of the NSO PV were designed. Sanger methodology generated sequences from which new specific primers were designed for the primer-walking approach. The NSO PV genome consists of 8085 nucleotides and contains an early region composed of E6, E7, E1, and E2 open reading frames (ORFs), an E4 ORF (contained within E2) lacking an in-frame proximal ATG start codon, an unusually long (907 nucleotide) stretch lacking any ORFs, a late region that contains the capsid genes L2 and L1, and a non-coding regulatory region (ncRR). This NSO PV has been tentatively named Enhydra lutris kenyoni PV2 (ElkPV2). Pairwise and multiple sequence alignments of the complete L1 ORF nucleotides and concatenated E1-E2-L1 amino acid sequences showed that the NSO PV is a novel PV, phylogenetically most closely related to southern sea otter PV1. The carboxy end of the E6 oncoprotein does not contain the PDZ-binding motif with a strong correlation with oncogenicity, suggesting a low-risk PV, which is in agreement with histopathological findings. However, the ElkPV2 E7 oncoprotein does contain the retinoblastoma (pRb) binding domain LXCXE (LQCYE in ElkPV2), associated with oncogenicity in some high-risk PVs. Further studies on the prevalence and clinical significance of ElkPV2 infections in NSO are needed.

The first Mediterranean record of the pomacanthid Holacanthus africanus, caught within the Maltese waters, was assigned based on morphological and meristic characters. However, molecular and genetic analyses are required to confirm the taxonomic determination and avoid misidentification given the abundance of closely-related Pomacanthidae species and the biogeographic significance of this record for the Mediterranean. At the species level, the analyzed specimens gave a 99.7% identity match with H. africanus. This study represents yet another example of molecular analyses supplementing the conclusions of conventional morphological identification exercises. [ABSTRACT FROM AUTHOR]

• Testis size is highly heritable in pigs. • Quadratic relationship between sire testis area and female reproductive performance. • Linear relationship between sire testis width and female reproductive performance. • Results suggest the use of testis size as parameter for culling purposes in pigs. Selection for female farrowing performance is challenging to the swine industry due to the low heritability. Previous studies have suggested testis size as an indicator of reproductive performance. Thus, to determine the effectiveness of measuring testis size to identify sires of reproductive superior sows, 161 Yorkshire and Landrace boars were measured for width (TW) and area (TA). Farrowing performance was collected for 384 sows, daughters of 13 of the 161 boars. For heritability estimates (h 2), the fixed effects of age (boar traits only), breed, contemporary group (CG), and parity (sow traits only), and the random effects of animal and permanent environment (sow traits only) were included in the model. Poisson phenotypic regression of the reproductive traits of daughters on the testis size of sires was performed including the fixed effects of parity, breeds of sow and sire, and TW or TA, and the random effects of sow and CG. For testis size, h 2 were 0.69 and 0.66 for TA and TW, respectively. For reproductive traits, h2 ranged from 0.01 to 0.18. There were quadratic and linear relationships (P < 0.05) between reproductive traits in sows with TA and TW, respectively. Optimal performance for survival traits was obtained when TA of sires was within 17.2–18.5 cm2, which did not overlap with the range that resulted in greater mortality (15.8–16.3 cm2). With regards to TW, there was a linear increase of survival traits (P < 0.05) as TW increased, but not mortality (P ≥ 0.11). Phenotypic assessment of testis size of sires may be a useful tool to cull animals for breeding, improving female performance. [ABSTRACT FROM AUTHOR]