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The present study aimed to elucidate the population structure and genetic diversity along with the estimation of genealogical parameters in Vrindavani cattle using pedigree data. The study was based on pedigree data on 12,718 animals, spread across multiple generations during a 52-year period (between 1971 and 2023). The pedigree data was used to estimate different population genealogical parameters including the generation interval; pedigree completeness; rate and level of inbreeding; effective population size; and parameters characterizing the probabilities of gene origin. The ENDOG program was used for estimation of different parameters while using population after 2010 as reference cohort. The results revealed the maximum number of generations (MG) to be 13, while the numbers of completed (CG) and equivalent generations (EqG) were 3.23 and 1.95, respectively. The mean generation interval for the population was 6.9 years. The average inbreeding coefficient of animals in the whole and reference population was 1.11 and 3.44%, respectively; with 0.68% rate of inbreeding per generation. The average additive relationship among all the animals and those in the reference population was 1.16 and 5.49%, respectively. The average effective population sizes for the maximum, equivalent, and complete generations were 115.56, 56.42, and 46.02, respectively. The effective population size on the basis of regression and log-regression on birth date was 77.40 and 71.24, respectively. The probabilities of gene origin were estimated by the effective number of founders (fe) and ancestors (fa), which was 115 and 78, respectively. The fe/fa ratio in the reference population was 1.20, indicating that occasional bottlenecks may have occurred in the population. The analysis revealed a loss of 5.3% of total heterozygosity as compared to base population, though significant variability exists in the latest generations. The results revealed that considerable genetic variability exists within the population that may be exploited through appropriate breed improvement programs targeting various economic traits. [ABSTRACT FROM AUTHOR]

Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm‐to‐wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidisation protocols may, on occasion, produce 'failed triploids' displaying diploidy, aneuploidy and aberrant inheritance. The potentially negative consequences for conservation and animal welfare motivate the need for methods to evaluate the success of ploidy‐manipulation protocols early in the production process. We developed a semi‐automated version of the MAC‐PR (microsatellite DNA allele counting – peak ratios) method to resolve the allelic configuration of large numbers of individuals across a panel of microsatellite markers that can be used to infer ploidy, pedigree and inheritance aberrations. We demonstrate an application of the approach using material from a series of Atlantic salmon (Salmo salar) breeding experiments where ploidy was manipulated using a hydrostatic pressure treatment. We validated the approach to infer ploidy against blood smears, finding a > 99% agreement between these methods, and demonstrate its potential utility to infer ploidy as early as the embryonic stage. Furthermore, we present tools to assign diploid and triploid progeny to families and to detect aberrant inheritance, which may be useful for breeding programmes that utilise ploidy manipulation techniques. The approach adds to the ploidy verification toolbox. The increased precision in detecting ploidy and inheritance aberrations will facilitate the ability of triploidisation programmes to prevent farm‐to‐wild introgression. [ABSTRACT FROM AUTHOR]

Kennel club registrations have been used in a number of studies to estimate ownership levels and fashion trends among dog breeds. They cannot, however, give a complete overview of the contemporary trade in pet dogs, and additionally, may be particularly poor at monitoring trends among some welfare-vulnerable breeds. Here, we compared data from online advertisements for the UK sales of single-breed dogs over an 18-month period, with equivalent data (including for prior and subsequent years) from the UK Kennel Club. Kennel Club registration rates and breed popularity rates online were positively correlated. However, some breeds, including the Jack Russell terrier, Border collie and Chihuahua were considerably over-represented in online advertisements when compared with Kennel Club registrations, indicating a hidden market for certain breeds. In addition, the online dataset provided information on the sale and re-homing of adult dogs, showing high rates of adult homing of the Staffordshire bull terrier, Siberian husky and Rottweiler. We conclude that online pet-sales websites are an important and complementary source of data about the market in, and popularity of, a wide range of dog breeds. [ABSTRACT FROM AUTHOR]

Background: Cascade testing can offer improved surveillance and timely introduction of clinical management for the at-risk biological relatives. Data on cascade testing and costs in mitochondrial diseases are lacking. To address this gap, we performed a cross-sectional retrospective study to provide a framework for cascade testing in mitochondrial diseases, to estimate the eligibility versus real-time uptake of cascade testing and to evaluate the cost of the genetic diagnosis of index cases and the cost of predictive cascade testing. Methods: Data was collected through retrospective chart review. The variant inheritance pattern guided the identification of eligible first-degree relatives: (i) Males with mitochondrial DNA (mtDNA) single nucleotide variants (SNVs) – siblings and mothers. (ii) Females with mtDNA SNVs – siblings, mothers and offspring. (iii) Autosomal Dominant (AD) nuclear DNA (nDNA) variants – siblings, offspring and both parents. (iv) Autosomal Recessive (AR) nDNA variants – siblings. Results: We recruited 99 participants from the Adult Mitochondrial Disease Clinic in Sydney. The uptake of cascade testing was 55.2% in the mtDNA group, 55.8% in the AD nDNA group and 0% in AR nDNA group. Of the relatives in mtDNA group who underwent cascade testing, 65.4% were symptomatic, 20.5% were oligosymptomatic and 14.1% were asymptomatic. The mean cost of cascade testing for eligible first-degree relatives (mtDNA group: $694.7; AD nDNA group: $899.1) was lower than the corresponding index case (mtDNA group: $4578.4; AD nDNA group: $5715.1) (p < 0.001). Conclusion: The demand for cascade testing in mitochondrial diseases varies according to the genotype and inheritance pattern. The real-time uptake of cascade testing can be influenced by multiple factors. Early diagnosis of at-risk biological relatives of index cases through cascade testing, confirms the diagnosis in those who are symptomatic and facilitates implementation of surveillance strategies and clinical care at an early stage of the disease. [ABSTRACT FROM AUTHOR]

Simple Summary: Inbreeding increases homozygosity, often leading to the co-expression of recessive deleterious alleles and a reduction in genetic diversity. Traditional methods involve pedigree-based analysis, but high-density arrays have enabled precise estimations using genomic markers. A study comparing genomic inbreeding coefficients from DNA marker data with conventional coefficients from pedigree information in Korean commercial pig breeds reveals differences in inbreeding levels and trends among breeds. The finding highlights differences in inbreeding levels and trends among breeds, emphasizing the importance of using both genomic and conventional methods for a comprehensive understanding of inbreeding, which is crucial for effective breeding programs and maintaining genetic diversity. The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated and compared various genomic and pedigree inbreeding coefficients using different models and approaches. A total of 709,384 ROH segments in Duroc, 816,898 in Landrace, and 1,401,781 in Yorkshire, with average lengths of 53.59 Mb, 56.21 Mb, and 53.46 Mb, respectively, were identified. Relatively, the Yorkshire breed had the shortest ROH segments, whereas the Landrace breed had the longest mean ROH segments. Sus scrofa chromosome 1 (SSC1) had the highest chromosomal coverage by ROH across all breeds. Across breeds, an absolute correlation (1.0) was seen between FROH total and FROH1–2Mb, showing that short ROH were the primary contributors to overall FROH values. The overall association between genomic and conventional inbreeding was weak, with values ranging from 0.058 to 0.140. In contrast, total genomic inbreeding (FROH) and ROH classes showed a strong association, ranging from 0.663 to 1.00, across the genotypes. The results of genomic and conventional inbreeding estimates improve our understanding of the genetic diversity among genotypes. [ABSTRACT FROM AUTHOR]

Understanding somatic mutations and structural variations in domestic pigs (Sus scrofa domestica) is critical due to their increasing importance as model organisms in biomedical research. In this study, we conducted a comprehensive analysis through whole-genome sequencing of skin, organs, and blood samples. By examining two pig pedigrees, we investigated the inheritance and sharedness of structural variants among fathers, mothers, and offsprings. Utilizing single-cell clonal expansion techniques, we observed significant variations in the number of somatic mutations across different tissues. An in-house developed pipeline enabled precise filtering and analysis of these mutations, resulting in the construction of individual phylogenetic trees for two pigs. These trees explored the developmental relationships between different tissues, revealing insights into clonal expansions from various anatomical locations. This study enhances the understanding of pig genomes, affirming their increasing value in clinical and genomic research, and provides a foundation for future studies in other animals, paralleling previous studies in mice and humans. This approach not only deepens our understanding of mammalian genomic variations but also strengthens the role of pigs as a crucial model in human health and disease research. [ABSTRACT FROM AUTHOR]

Small populations of endangered species risk losing already eroded genetic diversity, important for adaptive potential, through the effects of genetic drift. The magnitude of drift can be mitigated by maximising the effective population size, as is the goal of genetic management strategies. Different mating systems, specifically those leading to reproductive skew, exacerbate genetic drift by distorting contributions. In the absence of an active management strategy, reproductive skew will have long-term effects on the genetic composition of a population, particularly where admixture is present. Here we examine the contrasting effects of conservation management strategies in two ex situ populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli), one managed as a semi-wild population in South Africa (SAx), and one managed under a mean-kinship breeding strategy in European zoos. We use molecular data to reconstruct pedigrees for both populations and validate the method using the zoo studbook. Using the reconstructed pedigree and studbook we show there is male sex-specific skew in both populations. However, the zoo's mean-kinship breeding strategy effectively reduces reproductive skew in comparison to a semi-wild population with little genetic management. We also show that strong male reproductive skew in SAx has resulted in extensive admixture, which may require a re-evaluation of the population's original intended role in the black rhino meta-population. With a high potential for admixture in many ex situ populations of endangered species, molecular and pedigree data remain vital tools for populations needing to balance drift and selection. [ABSTRACT FROM AUTHOR]

Copyright of Urban Mass Transit is the property of Urban Mass Transit Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Serbia preserves a high number of local grape varieties, which have been cultivated across thecountry forcenturies.Now, these ancient varieties are in the spotlight, and there is a global trend towards their recovery and characterization because they can revitalize regional, national and international grape and wine sectors. In addition, their genetic study can be useful to find new pedigree relationships to reveal how local varietal assortment evolve dover time. Here, thegeneticcharacterizationof138 grapevines from old Serbian vineyards revealed 59 different genetic profiles, 49 of which were identified as grapevine varieties whose origin in the country could be linked to some major Serbian historical periods.Most of the genetic profiles found in this work arranged in a complex pedigree network that integrates numerous grapevine varieties from diverse Balkan countries, agreeing with an intense exchange of plant material among Balkan regions for centuries. This analysis identified some varieties as important founders of Balkan genetic resources, like 'Alba Imputotato', 'Braghina Rosie', 'Coarna Alba', and 'Vulpea'. After deepening into their genealogy, these major direct founders might have ultimately derived from 'Visparola', an ancient variety of likely Balkan origin with a major founding role in some European regions. Our results also indicated the genetic singularity of the grapevine resources fromthe Balkanswhen compared to those fromother relevant winemaking regions, supporting the interest of their detailed study to evaluate their oenological potential and for the eventual identification of useful traits tocounteract current viticulture challenges. [ABSTRACT FROM AUTHOR]

The preferred tool for conceptualizing, determining, and claiming relations of kinship, ancestry, and descent among humans are diagrams. For this reason, and at the same time to avoid a reduction to biology as transported by terms such as kinship, ancestry, and descent, we introduce the expression diagrammatics of relatedness. We seek to understand the enormous influence that especially tree diagrams have had as a way to express and engage with human relatedness, but hold that this success can only be adequately understood by attending to what in fact are broader diagrammatic practices. These practices bring to light that diagrams of relatedness do not simply make visible natural connections, but create or deny relations in particular ways and for particular reasons. In this special section, contributors investigate diagrams of relatedness in genealogy, heredity, as well as biological and social anthropology. Conceiving of diagrams as techniques that transcend such binaries as 'thought and action' and 'image and text', we aim at an understanding of how they were constructed and how they functioned in particular epistemic, cultural, and political contexts. [ABSTRACT FROM AUTHOR]

Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree‐based inbreeding coefficients. However, with the development of single‐nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding depression in 6 growth and 2 reproductive traits in the Asturiana de los Valles cattle breed using both genealogical and molecular information. The pedigree group comprised 225,848 records and an average equivalent number of complete generations of 2.3. The molecular data comprised genotypes of 2693 animals using the Affymetrix medium‐density chip. Using the pedigree information, three different inbreeding coefficients were estimated for the genotyped animals: the full pedigree coefficient (FPED), and the recent and ancient inbreeding coefficients based on the information of the last three generations (FPED<3G) and until the last three generations (FPED>3G), respectively. Using the molecular data, seven inbreeding coefficients were calculated. Four of them were estimated based on runs of homozygosity (ROH), considering (1) the total length (FROH), (2) segments shorter than 4 megabases (FROH<4), (3) between 4 and 17 megabases (FROH4‐17), and (4) longer than 17 Mb (FROH>17). Additionally, the three inbreeding coefficients implemented in the Plink software (FHAT1‐3) were estimated. Inbreeding depression was estimated using linear mixed‐effects model with inbreeding coefficients used as covariates. All analysed traits (birth weight, preweaning average daily gain, weaning weight adjusted at 180 days, carcass weight, calving ease, age at first calving, calving interval) showed a statistically significant non‐zero effect of inbreeding depression estimated from the pedigree group, except for the Postweaning Average Daily Gain trait. When inbreeding coefficients were based on the genomic group, statistically significant inbreeding depression was observed for two traits, Preweaning Average Daily Gain and Weaning Weight based on FROH, FROH>17, and FHAT3 inbreeding coefficients. Nevertheless, similar to inbreeding depression estimated based on pedigree information, estimates of inbreeding depression based on genomic information had no relevant economic impact. Despite this, from a long‐term perspective, genotyped data could be included to maximize genetic progress in genetic programs following an optimal genetic contribution strategy and to consider individual inbreeding load instead global inbreeding. ROH islands were identified on chromosomes 2, 3, 8, 10, and 16. Such regions contain several candidate genes for growth development, intramuscular fat, body weight and lipid metabolism that are related to production traits selected in Asturiana de los Valles breed. [ABSTRACT FROM AUTHOR]

The marmoset is a fundamental nonhuman primate model for the study of aging, neurobiology, and many other topics. Genetic management of captive marmoset colonies is complicated by frequent chimerism in the blood and other tissues, a lack of tools to enable cost‐effective, genome‐wide interrogation of variation, and historic mergers and migrations of animals between colonies. We implemented genotype‐by‐sequencing (GBS) of hair follicle derived DNA (a minimally chimeric DNA source) of 82 marmosets housed at the Southwest National Primate Research Center (SNPRC). Our primary goals were the genetic characterization of our marmoset population for pedigree verification and colony management and to inform the scientific community of the functional genetic makeup of this valuable resource. We used the GBS data to reconstruct the genetic legacy of recent mergers between colonies, to identify genetically related animals whose relationships were previously unknown due to incomplete pedigree information, and to show that animals in the SNPRC colony appear to exhibit low levels of inbreeding. Of the >99,000 single‐nucleotide variants (SNVs) that we characterized, >9800 are located within gene regions known to harbor pathogenic variants of clinical significance in humans. Overall, we show the combination of low‐resolution (sparse) genotyping using hair follicle DNA is a powerful strategy for the genetic management of captive marmoset colonies and for identifying potential SNVs for the development of biomedical research models. Research Highlights: Genotype‐by‐sequencing of hair follicle DNA allows effective genetic characterization of captive marmosets for colony management.Ancestry analysis of genetic data reflects recent colony mergers and site‐specific genetic characteristics.Genetic data augments pedigree records to reveal previously unknown relationships in a captive population. [ABSTRACT FROM AUTHOR]

For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus nonreproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found more than 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the nonbreeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than nonbreeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R  = −0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges. [ABSTRACT FROM AUTHOR]

Background: Haemochromatosis is a genetic disease characterized by the excessive deposition of iron in various tissues and organs, eventually results in organ damage including cirrhosis, diabetes, cardiomyopathy, etc. SLC40A1-related haemochromatosis is associated with gain-of-function mutations in the SLC40A1 gene, which encodes ferroportin. While sporadic reports of this condition exist in mainland China, the understanding of the phenotype and genetic pattern associated with the SLC40A1 p.Y333H mutation remains incomplete. Case presentation: We report a pedigree with heterozygous p.Y333H mutation in Chinese Han population. The proband is a 64-year-old man complaining of persistent abnormality of liver enzyme levels for 1 year, with a history of knee joint pain, diabetes and skin pigmentation. He displayed markedly elevated serum ferritin level and transferrin saturation. Magnetic resonance imaging showed iron deposition in the liver, spleen, and pancreas, along with cirrhosis and splenomegaly. Whole exome sequencing identified a heterozygous allelic variant c.997T > C (p.Y333H). Genetic screening of family members identified four first-degree relatives and three second-degree relatives having the same mutation. Additional cases with this mutation from two published studies were included. Among the probands and screened relatives, all eight males aged over 30 y had ferritin level > 1000 µg/L, transferrin saturation > 90%. Four patients with organ damage in the present study received therapeutic phlebotomy, alleviating clinical symptoms and improving in transferrin saturation and serum ferritin. Conclusions: This study reports the largest pedigree with heterozygous SLC40A1 p.Y333H mutation in the Chinese population to date. In Chinese families, males over 30 years old with hemochromatosis due to SLC40A1 p.Y333H mutation exhibit severe iron overload phenotypes. [ABSTRACT FROM AUTHOR]

Changes in wool prices, labour costs and animal welfare have sparked interest in several new sheep traits. Shedding, the ability of moulting or seasonal wool loss in sheep, is one of them. Here, we aimed to develop breeding values for shedding using existing data from New Zealand flocks. We used breeder-collected shedding scores, 0 = 'no shedding on any part of the body' to 10 = 'wool shed fully from all the body', for Wiltshire and Wiltshire-composite lambs born between 2003 and 2022. After QC, 20,653 phenotypic records from 25,066 animals with pedigree information (393 sires and 7439 dams from 12 flocks) were included in the analyses. Genetic parameters and breeding values were obtained using a genetic additive model with pedigree data (BLUP model), assuming shedding scores were quantitative. The genetic model incorporated the following variables: date of birth, sex, birth and rearing rank, age of dam and contemporary group. We found a high heritability for lamb shedding, 0.54 (0.02), and estimated a low-to-moderate prediction accuracy of breeding values (ranging from 0.09 to 0.36) using forward-validation. Our results confirmed that shedding can be subject to selection and that pedigree-based breeding values for this trait can be a useful tool for breeders. [ABSTRACT FROM AUTHOR]

Copyright of Plexus Medical Journal (PMJ) is the property of Sebelas Maret University, Faculty of Medicine / Universitas Sebelas Maret, Fakultas Kedokteran and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Knowledge of the parental origin of crop species is a prerequisite for formulating effective strategies for genetic conservation, management, and utilisation of genotypes in breeding programmes and genetic studies. In the case of the potato, although pedigree information is well documented, the possible lack of accurate pedigree data for certain cultivars constitutes a loss of opportunity to exploit the selection gain, the precise targeting of a market niche, or other breeding objectives. In this study, the genetic profiles of 1249 varieties were examined using a set of 35 polymorphic simple sequence repeats (SSR) markers with the available pedigree information to achieve pedigree validation. The maximum likelihood (LOD) was used to validate pedigree information of potato accessions for which the genetic data of at least one parent was available in the dataset. Our results showed that among the accessions for which both parents were genotyped, 81.7% presented a validated pedigree, while 18.3% presented a pedigree conflict (for at least one parent). Among the accessions for which only one parent was available in the dataset, 91.3% presented a validated pedigree, while 8.7% presented a pedigree conflict. Then, pedigree reconstruction was investigated to determine the most likely parent candidates for varieties whose pedigree is either questionable or lacking information. [ABSTRACT FROM AUTHOR]

Academia today is deeply hierarchical and continues to be centered around perceptions of prestige and symbolic capital. The symbolic capital, or pedigree, associated with the training one receives at the graduate level greatly informs how academics navigate their careers and how they advance professionally. In investigating the formation of the professional habitus of Indonesian academics, we are interested in how their graduate training informs both their career progression and their teaching practices. We theorize graduate training using the terms 'hybrid' for the participants who have a mix of overseas and domestic training and 'homegrown' for those who were educated solely in Indonesia. The data suggests that hybrid academics in Indonesia are more open to innovating their teaching practice and advance at a quicker pace than homegrown academics. [ABSTRACT FROM AUTHOR]

Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort's fingerprint genomic sites. The FPFinder was developed based on the term frequency–inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future. [ABSTRACT FROM AUTHOR]

Key Clinical Message: Maternally inherited diabetes and deafness (MIDD) is often caused by the m.3243A > G mutation in mitochondrial DNA. Unfortunately, the characteristics of MIDD, especially long‐term outcomes and heteroplasmic changes, have not been well described previously. The purpose of this study was to describe the clinical and genetic features of a family with MIDD after 10 years of follow‐up.A 33‐year‐old male patient with typical characteristics of MIDD, including early‐onset diabetes, deafness, and low body mass index, was admitted to our department. Further investigation revealed that the vast majority of his maternal relatives suffered from diabetes with or without deafness. A detailed family history was then requested from the patient and a pedigree was constructed. The patient suspected of MIDD was screened for mutations using whole mitochondrial DNA sequencing. Candidate pathogenic variants were then validated in other family members through Sanger sequencing. The patient was diagnosed with MIDD, with inherited m.3243A > G mutation in the mitochondrially encoded tRNA leucine 1 (MT‐TL1) gene, after 10 years of symptom onset. The patient was then treated with insulin and coenzyme Q10 to improve mitochondrial function. During the follow‐up period, his fasting blood glucose and HbA1c levels were improved and the incidence of diabetic ketoacidosis was significantly reduced. Our findings indicate that whole mitochondrial DNA sequencing should be considered for patients suspected of MIDD to improve the efficiency of diagnosis and prognosis. [ABSTRACT FROM AUTHOR]

Impacts of immigration on micro‐evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi‐generational genetic legacies have not been explicitly quantified in natural meta‐populations, precluding inference on how movements translate into effective gene flow and eco‐evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi‐generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis‐enhanced introgression. However, while contributions from female immigrants exceeded those from female natives by up to three‐fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, altering multiple eco‐evolutionary implications of immigration. [ABSTRACT FROM AUTHOR]

Background: Shih Tzus are a popular dog breed in the UK although there is relatively little reported information on their health. This study aimed to characterise the demography, common disorders and mortality of Shih Tzus under primary veterinary care during 2016 in the UK using de-identified clinical records from the VetCompass™ Programme. Results: The study population of 336,865 dogs under veterinary care during 2016 included 11,082 Shih Tzus (3.3%). The median age was 4.1 years (IQR: 2.1–7.1, range: 0.3–20.4) and mean adult bodyweight was 7.9 kg (SD: 1.9 kg). Annual proportional births increased from 2.2% of all dog births in 2005 to 3.8% in 2013, dropping to 3.3% by 2016. From a random subset of 2,423 Shih Tzus that had information extracted on disorders diagnosed during 2016, the most prevalent fine-level precision disorders were periodontal disease (n = 229, prevalence 9.5%, 95% CI: 8.4–10.7), anal sac impaction (180, 7.4%, 95% CI: 6.5–8.5) and ear disorders (134, 5.5%, 95% CI: 4.7–6.5). The most prevalent grouped-level precision disorders were cutaneous (n = 402, prevalence: 16.6%, 95% CI: 15.2–18.1), dental (322, 13.3%, 95% CI: 12.0–14.7), and ophthalmological (289, 11.9%, 95% CI: 10.7–13.3). Males were more likely than females to be diagnosed with skin disorders (P = 0.007) and musculoskeletal disorders (P = 0.010) while females were more likely than males to be diagnosed with hernias (P = 0.005). The median age of death was 12.7 years (IQR 8.7–14.3, range 2.0–19.9) and did not differ statistically between males and females. The most common grouped causes of death were enteropathy (7.9%, 95% CI: 3.9–15.4), heart disease (7.9%, 95% CI: 3.9–15.4) and poor quality of life (7.9%, 95% CI: 3.9–15.4). Conclusions: Periodontal disease, anal sac impaction and ear disorders were identified as common health issues. Shih Tzus had higher prevalence of anal sac impaction, umbilical hernias and eye problems than reported previously in dogs overall, suggesting potential predispositions. Shih Tzus appear to be relatively long-lived compared to previous reports of lifespan in dogs overall. The results can inform veterinarians and owners on priority disorders for monitoring to protect welfare. Oral hygiene was highlighted as a healthcare priority. Plain English summary: The Shih Tzu is a popular small breed of dog in the UK. However, there is little information on common health conditions affecting this breed. This study aimed to describe the demography, common disorders, and causes of death of Shih Tzus in the UK in 2016 using the VetCompass™ Programme, which holds a database of anonymized clinical records of dogs attending primary-care veterinary practices in the UK. The study included 11,082 Shih Tzus (3.3%) from 336,865 dogs under veterinary care in the UK in VetCompass™ in 2016. The popularity of the Shih Tzu increased slightly from 2005 to 2013 but showed signs of decline towards 2016. The average age of Shih Tzus in the study was 4.1 years and the average adult bodyweight was 7.9 kg. The most common disorders affecting Shih Tzus in the study were periodontal disease (inflammation of the gums and tissue around the teeth, affecting 9.5% of Shih Tzus), anal sac impaction (7.4%) and ear disorders (5.5%). Male Shih Tzus were more likely than females to have skin and musculoskeletal disorders (conditions affecting bones, muscles and joints), while female Shih Tzus were more likely be diagnosed with hernias (when internal tissues push out through weakened muscle tissues). Shih Tzus had higher prevalence of anal sac impaction, umbilical hernias and eye problems than previously reported in dogs overall, suggesting potential predispositions. The average age at death of Shih Tzus was 12.7 years of age and the most common causes of death were enteropathy (gastrointestinal diseases causing signs such as diarrhoea and vomiting, 7.9%), heart disease (7.9%) and poor quality of life (7.9%). This study demonstrated the value of analysis of veterinary clinical records to increase our understanding of common health problems affecting dogs in the UK. The results can help both current and prospective Shih Tzu owners, and veterinarians, in prioritising preventative healthcare for Shih Tzus. For example, the most common disorder in Shih Tzus was periodontal disease, suggesting that increased preventative dental checkups and toothbrushing could improve welfare, especially if implemented from an early age. [ABSTRACT FROM AUTHOR]

Background: The English Cocker Spaniel (ECS) is one of the most popular dog breeds in the UK but information on disorder predisposition and protection is limited. Using anonymised veterinary clinical data from the VetCompass™ Programme, this study aimed to compare disorder predisposition and protection between the ECS and the remaining dogs under primary veterinary care in the UK during 2016. Electronic patient records for random samples of ECS and non-ECS were reviewed. The most common disorders diagnosed during 2016 were extracted and compared using multivariable logistic regression, controlling for confounders. Results: The analysis included random samples of 2510/10,313 (24.3%) ECS and 7813/326,552 (2.39%) non-ECS. After accounting for confounding by age, sex, bodyweight within breed-sex, insurance status and veterinary practice group, the ECS had increased odds of 21/43 (48.85%) disorders at fine-level precision, with highest odds for aural discharge (odds ratio (OR) 14.66, 95% confidence interval (CI): 7.73–30.90, P < 0.001) and keratoconjunctivitis sicca (OR 7.64, 95% CI: 4.33–14.14, P < 0.001) and lowest odds for atopic dermatitis (OR 0.14, 95% CI: 0.05–0.31, P < 0.001) and allergy (OR 0.14, 95% CI: 0.06–0.28, P < 0.001). Conclusions: This study provides evidence for strong predisposition to aural and ocular disorders and protection from hypersensitivity disorders in the ECS. These results can aid dog owners, breeders, and veterinarians to better monitor health in ECS, and promote earlier diagnosis with improved prognosis. Further, the results can help breeding organisations establish key priorities the health-based reforms of the ECS. [ABSTRACT FROM AUTHOR]

The application of molecular tools to population management can improve the long-term genetic viability of ex situ populations. In this study, we aimed to understand the implications of integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer's pochard (Aythya baeri), in North America. Single nucleotide polymorphism data were generated for 141 Baer's pochard using double digest restriction site-associated DNA sequencing and empirical kinships were derived and integrated into the population management software PMx. Analyses suggested 37.7% of pairwise relationships previously assumed to be unrelated were first, second, or third-order relatives. We determined that most genetic summary statistics were impacted through the calculation of the population's mean kinship, which increased from M K ¯ = 0.0772 to M K ¯ = 0.2074 after empirical kinships were integrated into our analyses. Our results also revealed the importance of understanding how molecular kinships derived from a particular estimator are scaled, if the scale differs significantly from pedigree-based kinships. We describe the theory behind the genetic metrics impacted and provide general guidance on incorporating empirical kinships into ex situ population management as well as provide suggestions for sampling strategies to minimize the biases inherent in merging two types of kinship estimators. [ABSTRACT FROM AUTHOR]

Purpose: Norrie disease (ND) is a rare X‐linked recessive disorder characteristic of early childhood blindness. While several mutations in the NDP gene have been reported as causative for ND, the genetic etiology remains unknown for many patients. This study aims to describe a novel mutation and explore the clinical manifestations in a Chinese family with two affected males. Methods: Exome sequencing (ES) was employed to identify the causative gene in a four‐generation pedigree. Sanger sequencing was subsequently utilized to validate the mutation detected by ES in additional family members. Ophthalmologic examination and diagnostic imaging relevant to ND were conducted. Results: The proband (IV:2), an 8‐month‐old male infant, presented with binocular retinal detachment. DNA sequencing revealed a novel heterozygous missense mutation (c.174G>C) within the NDP gene in the proband. This mutation affected highly conserved residues and was predicted to disrupt the normal protein structure. Furthermore, the variant co‐segregated with the disease phenotypes within the family. Conclusions: Our findings identified a novel missense mutation in the NDP gene associated with Norrie disease in China, expanding the mutation spectrum associated with ND. This discovery holds diagnostic, prognostic, and genetic counseling implications for affected individuals. [ABSTRACT FROM AUTHOR]

Vaccinium corymbosum (L.) is a plant native to North America and belongs to the genus Vaccinium L., the Ericales order, family Ericaceae, Subfamily Vaccinioideae. Blueberries are classified under the family Ericaceae, subfamily Vacciniaceae, genus Vaccinium, and subgenus Cyanococcus. They are most commonly found growing in acidic and infertile soil conditions. Highbush blueberries have a higher total sugar content compared to other berries of the Vaccinium genus. The first blueberry crop in Romania was established in Bilcesti, Arges. Since 1980, blueberry breeding has been carried out at the Research Institute for Fruit Growing Pitesti - Maracineni, Romania, using different origins and parent plants. Controlled hybridization is used in the breeding process, where the parents or genitors are chosen based on the desired blueberry breeding objectives. The aim of this study is to expand the knowledge base on the pedigree and biometrical traits of Romanian blueberry cultivars. [ABSTRACT FROM AUTHOR]

Background: The Shar Pei is a common dog breed with a distinctive appearance caused by hyaluronosis that has been linked with several health conditions. Anonymised primary-care veterinary clinical records were explored to extract data on the demography, common disorders and mortality of Shar Pei in the UK in 2013. Results: The study population of 455,557 dogs included 1913 (0.42%) Shar Pei. The mean adult bodyweight was 22.26 kg. The most prevalent fine-level precision disorders were entropion (prevalence 17.88%, 95% CI: 16.16-19.59), otitis externa (16.36%, 95% CI: 14.70-18.02), ear disorders (6.69%, 95% CI: 5.57-7.81), aggression (5.23%, 95% CI: 4.23-6.22), and pyoderma (4.29%, 95% CI: 3.38-5.19). The most prevalent disorder groups were ophthalmologic (prevalence = 22.27%, 95% CI: 20.40-24.13), dermatological (21.01%, 95% CI: 19.19-22.84), aural (18.66%, 95% CI: 16.92-20.41), traumatic injury (7.53%, 95% CI: 6.35-8.71) and behavioural (7.21%, 95% CI: 6.05-8.37). The median longevity of 190 Shar Pei that died during the study period was 7.28 years (IQR 5.04-10.05, range 0.04-15.04). Of 184 deaths with a recorded method of death, 157 (85.33%) deaths involved euthanasia and 27 (14.67%) deaths were unassisted. Among 136 (71.58%) deaths with a recorded biomedical cause of death, the most common causes of death at group level precision were neoplasia (15.44%, 95% CI: 9.37-21.51), renal disorders (13.24%, 95% CI: 7.54-18.93), and behavioural disorders (11.03%, 95% CI: 5.76-16.29). Conclusions: Almost one fifth of Shar Pei receive veterinary care each year for entropion, a condition linked strongly with the extreme conformation of thickened and folded skin and bristly hair that characterises the Shar Pei breed. Several other common disorders are also linked to hyaluronosis. Current UK legislation can help support efforts to avoid breeding or acquiring animals with extreme conformations and to promote adequate veterinary care for already-owned animals with extreme conformations. Plain English summary: The Shar Pei dog breed is instantly recognisable by their copious loose folded skin and bristly coat, with Shar Pei translating from Chinese as 'sand paper skin'. Although originally a fighting, hunting and guarding dog in China, the Shar Pei breed was re-invented in the US as a companion animal in the late 1970s where a more wrinkled and heavy-set American 'meat mouth' variety replaced the traditional 'bone mouth' variety originally popular in China. However, the underlying disease of hyaluronosis that causes the characteristic extreme appearance of the Shar Pei has also been linked with several other health problems in the breed such as in-turned eyelids (entropion) and ear disease. Using anonymised veterinary clinical records collected within the VetCompass Programme at the Royal Veterinary College (RVC), Shar Pei made up 0.4% of all dogs in the UK in 2013 and had an average adult bodyweight of 22 kg. The most common specific disorders diagnosed in Shar Pei were in-turned eyelids (17.88%), ear infection (16.36%), ear problems (6.69%), aggression (5.23%), and skin infection (4.29%). Among the 30 most common specific disorders, females were more likely to show in-turned eyelids and conjunctivitis, while males were more likely to show aggression and infected paws. Once the disorders were grouped, the most common disorder groups were eye disorders (22.27%), skin (21.01%), ear (18.66%), traumatic injury (7.53%), and behavioural (7.21%). The average lifespan of Shar Pei was 7.28 years. The most common causes of death were cancer (15.44%,), kidney disorders (13.24%), and behavioural disorders (11.03%). This study highlights that almost one fifth of the breed receive veterinary care each year for in-turned eyelids that can lead to extreme pain and are linked to the thickened and folded skin that humans find so appealing in this breed. Current UK legislation can help support concerted efforts from all animal welfare stakeholders to avoid breeding or acquiring animals with these and other extreme conformations and to promote adequate veterinary care for already-owned animals with extreme conformations. [ABSTRACT FROM AUTHOR]

In countries where farming is largely subsistence, no pedigree records of farm animals are maintained at farmers' herd and scientific mating plans are not observed which leads to the accumulation of inbreeding and loss of production potential. Microsatellites have been widely used as reliable molecular markers to measure inbreeding. We attempted to correlate autozygosity estimated from microsatellite data with the inbreeding coefficient (F) calculated from pedigree data in Vrindavani crossbred cattle developed in India. The inbreeding coefficient was calculated from the pedigree of ninety-six Vrindavani cattle. Animals were further grouped into three groups viz. acceptable/low (F: 0–5%), moderate (F: 5–10%) and high (F: ≥10%), based on their inbreeding coefficients. The overall mean of the inbreeding coefficient was found to be 0.070 ± 0.007. A panel of twenty-five bovine-specific loci were chosen for the study according to ISAG/FAO. The mean FIS,FST, and FIT values were 0.0548 ± 0.025, 0.012 ± 0.001 and 0.0417 ± 0.025, respectively. There was no significant correlation between the FIS values obtained and the pedigree F values. The locus-wise individual autozygosity was estimated using the method-of-moments estimator (MME) formula for locus-specific autozygosity. The autozygosities ascribing to CSSM66 and TGLA53 were found to be significantly (p <.01 and p <.05, respectively) correlated with pedigree F values. [ABSTRACT FROM AUTHOR]

Simple Summary: The genetic variants responsible for lethal recurrent breast cancer are not yet recognized. Five sets of cousins with recurrent breast cancer who belonged to high-risk pedigrees were sequenced to identify rare, shared candidate predisposition variants in the pedigrees. The candidates were tested for association with breast cancer risk in other populations, and additional breast cancer cases were assayed for some of the candidate variants to test for co-segregation of the variants in pedigrees. One hundred and eighty-one rare candidate predisposition variants were shared in at least one cousin pair. A rare variant in MDH2 was found to segregate with breast-cancer-affected relatives in one extended pedigree. This small sequencing study identified a set of strong candidate variants for inherited predisposition for breast cancer recurrence, including MDH2, which should be pursued in other resources. A significant fraction of breast cancer recurs, with lethal outcome, but specific genetic variants responsible have yet to be identified. Five cousin pairs with recurrent breast cancer from pedigrees with a statistical excess of recurrent breast cancer were sequenced to identify rare, shared candidate predisposition variants. The candidates were tested for association with breast cancer risk with UKBiobank data. Additional breast cancer cases were assayed for a subset of candidate variants to test for co-segregation. Three-dimensional protein structure prediction methods were used to investigate how the mutation under consideration is predicted to change structural and electrostatic properties in the mutated protein. One hundred and eighty-one rare candidate predisposition variants were shared in at least one cousin pair from a high-risk pedigree. A rare variant in MDH2 was found to segregate with breast-cancer-affected relatives in one extended pedigree. MDH2 is an estrogen-stimulated gene encoding the protein malate dehydrogenase, which catalyzes the reversible oxidation of malate to oxaloacetate. The molecular simulation results strongly suggest that the mutation changes the NAD+ binding pocket electrostatics of MDH2. This small sequencing study, using a powerful approach based on recurrent breast cancer cases from high-risk pedigrees, identified a set of strong candidate variants for inherited predisposition for breast cancer recurrence, including MDH2, which should be pursued in other resources. [ABSTRACT FROM AUTHOR]

Background: Polycystic kidney disease (PKD), an inheritance disorder which is the fourth leading cause of the end-stage renal disease. The inheritance pattern can be diagnosed and confirmed by pedigree analysis. The aim of the present research was to determine the type and frequency of PKD using pedigree analysis. Materials and Methods: The present research was designed as a cross-sectional descriptive study. Thirty-eight adult Bangladeshi PKD patients were recruited using a selection checklist from the Department of Nephrology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh. Data were collected using a data collection sheet after taking informed written consent. The pedigree was drawn using the genetic pedigree chart creation software f-tree V4.0.6. The percentage frequencies of different types of pedigree were calculated using the Statistical Package for the Social Sciences software, version 23. Results: A total of 24 (63.20%) had a positive family history and 36.80% (14) had no positive family history. All of the patients with a positive family history had vertical transmission; male and female were equally inheriting the gene. Out of these 24 patients, 4.17% (one), 8.33% (two), and 16.67% (four) had a homozygous/heterozygous state, skip generation, and male to male transmission, respectively. Conclusions: Pedigree analysis of PKD patients showed an increased value in early diagnosis and better management and prognosis of the disease. [ABSTRACT FROM AUTHOR]

In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (FPED) and genomic data based on runs of homozygosity (ROH) in the genome (FROH) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree‐based inbreeding coefficients were lower than ROH‐based inbreeding values. The correlations between pedigree and ROH‐based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree‐based inbreeding affected only sperm motility while ROH‐based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (FPED10) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised. [ABSTRACT FROM AUTHOR]

The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site‐choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine‐scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery‐origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound. [ABSTRACT FROM AUTHOR]

Objective: Gitelman syndrome (GS) is an autosomal recessive tubulopathy resulting from inactivating mutations in the SLC12A3 gene that encodes the thiazide‐sensitive sodium‐chloride cotransporter (NCC). To date, more than 500 mutations have been identified in the SLC12A3 gene. In this study, we identified two new mutations in the SLC12A3 gene in two Chinese GS pedigrees. Design, Patients and Measurements: The clinical characteristics and laboratory examination of two suspected GS patients in our hospital were analyzed. In addition, two pedigrees including 11 members and 2 patients underwent SLC12A3 gene analysis. Results: Both patients were middle‐aged women with characteristics of hypokalemic metabolic alkalosis, hypomagnesemia, low level of urinary calcium and the elevated levels of renin‐angiotensin‐aldosterone system. So, they were clinically diagnosed as GS. Patient 2 also had type 2 diabetes and Graves' disease. Both patients were found to carry two mutations of SLC12A3 gene by Sanger direct sequencing, which were all compound heterozygous mutations. We identified three mutations in these two Chinese GS pedigrees, one of which was c.179C>T (Thr60Met). The novel c.2159G>T (p. Gly720Val) and c.2675T>C (p. Leu892Pro) mutations were strongly predicted to be pathogenic using four network programs—Polyphen‐2, SIFT, Mutation Taster and LRT. Conclusions: We identified two novel SLC12A3 genetic variant [c.2159G>T (p.Gly720Val) and c.2675T>C (p.Leu892Pro)] in two Chinese GS pedigrees. The discovery of new mutations has enriched the spectrum of SLC12A3 genotypes. [ABSTRACT FROM AUTHOR]

Reproductive skew occurs when a few individuals monopolize breeding output, which can act as a mechanism of natural selection. However, when population sizes become small, reproductive skew can depress effective population size and worsen inbreeding. Identifying the cause of reproductive skew is important for mitigating its effect on conservation of small populations. We hypothesized that superb parrots Polytelis swainsonii, which strongly select for the morphology of tree cavity nests, may be reproductively skewed toward pairs that monopolize access to nests. We use SNP genotyping to reconstruct a pedigree, estimate molecular relatedness and genetic diversity of wild superb parrot in the Australian Capital Territory. We successfully genotyped 181 nestlings (a census between 2015–2019) and showed they were the progeny of 34 monogamous breeding pairs. There was a strong reproductive skew – 21 pairs bred only once producing 40% of the nestlings, whereas 13 pairs bred two to four times, producing 60% of the total nestlings. Five of these repeat‐breeders produced 28% of all nestlings, which was nearly triple the productivity of one‐time breeders. Repeat breeders usually monopolized access to their nest cavities, but the few pairs that switched nests did not differ in fecundity from those that stayed. The cause of nest switching was unknown, but uninterrupted access to a suitable nest (not minor variations in morphology between nests) better predicted fitness of breeding superb parrots. Pedigrees offer powerful insights into demographic processes, and identifying reproductive skew early provides opportunities to proactively avoid irreversible loss of genetic diversity via conservation management. We identify new research questions based on our results to clarify the relationship between access to resources and breeding success. [ABSTRACT FROM AUTHOR]

Through fingerprinting analysis using reference microsatellite markers and comparing with the Vitis International Variety Catalogue (VIVC) database, it was possible to discover that in Brazil, the wine grape variety cultivated for over 70 years, called 'Peverella' (Variety number VIVC = 12963; National Register of Vine Varieties (Italy), code: 254) is actually the grape variety called 'Boschera' (Variety number VIVC = 1576; National Register of Vine Varieties (Italy), code: 326). This discovery makes wines produced in Brazil even rarer (with only approximately 10 hectares planted worldwide), presenting an additional means to promote and market this historic variety. [ABSTRACT FROM AUTHOR]

The aim of the study was to analyze the problem of constructing and interpreting human pedigrees, which include some signs that are easily detected during a clinical examination and the collection of primary history. Materials and methods. 2 pedigrees from own sources and 2 pedigrees of famous people from literary sources are presented. They serve as the examples of using the provided data for further medical and genealogical analysis. Results and discussion. The results indicate that pedigree analysis is a primary and informationally important tool for the further algorithm of diagnosis and treatment of subjects. The effect of the quantity, quality and testing level of the presented genealogical information for a full pedigree analysis and the use of its possibilities is demonstrated. Pedigree analysis demonstrated that the number of absolute units of quantitative information presented (total number of generations and members of the pedigree) and absolute units of qualitative information (traits/medical conditions listed and their level of detail) may not be associated with the value of genetic conclusions. It has been shown that the largest number of members in a generation is usually represented for the generation of the propositus. Thus, smaller pedigrees, where more units of information are represented per member, can be of greater value for genetic conclusions. An analysis of one's own pedigrees showed that, on average, less than one trait can be represented per person in the pedigree. Additionally, small pedigrees with available molecular genetic data may be of greatest value, even retrospectively. Conclusions. It is shown that pedigrees can represent valuable primary information for clinicians regarding the further algorithm of the subject dealing and serve as a tool for the scientific thinking development in the educational process [ABSTRACT FROM AUTHOR]

Background and Purpose: Lafora disease (LD) is a very rare autosomal recessive disorder manifesting primarily as fatal, congenital, and neurodegenerative epilepsies. We aimed to describe the MRI characteristics due to gene mutations in a Chinese pedigree with LD. Methods: Whole‐exome sequencing, muscle biopsy, pedigree analysis, and MRI analysis were conducted. Five family members (two of whom were affected by LD) were whole‐genome sequenced. Longitudinal changes in brain MRI volumes were analyzed by Freesurfer. Results: We identified a new intron heterozygous mutation in the EMP2A gene c.71 (exon 1) G>A in a Chinese LD pedigree that was characterized by refractory seizures, progressive vision impairment, and declines in motor and cognitive functions. The patient suffered generalized tonic–clonic seizures since the age of 15 years and had severe forms of progressive myoclonic seizure. She eventually died after being admitted to the intensive care unit due to status epilepticus at the age of 24 years. Period acid Schiff staining showed positive polyglucosan particles in muscle biopsy specimens. Regions of atrophy in the whole brain, and especially in the hippocampus, were detected. Conclusions: We identified a new heterozygous mutation (c.71+1G>A) in a Chinese LD pedigree, which broadens the mutation spectrum of LD genes. We found that the patient exhibited brain volumetric atrophy along with rapidly worsening symptoms. These results contribute to our understanding of LD. [ABSTRACT FROM AUTHOR]

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Common vetch is one of the most profitable forage legumes due to its versatility in end-use which includes grain, hay, green manure, and silage. Furthermore, common vetch is one of the best crops to rotate with cereals as it can increase soil fertility which results in higher yield in cereal crops. The National Vetch Breeding Program located in South Australia is focused on developing new vetch varieties with higher grain and dry matter yields, better resistance to major diseases, and wider adaptability to Australian cropping environments. As part of this program, a study was conducted with 35 field trials from 2015 to 2021 in South Australia, Western Australia, Victoria, and New South Wales with the objective of determining the best parents for future crosses and the vetch lines with highest commercial value in terms of grain yield production. A total of 392 varieties were evaluated. The individual field trials were combined in a multi-environment trial data, where each trial is identified as an environment. Multiplicative mixed models were used to analyze the data and a factor analytic approach to model the genetic by environment interaction effects. The pedigree of the lines was then assembled and incorporated into the analysis. This approach allowed to partition the total effects into additive and non-additive components. The total and additive genetic effects were inspected across and within environments for broad and specific selections of the lines with the best commercial value and the best parents. Summary measures of overall performance and stability were used to aid with selection of parents. To the best of our knowledge, this is the first study which used the pedigree information to breed common vetch. In this paper, the application of this statistical methodology has been successfully implemented with the inclusion of the pedigree improving the fit of the models to the data with most of the total genetic variation explained by the additive heritable component. The results of this study have shown the importance of including the pedigree information for common vetch breeding programs and have improved the ability of breeders to select superior commercial lines and parents. [ABSTRACT FROM AUTHOR]

A unique approach with rare resources was used to identify candidate variants predisposing to familial nonsquamous nonsmall‐cell lung cancers (NSNSCLC). We analyzed sequence data from NSNSCLC‐affected cousin pairs belonging to high‐risk lung cancer pedigrees identified in a genealogy of Utah linked to statewide cancer records to identify rare, shared candidate predisposition variants. Variants were tested for association with lung cancer risk in UK Biobank. Evidence for linkage with lung cancer was also reviewed in families from the Genetic Epidemiology of Lung Cancer Consortium. Protein prediction modeling compared the mutation with reference. We sequenced NSNSCLC‐affected cousin pairs from eight high‐risk lung cancer pedigrees and identified 66 rare candidate variants shared in the cousin pairs. One variant in the FGF5 gene also showed significant association with lung cancer in UKBiobank. This variant was observed in 3/163 additional sampled Utah lung cancer cases, 2 of whom were related in another independent pedigree. Modeling of the predicted protein predicted a second binding site for SO4 that may indicate binding differences. This unique study identified multiple candidate predisposition variants for NSNSCLC, including a rare variant in FGF5 that was significantly associated with lung cancer risk and that segregated with lung cancer in the two pedigrees in which it was observed. FGF5 is an oncogenic factor in several human cancers, and the mutation found here (W81C) changes the binding ability of heparan sulfate to FGF5, which might lead to its deregulation. These results support FGF5 as a potential NSNSCLC predisposition gene and present additional candidate predisposition variants. [ABSTRACT FROM AUTHOR]

Substantial numbers of variants of unknown significance (VUSs) have been identified in BRCA1/2 through genetic testing, which poses a significant clinical challenge because the contribution of these VUSs to cancer predisposition has not yet been determined. Here, we report 10 Japanese patients from seven families with breast or ovarian cancer harboring the BRCA2 c.7847C>T (p.Ser2616Phe) variant that was interpreted as a VUS. This variant recurs only in families from Japan and has not been reported in the global general population databases. A Japanese patient with Fanconi anemia with compound heterozygous variants c.7847C>T (p.Ser2616Phe) and c.475+1G>A in BRCA2 was reported. In silico predictions and quantitative cosegregation analysis suggest a high probability of pathogenicity. The clinical features of the variant carriers were not specific to, but were consistent with, those of patients with hereditary breast and ovarian cancer. A validated functional assay, called the mixed‐all‐nominated‐in‐one‐BRCA (MANO‐B) method and the accurate BRCA companion diagnostic (ABCD) test, demonstrated the deleterious effects of the variant. Altogether, following the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines, this variant satisfied the "PS3," "PM2," "PM3," and "PP3" criteria. We thus conclude that the BRCA2 c.7847C>T (p.Ser2616Phe) variant is a "likely pathogenic" variant that is specifically observed in the Japanese population, leading to a breast and ovarian cancer predisposition. [ABSTRACT FROM AUTHOR]

A dataset of high-quality 7k SNP profiles of 1,038 unique Eurasian grapevine varieties was used to infer the most likely grapevine migration events, a spatial ancestry estimation, and a model about the origin of Eurasian grapevine germplasm. The comparison of putative gene flow scenarios from Caucasus throughout Europe aided to fit the more reliable spreading routes around the Mediterranean Basin. The same dataset was also used to assess the population genetic diversity, structure, and relatedness of Italian varieties. These data suggested a different history between Northern and Southern Italian grapevines, appearing clearly split into two different clusters. Interestingly, the Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The same SNP panel was used to determine parental relationships, identifying the main parents of traditional Italian and closely related cultivars. The parentage network suggested that Italian germplasm largely originated from a few key parents distributed into several geographical areas of genetic influence, with more or less large overlaps. These key cultivars are ‘Bombino bianco’, ‘Garganega’/‘Grecanico’, ‘Mantonico bianco’, ‘Orsolina’/‘Coccalona nera’, ‘Muscat à petits grains blanc’, ‘Malvasia odorosissima’, ‘Sangiovese’, ‘Sciaccarello’, ‘Visparola’ and ‘Vulpea’. The pedigree reconstruction by fullsib and second-degree relationships highlighted the pivotal role of some cultivars, such as ‘Visparola’, until now scarcely known. A hypothetic migration of this variety from Southern to Northern Italy along the Eastern side, as well as ‘Sangiovese’ migration from Southern to Central Italy along the Western side might be supposed. Moreover, ‘Muscat à petits grains blanc’, mainly through its offspring ‘Malvasia odorosissima’, furnished a consistent contribution to the development of many aromatic grapes grown in the Northern-Western part of the Italian Peninsula. These results represent the most complete study of grapevine Italian population genetics that has been carried out until now on the Italian germplasm. [ABSTRACT FROM AUTHOR]

Individuals with specific language impairment (SLI) struggle with language acquisition despite average non-verbal intelligence and otherwise typical development. One SLI account focuses on grammar acquisition delay. The current study aimed to detect novel rare genetic variants associated with performance on a grammar assessment, the Test of Early Grammatical Impairment (TEGI), in English-speaking children. The TEGI was selected due to its sensitivity and specificity, consistently high heritability estimates, and its absence from all but one molecular genetic study. We performed whole exome sequencing (WES) in eight families with SLI (n = 74 total) and follow-up Sanger sequencing in additional unrelated probands (n = 146). We prioritized rare exonic variants shared by individuals with low TEGI performance (n = 34) from at least two families under two filtering workflows: (1) novel and (2) previously reported candidate genes. Candidate variants were observed on six new genes (PDHA2, PCDHB3, FURIN, NOL6, IQGAP3, and BAHCC1), and two genes previously reported for overall language ability (GLI3 and FLNB). We specifically suggest PCDHB3, a protocadherin gene, and NOL6 are critical for ribosome synthesis, as they are important targets of SLI investigation. The proposed SLI candidate genes associated with TEGI performance emphasize the utility of precise phenotyping and family-based genetic study. [ABSTRACT FROM AUTHOR]

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Background: Osteosarcoma is a malignant bone neoplasia that has high welfare consequences for affected dogs. Awareness of breed and canine conformational risk factors for osteosarcoma can assist with earlier diagnosis and improved clinical management. Study of osteosarcoma in dogs also offers translational value for humans. Anonymised clinical data within VetCompass on dogs under primary veterinary care in the UK were searched for osteosarcoma cases. Descriptive statistics reported overall and breed-specific prevalence. Risk factor analysis used multivariable logistic regression modelling. Results: From 905,552 study dogs, 331 osteosarcoma cases were confirmed yielding a one-year period prevalence of 0.037% (95% CI: 0.033–0.041). Breeds with the highest annual prevalence were the Scottish Deerhound (3.28%, 95% CI 0.90–8.18), Leonberger (1.48%, 95% CI 0.41- 3.75), Great Dane (0.87%, 95% CI 0.43- 1.55) and Rottweiler (0.84%, 95% CI 0.64–1.07). The median age at diagnosis was 9.64 years (IQR: 7.97–11.41). Following multivariable modelling, 11 breeds showed increased odds of osteosarcoma compared with crossbred dogs. Breeds with the highest odds included Scottish Deerhound (OR 118.40, 95% CI 41.12–340.95), Leonberger (OR 55.79, 95% CI 19.68–158.15), Great Dane (OR 34.24, 95% CI 17.81–65.83) and Rottweiler (OR 26.67, 95% CI 18.57–38.29). Compared with breeds with mesocephalic skull conformation, breeds with dolichocephalic skull conformation (OR 2.72, 95% CI 2.06–3.58) had increased odds while breeds with brachycephalic skull conformation showed reduced odds (OR 0.50, 95% CI 0.32–0.80). Chondrodystrophic breeds had 0.10 times the odds (95% CI 0.06–0.15) compared with non-chondrodystrophic breeds. Increasing adult bodyweight was associated with increasing odds of osteosarcoma. Conclusions: The current study cements the concept that breed, bodyweight and longer leg or longer skull length are all strong risk factors for osteosarcoma in dogs. With this awareness, veterinarians can update their clinical suspicion and judgement, breeders can select towards lower-risk animals, and researchers can robustly define more useful study populations for fundamental and translational bioscience. Plain English summary: Osteosarcoma describes a serious bone tumour. Affected dogs often show a bony or soft tissue swelling with severe pain. Canine and human osteosarcoma show similar patient characteristics, clinical course and tumour biology that make studies on canine osteosarcoma highly valuable to inform on the human disease. This study aimed to interrogate anonymised veterinary clinical data from the VetCompass Programme to explore whether demographic information on dogs such as breed, bodyweight and body shape could be useful to predict osteosarcoma. VetCompass shares anonymised veterinary clinical records for welfare-focused research. This study explored the records of 905,552 dogs under veterinary care in 2016 to identify all cases of osteosarcoma. Advanced statistical methods were used to evaluate links between demographic factors and the risk of osteosarcoma. From the overall study population of 905,552 dogs, there were 331 osteosarcoma cases identified to show a one-year period prevalence of 0.037%. The breeds with the highest frequency of osteosarcoma were the Scottish Deerhound (3.28%), Leonberger (1.48), Great Dane (0.87%), Rottweiler (0.84%) and Greyhound (0.62%). Eleven breeds showed increased risk of osteosarcoma compared with crossbred dogs. Breeds with the highest risk included Scottish Deerhound (× 118.40 times risk), Leonberger (× 55.79), Great Dane (× 34.24) and Rottweiler (× 26.67). Aging was progressively and strongly associated with increasing risk of osteosarcoma. Dogs weighing heavier that the average for their breed had 1.65 times the risk than animals weighing below the breed average. Insured dogs had 1.71 times the risk of being diagnosed with osteosarcoma compared with uninsured dogs which may indicate higher levels of healthcare given to insured dogs compared to uninsured dogs. Chondrodystrophic (short-legged) breeds had 0.10 times the risk of osteosarcoma compared with non-chondrodystrophic breeds. Compared with breeds with mesocephalic (average length) skull conformation, breeds with dolichocephalic (long) skull conformation (× 2.72) had increased odds of osteosarcoma while breeds with brachycephalic (short) skull conformation showed reduced risk (× 0.50). This study cements the concept that breed, bodyweight and longer leg or longer skull length all predispose to osteosarcoma in dogs. With this awareness, veterinarians can update their clinical suspicion and judgement, breeders can select towards lower-risk animals, and researchers can define more useful study populations for better research. [ABSTRACT FROM AUTHOR]

Background: The Boxer is a popular dog breed with a distinctive appearance. However, the breed has been linked with several health conditions, some of which have been associated with its moderately brachycephalic conformation and its white colouration. Anonymised primary-care veterinary clinical records were explored to extract data on the demography, common disorders and mortality of Boxers in the UK in 2016. Results: The study population of 336,865 dogs included 3,219 (0.96%) Boxers, of which 10.71% were recorded as white. The mean adult bodyweight was 30.43 kg (SD 5.73 kg). Annual disorder counts did not differ statistically between the sexes or between white and non-white Boxers. The most prevalent fine-level precision disorders were otitis externa (n = 230, 7.15%), epulis (188, 5.84%), corneal ulceration (161, 5.00%) and periodontal disease (149, 4.63%). Of the 34 most common fine-level disorders, none differed in prevalence between white and non-white dogs. The most prevalent disorder groups were skin disorder (n = 571, 17.74%), neoplasia (457, 14.20%) and ear disorder (335, 10.41%). White Boxers had higher prevalence than non-white Boxers for two disorder groups: dental disorder and brain disorder. The median longevity of 346 Boxers that died during the study was 10.46 years (IQR 9.00–11.98, range 2.76–18.00). Median longevity did not differ statistically between the sexes or between white and non-white Boxers. The most common grouped causes of death were death – unrecorded cause (n = 73, 21.10%), neoplasia (43, 12.43%) and brain disorder (33, 9.54%). Conclusions: There was minimal evidence of substantial health differences between white and non-white Boxers. Among the four most common disorders recorded in Boxers, two were typically common across all types of dogs (otitis externa and periodontal disease) while two suggested strong predispositions for the Boxer breed (epulis and corneal ulceration), showing the value of eliciting breed-specific disorder patterns for insights for potential health reforms. The overall longevity of Boxer dogs was consistent with other breeds of similar body size. Plain English summary: The Boxer is a medium-large sized, active dog with a short coat and a moderately flat-faced (brachycephalic) skull shape. Despite many decades of popularity in the UK, there is limited published evidence on the overall health profile of Boxers. White-coloured Boxers are thought to be at higher risk of deafness from birth and as a result, white Boxers have traditionally often been culled at birth by breeders. Using anonymised veterinary clinical records collected within the VetCompass Programme at the Royal Veterinary College (RVC), Boxers made up around 1% of all dogs in the UK in 2016, with an average adult bodyweight around 30 kg. The most common colours were brindle (22.82%), dark red (22.62%) and dark red multi-colour (20.92%), with 10.71% white Boxers. Across the 3,219 Boxers in the study, 73.97% had at least one disorder recorded during 2016. The average number of disorders per year did not differ statistically between female and male Boxers, or between white and non-white Boxers. The most common specific disorders in Boxers were ear infection (7.15%), gum mass (5.84%), eye ulcer (5.00%) and dental disease (4.63%). White and non-white dogs did not differ in their risk for any of the 34 most common specific disorders. Only two dogs in the study were recorded with deafness; one white and one non-white. The average lifespan of Boxers overall was 10.46 years. Lifespan did not differ statistically between female and male Boxers, or between white and non-white Boxers. This study identifies ongoing popularity for the Boxer in the UK, with around 10% of these Boxers being white. There was minimal evidence of health differences between male and female Boxers, or between white and non-white Boxers. Among the four most common disorders recorded in Boxers, two are typically common across all types of dogs (ear and dental disease) while two showed strong predisposition in the Boxer breed (gum mass and eye ulcer), suggesting the value of understanding breed-specific health patterns to prioritise health plans for each breed. The overall longevity of Boxer dogs was typical of other breeds of this body size. [ABSTRACT FROM AUTHOR]

Empathetic the inherited configuration of rapeseed cultivars is a precondition to consider phylogenetic pedigree, population structure, haplotype block in the target population. In this investigation, from different regions we have 85 rapeseeds (13rassica napus L.) cultivars. DNA was extracted by using C I A13 method. Phylogenetic pedigree, haplotype block and SNP hotspots, Population structure is analyzed by using the 5058 Single Nucleotide Polymorphisms SNP markers to this research 85 rapeseed cultivars were considered. Phylogenetic was analyzed by using Power Marker software and MEGA software, Haplo View was using to analysis the haplotype block, population structures were analyzed by using population structure software 2.3.4 manual user as K increasing sidewise from 1 into 10, recording AK valency shown at K=2 hence, 85 rapeseed cultivar were divided into two subcategories, P 1 subgroups including 13 cultivars and P2 subcategory including 72 cultivars, SNP hotspots determined by using map chart software. In this research, the haplotype block analysis presented that the SNP markers number in A sub genome is more than the C sub genome, the block numbers on chromosomes A06 and CO3 are greater than the other chromosomes and the lowest block number is on chromosome C09. The hotspots of SNP were defined by SNP position, mutation frequency, and the number of SNPs per 100Kbp on the chromosome. The phylogenetic pedigree was constructed, neighbor joining based on genetic similarity and kinship. In this study, 85 rapeseeds are branched into 12 major groups. [ABSTRACT FROM AUTHOR]

Background: The English Cocker Spaniel (ECS) is a common family dog in the UK. This study aimed to describe demography, morbidity, and mortality in ECS under primary veterinary care in the UK during 2016 using data from the VetCompass™ Programme. This study hypothesised that the prevalence of aggression is higher in male than female ECS, and higher in solid-coloured than bi-coloured ECS. Results: English Cocker Spaniels comprised 10,313/336,865 (3.06%) of dogs under primary veterinary care during 2016. The median age was 4.57 years (inter-quartile range (IQR) 2.25–8.01) and the median adult bodyweight was 15.05 kg (IQR 13.12–17.35). The annual proportional birth rate was relatively stable between 2.97–3.51% from 2005–2016. The most common specific diagnoses were periodontal disease (n = 486, prevalence 20.97%, 95% confidence interval (CI): 19.31–22.62), otitis externa (n = 234, 10.09%, 95% CI: 8.87–11.32), obesity (n = 229, 9.88%, 95% CI: 8.66–11.09), anal sac impaction (n = 187, 8.07%, 95% CI: 6.96–9.18), diarrhoea (n = 113, 4.87%, 95% CI: 4.00–5.75), and aggression (n = 93, 4.01%, 95% CI: 3.21–4.81). The prevalence of aggression was higher in males (4.95%) than in females (2.87%) (P = 0.015) and in solid-coloured (7.00%) than in bi-coloured dogs (3.66%) (P = 0.010). The median age at death was 11.44 years (IQR 9.46–13.47) and the most common grouped causes of death were neoplasia (n = 10, 9.26%, 95% CI: 3.79–14.73), mass-associated disorders (n = 9, 8.33%, 95% CI: 4.45–15.08), and collapse (n = 8, 7.41%, 95% CI: 3.80–13.94). Conclusions: Periodontal disease, otitis externa, and obesity are identified as the most common health issues for ECS, and neoplasia and mass-associated disorders as the most common reasons for death. The prevalence of aggression was higher in males and solid-coloured dogs. The results can aid veterinarians in giving evidence-based health and breed choice information to dog owners and highlights the importance of thorough oral examination and body condition score evaluation during routine veterinary examination of ECS. Plain English summary: The English Cocker Spaniel (ECS) is a popular family dog in the UK, but there is limited information regarding common disorders affecting the breed. The goal of this study was to describe demography (age, sex, neuter, and bodyweight), disease occurrence, lifespan, and reasons for death in ECS by using data from the VetCompass™ Programme. The VetCompass™ Programme collects information from anonymised clinical records of dogs attending first-opinion veterinary practices in the UK. This study hypothesised that aggression is more common in males than in females, and in solid-coloured than in bi-coloured ECS dogs. English Cocker Spaniels comprised 10,313/336,865 (3.06%) of dogs under primary veterinary care during 2016. Breed popularity did not vary much from 2005 to 2016, comprising around 3% of all dogs born each year. The average age of dogs in 2016 was 4.57 years and the average adult bodyweight was 15.05 kg. The most common disorders were periodontal disease (infection of the tissues that hold the teeth in place, affecting 20.97% of the dogs), inflammation of the external ear canal (10.09%), obesity (9.88%), anal sac impaction (8.07%), diarrhoea (4.87%), and aggression (4.01%). Aggression was more common in males (4.95%) than in females (2.87%) and in solid-coloured (7.00%) than in bi-coloured (3.66%) dogs. The frequency of aggression also varied across the four most common solid colours (black, liver, golden, red), with golden-coloured dogs showing the most aggression (12.08%). The average lifespan was 11.44 years and the most common cause of death was tumours. This study shows that first-opinion clinical records can help us to understand and enhance breed health. The results can guide veterinarians in giving breed-adapted information to owners of ECS and help breeders to optimise breeding decisions. Further, this information can be used by future ECS owners to make more informed decisions when acquiring a dog if avoidance of aggression is a key priority. Periodontal disease was the most common condition affecting the breed, which highlights the importance of regular veterinary dental checks and as well as tooth brushing in ECS. [ABSTRACT FROM AUTHOR]

An individual's lifetime reproductive success (LRS) measures its realized genetic contributions to the next generation, but how well does it predict this over longer periods? Here we use human genealogical data to estimate expected individual genetic contributions (IGC) and quantify the degree to which LRS, relative to other fitness proxies, predicts IGC over longer periods. This allows an identification of the life-history stages that are most important in shaping variation in IGC. We use historical genealogical data from two non-isolated local populations in Switzerland to estimate the stabilized IGC for 2230 individuals approximately 10 generations after they were born. We find that LRS explains 30% less variation in IGC than the best predictor of IGC, the number of grandoffspring. However, albeit less precise than the number of grandoffspring, we show that LRS does provide an unbiased prediction of IGC. Furthermore, it predicts IGC better than lifespan, and accounting for offspring survival to adulthood does not improve the explanatory power. Overall, our findings demonstrate the value of human genealogical data to evolutionary biology and suggest that reproduction—more than lifespan or offspring survival—impacts the long-term genetic contributions of historic humans, even in a population with appreciable migration. [ABSTRACT FROM AUTHOR]