Von-Hipple Lindau syndrome with family history: a case report and seventeen years follow-up study

Background

Von-Hipple Lindau syndrome is an uncommon autosomal dominant disorder. 17 years ago we diagnosed a young woman with VHL syndrome validated by Sanger sequencing, her family members were genetically tested as well, and 187 healthy people were randomly selected for VHL genetic testing as controls. We analyze the clinical and genetic characteristics of VHL syndrome in a Chinese lineage and with 17-year follow-up.

Case presentation

A woman was finally diagnosed with VHL syndrome due to the detection of a missense mutation c.353T > C in exon 2 of the short arm of chromosome 3, which resulted in a leucine substitution at amino acid 118 of the encoded protein by a proline, which may be thought the main cause of the disease. The same mutation was observed in two other family members, their clinical symptoms are not entirely identical. However, this mutation was not found in other family members or 187 healthy controls. She clinically presented with central nervous system hemangioblastomas, clear renal cell carcinoma, and pancreatic neuroendocrine neoplasms, despite the multi-organ involvement and several relapses during the disease, the patients survive well for she was treated with aggressive surgery early in the course of the plaguing symptoms, whereas patients who are not aggressively treated have a poorer prognosis.

Conclusion

The clinical presentation of VHL syndrome is atypical, and early identification and treatment of VHL syndrome is possible by genetic testing techniques. Multiple relapses occurred during the course of the disease, but early diagnosis and aggressive treatment allowed the patients to survive well.

Population Subdivision and Migration Assessment of Mangalica Pig Breeds Based on Pedigree Analysis

In conserving the genetic diversity of domestic animal breeds, strategies that emphasise between-breed diversity may not be optimal, as they neglect within-breed variation. The aim of the present study was to assess the extent of population subdivision in three Mangalica pig breeds and the contribution of migration to their substructure. Wright's FST coefficient was calculated based on genealogical data with breeding animals born between 1981 and 2023, with three colour variants (Blonde, Swallow-Belly and Red). These Wright's FST coefficients were analysed using multidimensional scaling to reveal the population substructure. The average FST coefficient was 0.04 for the Blonde breed and 0.047 for the Swallow-Belly and Red Mangalica breeds, while these parameters were lower in the active herds at 0.03 and 0.04, respectively. The migration of individuals between herds was 61.63% for the Blonde breed and 75.53% and 63.64% for the Swallow-Belly and Red Magalica breeds, respectively. No population substructure was observed in any of the Mangalica breeds, which can be explained by the extensive migration between herds.

Experience with cascade screening: A comprehensive family pedigree analysis of two index patients with Fabry disease

The wide range of clinical symptoms observed in patients with Fabry disease (FD) often leads to delays in diagnosis and initiation of treatment. Delayed initiation of therapy may result in end-organ damage, such as chronic renal failure, hypertrophic cardiomyopathy, and stroke. Although some tools are available to identify undiagnosed patients, new comprehensive screening methods are needed. In this study, the outcomes of the cascade screening applied to three index cases with FD from 2 familes were investigated. In the pedigree analysis, 280 individuals were included; out of them, 131 individuals underwent genetic testing and cascade screening for FD. During the screening program, a total of 45 individuals were diagnosed, with a diagnostic ratio of 1:15. The average age at diagnosis for all individuals was 30.9 ± 17.7 years, and %25 were pediatric cases (mean age 9.5 ± 5.9 years). Thirty affected relatives were diagnosed from the two index cases in Family 1 and 15 individuals were diagnosed from one index case in Family 2. There were 13 consanguineous marriages observed among 2 pedigres, in two both spouses  were affected, leading to two homozygous affected daughters in one couple. In regions where there is a high prevalence of consanguineous marriages, implementing the cascade screening approach to identify all individuals at risk can be beneficial for patients with FD, specifically women and children.

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Distinct patterns of inheritance shape life-history traits in steelhead trout

Life-history variation is the raw material of adaptation, and understanding its genetic and environmental underpinnings is key to designing effective conservation strategies. We used large-scale genetic pedigree reconstruction of anadromous steelhead trout (Oncorhynchus mykiss) from the Russian River, CA, USA, to elucidate sex-specific patterns of life-history traits and their heritability. SNP data from adults returning from sea over a 14-year period were used to identify 13,474 parent-offspring trios. These pedigrees were used to determine age structure, size distributions and family sizes for these fish, as well as to estimate the heritability of two key life-history traits, spawn date and age at maturity (first reproduction). Spawn date was highly heritable (h2  = 0.73) and had a cross-sex genetic correlation near unity. We provide the first estimate of heritability for age at maturity in ocean-going fish from this species and found it to be highly heritable (h2 from 0.29 to 0.62, depending on sex and method), with a much lower genetic correlation across sexes. We also evaluated genotypes at a migration-associated inversion polymorphism and found sex-specific correlations with age at maturity. The significant heritability of these two key reproductive traits in these imperiled fish, and their patterns of inheritance in the two sexes, is consistent with predictions of both natural and sexually antagonistic selection (sexes experience opposing selection pressures). This emphasizes the importance of anthropogenic factors, including hatchery practices and ecosystem modifications, in shaping the fitness of this species, thus providing important guidance for management and conservation efforts.

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR's ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

GRAMM: A new method for analysis of HLA in families

Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for stem cell transplants. Haplotype sharing detection requires the imputation of donor and recipient. We show that even in high-resolution typing when all alleles are known, there is a 15% error rate in haplotype phasing, and even more in low-resolution typings. Similarly, in related donors, the parents' haplotypes should be imputed to determine what haplotype each child inherited. We propose graph-based family imputation (GRAMM) to phase alleles in family pedigree HLA typing data, and in mother-cord blood unit pairs. We show that GRAMM has practically no phasing errors when pedigree data are available. We apply GRAMM to simulations with different typing resolutions as well as paired cord-mother typings, and show very high phasing accuracy, and improved allele imputation accuracy. We use GRAMM to detect recombination events and show that the rate of falsely detected recombination events (false-positive rate) in simulations is very low. We then apply recombination detection to typed families to estimate the recombination rate in Israeli and Australian population datasets. The estimated recombination rate has an upper bound of 10%-20% per family (1%-4% per individual).

Evaluating the utility of effective breeding size estimates for monitoring sea lamprey spawning abundance

Sea lamprey (Petromyzon marinus) is an invasive species that is a significant source of mortality for populations of valued fish species across the North American Great Lakes. Large annual control programs are needed to reduce the species' impacts; however, the number of successfully spawning adults cannot currently be accurately assessed. In this study, effective breeding size (N b) and the minimum number of spawning adults (N s) were estimated for larval cohorts from 17 tributaries across all five Great Lakes using single nucleotide polymorphisms (SNP) genotyped via RAD-capture sequencing. Reconstructed larval pedigrees showed substantial variability in the size and number of full- and half-sibling groups, N b (<1-367), and N s (5-545) among streams. Generalized linear models examining the effects of stream environmental characteristics and aspects of sampling regimes on N b and N s estimates identified sample size, the number of sampling sites, and drainage area as important factors predicting N b and N s. Correlations between N b, N s, and capture-mark-recapture estimates of adult census size (N c) increased when streams with small sample sizes (n < 50) were removed. Results collectively indicate that parameters estimated from genetic data can provide valuable information on spawning adults in a river system, especially if sampling regimes are standardized and physical stream covariates are included.

Temporal Changes in Demography and Genetic Diversity of Oriental Storks at the Stage of Long-Term Captive Propagation and Reintroduction Initiation

Captive propagation and reintroduction are the major steps in the ex-situ conservation of locally extirpated endangered species in a historical region. In a species restoration project conducted in South Korea, we examined temporal changes in demographics and genetic diversity of oriental storks (Ciconia boyciana). Demographic and genetic data from 1996-2018 were analyzed for 80% of all captive and recently reintroduced individuals. Founder establishment and pair formation induced increases in population size and genetic diversity during the early stage of captive propagation. The degree of genetic diversity was found to become saturated and stable with long-term captive propagation. However, this might be a concern for future genetic diversity of both captive and reintroduced populations simultaneously due to the extraction of captive populations at the early stage of reintroduction. Our findings suggest that periodic evaluation of genetic diversity and selection for releasing individuals, using effective genetic markers, would assist in balancing the genetic diversity of the captive and reintroduced oriental storks at the early stage of reintroduction.

Methods and Research Hotspots of Forensic Kinship Testing

Kinship testing is widely needed in forensic science practice. This paper reviews the definitions of common concepts, and summarizes the basic principles, advantages and disadvantages, and application scope of kinship analysis methods, including identity by state (IBS) method, likelihood ratio (LR) method, method of moment (MoM), and identity by descent (IBD) segment method. This paper also discusses the research hotspots of challenging kinship testing, complex kinship testing, forensic genetic genealogy analysis, and non-human biological samples.

An insight into population structure and genetic progress of Argentinean Holstein cattle

The objective of the present study was to investigate the most critical issues associated with the limited genetic progress evidenced in the Argentinean Holstein ("Holando Argentino") breed in the last 20 years (only 26% of the phenotypic trend in milk yield was due to genetics). The study comprised the analysis of population structure, realized genetic selection differentials, genetic progress and partition of genetic trends by sex and country of origin from 1936 to 2019 (1,045,582 records; 24,680 sires and 619,322 dams in the pedigree). Average inbreeding steadily increased in the last 15 generations (ΔF = 0.6%, which translates to Ne = 75). Partition of genetic trends revealed that local genetics made a negligible contribution to genetic progress, which for most traits was highly dependent on imported genetics (>80%). Mean generation intervals were fairly constant until 2009 (8-9 years for males and 5-6 years for females, respectively) and then decreased, especially in the paths of sires of bulls and dams of bulls (to 5 and 4 years, respectively) mostly due to the influence of imported sires. The reduction in generation intervals was counterbalanced by a marked deterioration of realized selection differentials, particularly in the path of sires of bulls that nevertheless made the largest contribution to genetic progress. In the last 20 years, realized selection differentials in this path went from 533.6 to 170.8 kg for milk yield and from 16.7 to 13.3 kg for protein yield (1.7-0.5 and 1.6-1.3 standard deviation units, respectively). Among all considered traits (milk yield, fat yield, protein yield, stature, final score and daughter pregnancy rate) in the analysed period, annual genetic gain was negative for milk yield, fairly constant for composition and conformation traits, and positive only in the case of daughter pregnancy rate. Considered together, these results suggest that limited genetic progress is due to the absence of a sound breeding programme that includes genomic selection and a carefully defined selection objective, together with the absence of stronger regulations in germplasm importation; however, other factors such as potential genetics by environment interactions cannot be ruled out.

Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆F_i), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆F_i in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with N_e < 50. The next most endangered breeds are exotic, country, and heath breeds, with average N_e of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average N_e of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds.

Hereditary coagulation factor VII deficiency caused by novel compound heterozygous mutations in a Chinese pedigree: A case report

BACKGROUND

Congenital coagulation factor VII (FVII) deficiency is a rare, autosomal-recessive haemorrhagic disorder with an estimated incidence of 1:500,000. This disorder is caused by mutations in the F7 gene.

CASE DESCRIPTION

Here, we report a pedigree of congenital FVII deficiency. The proband was a 30-year-old female with severely low FVII activity and a history of menorrhagia and epistaxis since her childhood who was subsequently diagnosed with congenital compound heterozygous FVII deficiency. A genetic study revealed a novel combination of compound heterozygous mutations (c.64G 〉 A, p.Gly22Ser and c.1027G 〉 A, p.Gly343Ser). Her father and older son had the c.64G 〉 A, p.Gly22Ser (heterozygous) mutation. Her mother and younger son had the c.1027G 〉 A, p.Gly343Ser (heterozygous) mutation. The predicted results of PolyPhen-2 and MutationTaster indicated that these mutations were probably damaging and disease-causing, respectively.

CONCLUSION

In this study, we identified a novel combination of genetic mutations that could expand the mutant library and help in elucidating the pathogenesis of hereditary human coagulation FVII deficiency. A novel combination of compound heterozygous mutations was reported for the first time in Chinese individuals.

Two-locus identity coefficients in pedigrees

This paper proposes a solution to a long-standing problem concerning the joint distribution of allelic identity by descent between two individuals at two linked loci. Such distributions have important applications across various fields of genetics, and detailed formulas for selected relationships appear scattered throughout the literature. However, these results were obtained essentially by brute force, with no efficient method available for general pedigrees. The recursive algorithm described in this paper, and its implementation in R, allow efficient calculation of two-locus identity coefficients in any pedigree. As a result, many existing procedures and techniques may, for the first time, be applied to complex and inbred relationships. Two such applications are discussed, concerning the expected likelihood ratio in forensic kinship testing, and variances in realized relatedness.

A 69 kbp Deletion at the Berry Color Locus Is Responsible for Berry Color Recovery in Vitis vinifera L. Cultivar 'Riesling Rot'

‘Riesling Weiss’ is a white grapevine variety famous worldwide for fruity wines with higher acidity. Hardly known is ‘Riesling Rot’, a red-berried variant of ‘Riesling Weiss’ that disappeared from commercial cultivation but has increased in awareness in the last decades. The question arises of which variant, white or red, is the original and, consequently, which cultivar is the true ancestor. Sequencing the berry color locus of ‘Riesling Rot’ revealed a new VvmybA gene variant in one of the two haplophases called VvmybA3/1RR. The allele displays homologous recombination of VvmybA3 and VvmybA1 with a deletion of about 69 kbp between both genes that restores VvmybA1 transcripts. Furthermore, analysis of ‘Riesling Weiss’, ‘Riesling Rot’, and the ancestor ‘Heunisch Weiss’ along chromosome 2 using SSR (simple sequence repeat) markers elucidated that the haplophase of ‘Riesling Weiss’ was inherited from the white-berried parent variety ‘Heunisch Weiss’. Since no color mutants of ‘Heunisch Weiss’ are described that could have served as allele donors, we concluded that, in contrast to the public opinion, ‘Riesling Rot’ resulted from a mutational event in ‘Riesling Weiss’ and not vice versa.

Pedigree analysis and estimates of effective breeding size characterize sea lamprey reproductive biology

The sea lamprey (Petromyzon marinus) is an invasive species in the Great Lakes and the focus of a large control and assessment program. Current assessment methods provide information on the census size of spawning adult sea lamprey in a small number of streams, but information characterizing reproductive success of spawning adults is rarely available. We used RAD-capture sequencing to genotype single nucleotide polymorphism (SNP) loci for ~1600 sea lamprey larvae collected from three streams in northern Michigan (Black Mallard, Pigeon, and Ocqueoc Rivers). Larval genotypes were used to reconstruct family pedigrees, which were combined with Gaussian mixture analyses to identify larval age classes for estimation of spawning population size. Two complementary estimates of effective breeding size (N b), as well as the extrapolated minimum number of spawners (N s), were also generated for each cohort. Reconstructed pedigrees highlighted inaccuracies of cohort assignments from traditionally used mixture analyses. However, combining genotype-based pedigree information with length-at-age assignment of cohort membership greatly improved cohort identification accuracy. Population estimates across all three streams sampled in this study indicate a small number of successfully spawning adults when barriers were in operation, implying that barriers limited adult spawning numbers but were not completely effective at blocking access to spawning habitats. Thus, the large numbers of larvae present in sampled systems were a poor indicator of spawning adult abundance. Overall, pedigree-based N b and N s estimates provide a promising and rapid assessment tool for sea lamprey and other species.

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non‐founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.

Estimating the Additive Heritability of Historiometric Eminence in a Super-Pedigree Comprised of Four Prominent Families

By merging analytical approaches from the fields of historiometrics and behavior genetics, a social pedigree-based estimate of the heritability of eminence is generated. Eminent individuals are identified using the Pantheon dataset. A single super-pedigree, comprised of four prominent and interrelated families (including the Wedgwood-Darwin, Arnold-Huxley, Keynes-Baha'u'lláh, and Benn-Rutherford pedigrees) is assembled, containing 30 eminent individuals out of 301 in total. Each eminent individual in the super-pedigree is assigned a relative measure of historical eminence (scaled from 1 to 100) with noneminent individuals assigned a score of 0. Utilizing a Bayesian pedigree-based heritability estimation procedure employing an informed prior, an additive heritability of eminence of .507 (95% CI [.434, .578]) was found. The finding that eminence is additively heritable is consistent with expectations from behavior-genetic studies of factors that are thought to underlie extraordinary accomplishment, which indicate that they are substantially additively heritable. Owing to the limited types of intermarriage present in the data, it was not possible to estimate the impact of nonadditive genetic contributions to heritability. Gene-by-environment interactions could not be estimated in the present analysis either; therefore, the finding that eminence is simply a function of additive genetic and nonshared environmental variance should be interpreted cautiously.

Distinct error rates for reference and nonreference genotypes estimated by pedigree analysis

Errors in genotype calling can have perverse effects on genetic analyses, confounding association studies, and obscuring rare variants. Analyses now routinely incorporate error rates to control for spurious findings. However, reliable estimates of the error rate can be difficult to obtain because of their variance between studies. Most studies also report only a single estimate of the error rate even though genotypes can be miscalled in more than one way. Here, we report a method for estimating the rates at which different types of genotyping errors occur at biallelic loci using pedigree information. Our method identifies potential genotyping errors by exploiting instances where the haplotypic phase has not been faithfully transmitted. The expected frequency of inconsistent phase depends on the combination of genotypes in a pedigree and the probability of miscalling each genotype. We develop a model that uses the differences in these frequencies to estimate rates for different types of genotype error. Simulations show that our method accurately estimates these error rates in a variety of scenarios. We apply this method to a dataset from the whole-genome sequencing of owl monkeys (Aotus nancymaae) in three-generation pedigrees. We find significant differences between estimates for different types of genotyping error, with the most common being homozygous reference sites miscalled as heterozygous and vice versa. The approach we describe is applicable to any set of genotypes where haplotypic phase can reliably be called and should prove useful in helping to control for false discoveries.

Novel factor VII gene mutations in six families with hereditary coagulation factor VII deficiency

Introduction

Hereditary human coagulation factor VII (FVII) deficiency is an inherited autosomal recessive hemorrhagic disease involving mutations in the F7 gene. The sites and types of F7 mutations may influence the coagulation activities of plasma FVII (FVII: C) and severity of hemorrhage symptoms. However, the specific mutations that impact FVII activity are not completely known.

Methods

We tested the coagulation functions and plasma activities of FVII in seven patients recruited from six families with hereditary FVII deficiency and sequenced the F7 gene of the patients and their families. Then, we analyzed the genetic information from the six families and predicted the structures of the mutated proteins.

Results

In this study, we detected 11 F7 mutations, including four novel mutations, in which the mutations p.Phe84Ser and p.Gly156Cys encoded the Gla and EGF domains of FVII, respectively, while the mutation p.Ser339Leu encoded the recognition site of the enzymatic protein and maintained the conformation of the catalytic domain structure. Meanwhile, the mutation in the 5′ untranslated region (UTR) was closely associated with the mRNA regulatory sequence.

Conclusion

We have identified novel genetic mutations and performed pedigree analysis that shed light on the pathogenesis of hereditary human coagulation FVII deficiency and may contribute to the development of treatments for this disease.

In this study, we performed coagulation index tests and gene sequencing on 7 hereditary FVII deficiency patients and their family members to explain the pathogenesis of the disease based on the analysis of their genetic information. Also, we compared the structures of newly discovered mutant proteins with the wild type and predicted their pathogenicity. To sum up, this study expands our insight on the pathogenesis of hereditary human coagulation FVII deficiency.

SERINC2 increases the risk of bipolar disorder in the Chinese population

BACKGROUND

Although common variants in a large collection of patients are associated with increased risk for bipolar disorder (BD), studies have only been able to predict 25%-45% of risks, suggesting that lots of variants that contribute to the risk for BD haven't been identified. Our study aims to identify novel BD risk genes.

METHODS

We performed whole-exome sequencing of 27 individuals from 6 BD multi-affected Chinese families to identify candidate variants. Targeted sequencing of one of the novel risk genes, SERINC2, in additional sporadic 717 BD patients and 312 healthy controls (HC) validated the association. Magnetic resonance imaging (MRI) were performed to evaluate the effect of the variant to brain structures from 213 subjects (4 BD subjects from a multi-affected family, 130 sporadic BD subjects and 79 HC control).

RESULTS

BD pedigrees had an increased burden of uncommon variants in extracellular matrix (ECM) and calcium ion binding. By large-scale sequencing we identified a novel recessive BD risk gene, SERINC2, which plays a role in synthesis of sphingolipid and phosphatidylserine (PS). MRI image results show the homozygous nonsense variant in SERINC2 affects the volume of white matter in cerebellum.

CONCLUSIONS

Our study identified SERINC2 as a risk gene of BD in the Chinese population.

Behçet's Syndrome in a Chinese Pedigree of NLRP3-Associated Autoinflammatory Disease: A Coexistence or Novel Presentation?

Objectives:NLRP3-associated autoinflammatory disease (NLRP3-AID) and Behçet's syndrome (BS) both belong to autoinflammatory diseases and rarely co-occur. Here we reported a Chinese pedigree of NLRP3-AID presented with BS.

Methods: We recorded a Chinese pedigree of NLRP3-AID presented with BS. Whole-exome sequencing was performed to find the hereditary susceptibility gene, and Sanger sequencing was performed on a consecutive cohort of 30 BS patients. We also reviewed the English literature on vasculitis associated with NLRP3-AID.

Results: The proband was a 45-year-old Chinese Han woman. She and her 12-year-old daughter presented with recurrent fevers, cold-induced urticaria, oral, and genital ulcers, conjunctivitis, uveitis, optic atrophy, erythema nodosum, headache, and hearing loss. They were initially suspected of having BS, and both responded poorly to corticosteroids and immunosuppressants, while anti-TNF therapy was moderately effective. Pedigree analysis revealed another four relatives with similar symptoms, and a heterozygous NLRP3 gene mutation c.1316C>T, p.Ala439Val was identified by whole-exome sequencing and Sanger sequencing. However, we did not discover NLRP3 gene mutation by Sanger sequencing in a confirmative cohort of 30 BS cases. A few case reports of vasculitis coexisting with NLRP3-AID, including a case of glomerulonephritis, and five cases of retinal vasculitis, were summarized through literature review.

Conclusions: Our study is the first report of NLRP3-AID associated with BS. The coexistence of NLRP3-AID and BS reveals the extensive heterogeneity of the pathogenesis of systemic autoinflammatory diseases and calls for specific therapeutics.

Heritability and Pedigree Analyses of Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca Mulatta)

In a colony of rhesus macaques at California National Primate Research Center (CNPRC), naturally occurring hypertrophic cardiomyopathy (HCM) classified by left ventricular hypertrophy without obvious underlying diseases has been identified during necropsy over the last two decades. A preliminary pedigree analysis suggested a strong genetic predisposition of this disease with a founder effect. However, the mode of inheritance was undetermined due to insufficient pedigree data. Since 2015, antemortem examination using echocardiographic examination as well as other cardiovascular analyses have been performed on large numbers of rhesus macaques at the colony. Based on antemortem examination, HCM was diagnosed in additional 65 rhesus macaques. Using HCM cases diagnosed based on antemortem and postmortem examinations, the heritability (h²) was estimated to determine the degree of genetic and environmental contributions to the development of HCM in rhesus macaques at the CNPRC. The calculated mean and median heritability (h²) of HCM in this colony of rhesus macaques were 0.5 and 0.51 (95% confidence interval; 0.14-0.82), respectively. This suggests genetics influence development of HCM in the colony of rhesus macaques. However, post-translational modifications and environmental factors are also likely to contribute the variability of phenotypic expression. Based on the pedigree analysis, an autosomal recessive trait was suspected, but an autosomal dominant mode of inheritance with incomplete penetrance was also possible. Further investigation with more data from siblings, offspring, and parents of HCM-affected rhesus macaques are warranted. Importantly, the findings of the present study support conducting genetic investigations such as whole genome sequencing to identify the causative variants of inherited HCM in rhesus macaques.

The Nero Lucano Pig Breed: Recovery and Variability

Simple Summary

The reduction of biodiversity determines the loss of species and breeds, with the consequent disappearance of production systems, knowledge, cultures and local traditions. The Nero Lucano pig is a native breed of Southern Italy (Basilicata region) recovered, starting from 2001, because of the high quality of its cured meat products. This study gives a picture of the low genetic variability of this breed. Knowledge of individual inbreeding levels allows for planning of interventions to reduce the negative effects of the low effective population size and, then, improve the efficiency of the actual recovery project.

Abstract

The Nero Lucano (NL) pig is a black coat colored breed characterized by a remarkable ability to adapt to the difficult territory and climatic conditions of Basilicata region in Southern Italy. In the second half of the twentieth century, technological innovation, agricultural evolution, new breeding methods and the demand for increasingly lean meat brought the breed almost to extinction. Only in 2001, thanks to local institutions such as: the Basilicata Region, the University of Basilicata, the Regional Breeders Association and the Medio Basento mountain community, the NL pig returned to populate the area with the consequent possibility to appreciate again its specific cured meat products. We analyzed the pedigrees recorded by the breeders and the Illumina Porcine SNP60 BeadChip genotypes in order to obtain the genetic structure of the NL pig. Results evidenced that this population is characterized by long mean generation intervals (up to 3.5 yr), low effective population size (down to 7.2) and high mean inbreeding coefficients (F_MOL = 0.53, F_ROH = 0.39). This picture highlights the low level of genetic variability and the critical issues to be faced for the complete recovery of this population.

Feingold syndrome type 2 in a patient from China

Feingold syndrome type 2 (FGLDS2, MIM614326) is a genetic congenital malformation syndrome, caused by germline heterozygous deletion of MIR17HG on chromosome 13q31, which is extremely rare worldwide. To date, less than 25 patients have been described in the literature. Here, we report on a 3-year-old girl presented with hip dysplasia, polysyndactyly of the left thumb, brachymesophalangy of the fifth digit, microcephaly, intellectual disability, and growth delay. This is likely to be the first case of Feingold syndrome type 2 ever discovered among Chinese population. Through genetic testing and pedigree analysis, she was identified to have a de novo 4.8-Mb microdeletion at chromosome 13q31.3-q32.1, encompassing MIR17HG, GPC5, and GPC6. Additionally, we detected two common compound heterozygous variants (c.919-2A>G and c.147C>G) in SLC26A4 encoding pendrin protein, as well as a novel heterozygous variant c.985_988del in COMP encoding cartilage oligomeric matrix protein. This case report aims to analyze the microdeletion and the three types of variant detected in the patient, and to explore the association between the genotype and phenotype in patients with Feingold syndrome type 2, which may contribute to further understanding and future diagnosis of this disorder.

Pedigree and Molecular Analyses in the Assessment of Genetic Variability of the Polish Greyhound

Simple Summary

The Polish Greyhound is an old Polish breed. The first descriptions of hunting with greyhounds can be found in the hunting literature of the 16th century, and the first detailed description of a greyhound comes from 1600. The Polish Greyhound probably originates from the Saluki-type Asian greyhounds. The population of this breed is very small and limited mainly to the territory of its country of origin (Poland). Pedigree books were opened for this breed in 1981. The narrow gene pool necessitated mating relatives, resulting in the appearance of various genetic diseases in the breed. The analysis of Polish Greyhound pedigrees registered in the pedigree books from the time of the registration of the breed and molecular tests facilitated calculation of the degree of relatedness in the breed and to design future breeding plans, taking into account that a 2.56% increase in inbreeding per complete generation will be observed if the current breeding program and similar matings are maintained.

Abstract

The aim of the study was to assess the genetic variability of the Polish Greyhound population based on pedigree analysis and molecular DNA testing and to determine the degree of relatedness among individuals in the population. Pedigree data of 912 Polish Greyhounds recorded in pedigree books since they were opened for this breed were analyzed. For molecular testing, DNA was obtained from cheek swabs taken from 235 dogs of the tested breed. A panel of 21 markers (Short Tandem Repeat—STR) was used. The mean inbreeding determined for the Polish Greyhound population based on pedigree analyses was low and amounted to 11.8%, but as many as 872 individuals of the 912 dogs in the studied population were inbred. A total of 83 founders (at least one unknown parent) were identified, among which 27 founders had both unknown parents. Full-sibling groups consisted of 130 individuals, with a minimum and maximum litter size of 2 and 16, respectively. The average litter size was 5.969. Gene diversity calculated based on the mean kinship matrix was 0.862 and the population mean kinship was 0.138. The founder genome equivalent based on the mean kinship matrix was 3.61; the founder genome surviving level was 12.34; the mean Ne was estimated at 21.76; and the Ne/N ratio was 0.135. The FIS inbreeding coefficient for 21 STR was negative, and the mean FIS value for all loci had a low negative value (−0.018). These values suggest a low level of inbreeding in the examined breed as well as the avoidance of mating related animals.

The Economic Impact of Exchanging Breeding Material: Assessing Winter Wheat Production in Germany

Climate change impacts imply that the stabilization and improvement of agricultural production systems using technological innovations has become vital. Improvements in plant breeding are integral to such innovations. In the context of German crop breeding programs, the economic impact of exchanging genetic material has yet to be determined. To this end, we analyze in this impact assessment the economic effects on German winter wheat production that are attributable to exchanging parental material amongst breeders in the breeding process. This exchange is supported by the breeders' exemption, which is an integral part of the German plant variety protection legislation. It ensures that breeders can freely use licensed varieties created by other breeders for their own breeding activities and aims to speed up the development of improved varieties. For our analysis, we created a unique data set that combines variety-specific grain yield, adoption, and pedigree information of 133 winter wheat varieties. We determined the parental pedigree of each variety to see if a variety was created by interbreeding varieties that are internal or external to its specific breeder. Our study is the first that analyzes the economic impact of exchanging genetic material in German breeding programs. We found that more than 90 % of the tested varieties were bred with exchanged parental material, whereby the majority had two external parents. Also, these varieties were planted on an 8.5 times larger area than the varieties that were bred with two internal parents. Due to lower adoption, these only contributed 11 % to the overall winter wheat production in Germany, even though they yielded more. We used an economic surplus model to measure the benefits of exchanging parental breeding material on German winter wheat production. This resulted in an overall estimated economic surplus of 19.2 to 22.0 billion EUR from production year 1972 to 2018. This implies tremendous returns to using the breeder's exemption, which, from an economic perspective, is almost cost-free for the breeder. We conclude that the exchange of breeding material contributes to improving Germany's agricultural production and fosters the development of climate-resilient production systems and global food security.

Deciphering the Genetics of Primary Angioedema with Normal Levels of C1 Inhibitor

The genetic alteration underlying the great majority of primary angioedema with normal C1 inhibitor (nl-C1-INH-HAE) cases remains unknown. To search for variants associated with nl-C1-INH-HAE, we genotyped 133 unrelated nl-C1-INH-HAE patients using a custom next-generation sequencing platform targeting 55 genes possibly involved in angioedema pathogenesis. Patients already diagnosed with F12 alterations as well as those with histaminergic acquired angioedema were excluded. A variant pathogenicity curation strategy was followed, including a comparison of the results with those of genotyping 169 patients with hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE), and only filtered-in variants were studied further. Among the examined nl-C1-INH-HAE patients, carriers of neither the ANGPT1 p.Ala119Ser nor the KNG1 p.Met379Lys variant were found, whereas the PLG p.Lys330Glu was detected in four (3%) unrelated probands (one homozygote). In total, 182 different variants were curated, 21 of which represented novel mutations. Although the frequency of variants per gene was comparable between nl-C1-INH-HAE and C1-INH-HAE, variants of the KNG1 and XPNPEP1 genes were detected only in nl-C1-INH-HAE patients (six and three, respectively). Twenty-seven filtered variants in 23 different genes were detected in nl-C1-INH-HAE more than once, whereas 69/133 nl-C1-INH-HAE patients had compound heterozygotes of filtered variants located in the same or different genes. Pedigree analysis was performed where feasible. Our results indicate the role that alterations in some genes, like KNG1, may play in disease pathogenesis, the complex trait that is possibly underlying in some cases, and the existence of hitherto unrecognized disease endotypes.

Deciphering the Genetics of Primary Angioedema with Normal Levels of C1 Inhibitor

The genetic alteration underlying the great majority of primary angioedema with normal C1 inhibitor (nl-C1-INH-HAE) cases remains unknown. To search for variants associated with nl-C1-INH-HAE, we genotyped 133 unrelated nl-C1-INH-HAE patients using a custom next-generation sequencing platform targeting 55 genes possibly involved in angioedema pathogenesis. Patients already diagnosed with F12 alterations as well as those with histaminergic acquired angioedema were excluded. A variant pathogenicity curation strategy was followed, including a comparison of the results with those of genotyping 169 patients with hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE), and only filtered-in variants were studied further. Among the examined nl-C1-INH-HAE patients, carriers of neither the ANGPT1 p.Ala119Ser nor the KNG1 p.Met379Lys variant were found, whereas the PLG p.Lys330Glu was detected in four (3%) unrelated probands (one homozygote). In total, 182 different variants were curated, 21 of which represented novel mutations. Although the frequency of variants per gene was comparable between nl-C1-INH-HAE and C1-INH-HAE, variants of the KNG1 and XPNPEP1 genes were detected only in nl-C1-INH-HAE patients (six and three, respectively). Twenty-seven filtered variants in 23 different genes were detected in nl-C1-INH-HAE more than once, whereas 69/133 nl-C1-INH-HAE patients had compound heterozygotes of filtered variants located in the same or different genes. Pedigree analysis was performed where feasible. Our results indicate the role that alterations in some genes, like KNG1, may play in disease pathogenesis, the complex trait that is possibly underlying in some cases, and the existence of hitherto unrecognized disease endotypes.

Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Simple Summary

Dogs are an important part of society. The Polish Lowland Sheepdog (PON) is one of 353 of the world’s largest cynological organization listed dog breeds. Breeds with small population sizes, like the PONs, are often characterized by high inbreeding rates and thus an increased risk of congenital diseases. To examine the endangerment of the PONs, measures for genetic diversity and inbreeding were calculated for the German PON population. The study showed that the PONs had to be classified as a minimally endangered population according to threshold values specified by the European Association for Animal Production. However, the very recent trend showed a slight improvement.

Abstract

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients F_Ped based on pedigree data and F_ROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r^² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

Analysis of Genetic Diversity in the Czech Spotted Dog

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed-the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity-which was calculated based on the reference population and pedigree completeness-were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.

Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records

* Correspondence: andrea [...].

[Congenital flexural deformity in 93 calves - appearance, treatment techniques and results of pedigree analysis]

INTRODUCTION

Contracture of the flexor tendons (CFT) is very common in calves and it is usually diagnosed within the first few days after birth (congenital flexural deformity). However, CFT can appear even in older calves caused by chronic pain. The aetiology of CFT is still unknown. In this study, the distribution of sex, age, breed, the severity of flexural deformity, concurrent presence of other diseases, applied treatment methods for flexural deformity, and the outcome of calves with CFT, which were examined at the University Clinic for Ruminants in Vienna from 2001 to 2016, were evaluated retrospectively. 93 calves were admitted with CFT in the observation period. 70 (75.3%) calves were male and 78 (83.9%) of the affected animals were Simmental calves. The age of calves with CFT varied from one day to 41 days. Twenty-six calves suffered exclusively from CFT, and CFT was diagnosed as an additional finding in 67 calves. 91 animals (97.8%) showed CFT on the front limbs, 79 of them (84.9%) on both front limbs. The distribution of the severity scores was as follows: 69 calves (74.2%) had score 1, 17 calves (18.3%) had score 2, three calves (3.2%) had score 3. Three additional calves (3.2%) had a score 1 CFT on one front limb and a score 2 CFT on the other front limb, and one additional calf showed all three scores on both front limbs and one hind limb. 69 patients (74.2%) could be discharged with a significant improvement in CFT after treatment and 24 calves (25.8%) had to be euthanized due to other severe diseases. The results of the applied pedigree analysis do not show that a single gene mutation is the cause for the development of CFT, but rather a complex hereditary pattern has to be assumed. Depending on the severity of CFT and the presence of other concurrent diseases, an early and consistent therapy has to be carried out to achieve the highest possible success. Since animals with CFT are usually restricted in their movement, sufficient colostrum intake must be ensured within the first hours of life.

A novel mutation combining with rs66612022 in a Chinese pedigree suggests a new pathogenesis to osteogenesis imperfecta via whole genome sequencing

Osteogenesis imperfecta (OI) is a rare heritable disease with systemic connective tissue disorder. Most of the patients represent autosomal dominant form of OI, and are usually resulting from the mutations in type I collagen genes. However, the gene mutations reported previously only account for ∼70% of the OI cases. Here, in a Chinese OI family, we examined seven patients and nine normal individuals using the whole genome sequencing and molecular genetic analysis. The mutation of rs66612022 (COL1A2:p.Gly328Ser) related to glycine substitution was found in the seven patients. Moreover, we identified a novel missense mutation (HMMR:p.Glu2Gln). Interestingly, the individuals of this family with both the mutations were suffering from OI, while the others carried one or none of them are normal. The mutations of COL1A2 and HMMR and their combined effect on OI would further expand the genetic spectrum of OI.

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent-offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.

Population Structure Analysis of the Border Collie Dog Breed in Hungary

Pedigree data of the Border Collie dog breed were collected in Hungary to examine genetic diversity within the breed and its different lines. The database was based on available herd books dating from the development of the breed (in the late 1800s) to the present day. The constructed pedigree file consisted of 13,339 individuals, of which 1566 dogs (born between 2010 and 2016) composed the alive reference population which was active from breeding perspective. The breed is subdivided by phenotype, showing a thicker coat, harmonic movement, a wide skull, and heavier bones for the show type, and a thinner or sometimes short coat and smaller body for the working line, while the mixed line is quite heterogeneous (a combination of the above). Thus, the reference population was dissected according to the existing lines. The number of founders was 894, but eight individuals were responsible for contributing 50% of the genetic variability. The reference population had a pedigree completeness of 99.6% up to 15 generations and an inbreeding coefficient of 9.86%. Due to the changing breed standards and the requirements of the potential buyers, the effective population size substantially decreased between 2010 and 2016. Generation intervals varied between 4.09 and 4.71 years, where the sire paths were longer due to the later initial age of breeding in males compared to females. Genetic differences among the existing lines calculated by fixation indices are not significant; nonetheless ancestral inbreeding coefficients are able to show contrasts.

The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize

Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequenced maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZS-related lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.

Identifying a large number of high-yield genes in rice by pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 gene knockout

Repeated artificial selection of a complex trait facilitates the identification of genes underlying the trait, especially if multiple selected descendant lines are available. Here we developed a pedigree-based approach to identify genes underlying the Green Revolution (GR) phenotype. From a pedigree analysis, we selected 30 cultivars including the "miracle rice" IR8, a GR landmark, its ancestors and descendants, and also other related cultivars for identifying high-yield genes. Through sequencing of these genomes, we identified 28 ancestral chromosomal blocks that were maintained in all the high-yield cultivars under study. In these blocks, we identified six genes of known function, including the GR gene sd1, and 123 loci with genes of unknown function. We randomly selected 57 genes from the 123 loci for knockout or knockdown studies and found that a high proportion of these genes are essential or have phenotypic effects related to rice production. Notably, knockout lines have significant changes in plant height (P < 0.003), a key GR trait, compared with wild-type lines. Some gene knockouts or knockdowns were especially interesting. For example, knockout of Os10g0555100, a putative glucosyltransferase gene, showed both reduced growth and altered panicle architecture. In addition, we found that in some retained chromosome blocks several GR-related genes were clustered, although they have unrelated sequences, suggesting clustering of genes with similar functions. In conclusion, we have identified many high-yield genes in rice. Our method provides a powerful means to identify genes associated with a specific trait.

Association between the p.V37I variant of GJB2 and hearing loss: a pedigree and meta-analysis

Pathogenic variants in the gap junction protein beta-2 (GJB2) gene are the most common cause of hearing loss. Of these, the p.V37I variant of GJB2 has a high allele frequency (up to 10%) in East Asians. Characterization of the phenotypic spectrum associated with p.V37I, as well as the role of this variant in the onset of hearing loss could have a remarkable effect on future diagnostic strategies. Here, we performed a pedigree analysis of unrelated families exhibiting various hearing phenotypes, and then conducted a meta-analysis to comprehensively assess the association between the p.V37I and the risk of hearing loss. Pedigree analyses showed that both homozygous p.V37I variants, as well as compound heterozygous p.V37I with other GJB2 pathogenic variants, contributed to various phenotypes of hearing loss. Meanwhile, meta-analysis demonstrated that, compared with those in the wild type group, both p.V37I homozygotes and compound heterozygous p.V37I variants were at significantly higher risk of developing hearing loss (odds ratios = 7.14 and 3.63; 95% confidence intervals = 3.01-16.95 and 1.38–9.54, respectively). Conversely, heterozygous p.V37I variants alone did not increase the risk of hearing loss. Given the high allele carriage rate of p.V37I (up to 10%) within the general population, our work not only provides information that might influence future genetic screening policies, but also offers insight into clinical risk evaluation and genetic counseling regarding hearing loss.

Pedigree analysis, diagnosis and treatment in Von Hippel-Lindau syndrome: A report of three cases

The objective of the present study was to systematically investigate the clinical features, diagnosis and therapeutic treatment of Von Hippel-Lindau (VHL) syndrome in order to improve understanding of this disease. A total of 3 cases of VHL syndrome treated at the Affiliated Hospital of Zunyi Medical College (Zunyi, China) between September 2014 and October 2015 were retrospectively analyzed. The associated literature was reviewed, and the diagnostic and therapeutic features were discussed. Case 1 was diagnosed as VHL syndrome accompanied by a renal tumor on the right side, and radical tumor resection in the right kidney was performed. Postoperative pathological examination indicated clear cell carcinoma. Case 2 was diagnosed as VHL syndrome accompanied by bilateral adrenal pheochromocytoma. The left-side adrenal tumor was removed, and postoperative pathological analysis was suggestive of adrenal pheochromocytoma. Case 3 visited the hospital due to the presence of masses on the left and right sides of the kidney, but did not undergo surgery for personal reasons. Follow-ups were scheduled subsequent to surgery at another hospital. The diagnosis in all 3 cases was confirmed by genetic testing, where VHL mutations were detected in all patients. Following surgery, pedigree and genetic analysis was performed in all 3 pedigrees and VHL mutations were identified in 7 family members. The diagnosis of VHL syndrome should be based on the clinical manifestation of the patients and the results of genetic tests. DNA analysis of mutations is the main method for diagnosis. An appropriate surgical plan should be formulated based on the site, size and number of tumors, and the condition of the patient. Since VHL syndrome is an inheritable genetic disorder and relapse following surgery is common, pedigree analysis of the patient and lifelong follow-ups are essential. Additionally, physicians should pay attention to VHL syndrome in order to avoid missing diagnosis or misdiagnosis.

Investigation of inflammatory bowel disease risk factors in 4 families in central China

The prevalence of inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is increasing markedly in China. The present study performed pedigree analysis of 4 families with a history of IBD and investigated the association of genetic and environmental factors with susceptibility to IBD. A total of 10 IBD patients (8 CD patients and 2 UC patients) and 90 family members were included in the present study. The clinical characteristics of familial subjects were compared with those of patients with sporadic IBD. Previously reported mutations, namely interleukin-10 receptor (IL10R)-A Thr84Ile, IL10RA Gly141Arg, IL10RB Trp159X, X-linked inhibitor of apoptosis (XIAP) Cys203Tyr, nucleotide-binding oligomerization domain-containing protein 2 (NOD2) Arg702Trp, NOD2 Gly908Arg and NOD2 Leu1007fsinsC, were screened in the patients with IBD, and selected demographic factors were compared between the patients and their unaffected family members. It was observed that single-gene and multi-gene inheritance patterns contributed to IBD in Chinese families. Based on data from the registry system, the ratio of patients with a family history of IBD was 1.25%, which was lower than that in the Western population. First-degree relatives were found to be more susceptible to IBD, and siblings were affected more frequently. Furthermore, the median age of diagnosis was younger in familial patients than in sporadic patients (29.0 vs. 36.0 for CD; 35.5 vs. 41.0 for UC). However, none of the 7 susceptibility loci were present in any of the familial patients. Immigration was a significant risk factor of IBD (odds ratio: 4.667; 95% confidence interval: 1.165-18.690; P=0.021). In conclusion, genetic heterogeneity exits between Chinese families with IBD and the Western population. The present findings suggest that genetic background and environmental factors serve a role in the pathogenesis of IBD.

Pedigree Analysis of Familial Primary Concomitant Horizontal Strabismus in Northern India

PURPOSE

Familial clustering of common forms of primary strabismus like esotropia (ET) and exotropia (XT) is observed in a proportion of the strabismus cohort. The genetic components of this remain unidentified. Linkage studies have demonstrated susceptibility locus for primary strabismus at the STBMS1 locus on 7p22.1 as well as other loci on 4q28.3 and 7q31.2. Recently next generation sequencing (NGS) technology has emerged as a powerful tool in discovery genomics and a large number of novel disease-causing variants are being reported. In this study, we recruited informative families for subsequent genetic analysis for disease-causing variant identification.

METHODS

All consecutive families with two or more affected members with primary concomitant horizontal strabismus were prospectively recruited at the ophthalmic outpatients department (OPD) of Lady Hardinge Medical College, New Delhi, from August 2014 to February 2017. Detailed phenotypic evaluation and pedigree documentation was performed.

RESULTS

Of the 39 recruited families of north Indian origin, 18 families each had affected family members demonstrating either ET or XT. 100% concordance of the phenotype in the affected family members was observed in these families. While vertical transmission was observed in 17/18 families with XT, 7 with ET had affected members across one generation, 2 demonstrated consanguineous pedigree, and 2 comprised identical twin families. In 3 families, a combination of ET and XT was noted. This comprised one family with the ET and XT patients being from 2 separate arms of the family related by marriage, one family where one sibling had XT and the other had ET, and another family where the maternal aunt of the affected proband with ET had XT.

CONCLUSIONS

Subjects with familial primary concomitant strabismus recruited in this study may provide a valuable resource to unravel the genetic determinants of this condition, which is a common disorder of early childhood with high ophthalmic morbidity.

Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation

Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity. Estimates of marginal contributions of ancestors suggest that the bottlenecks arose mainly because related stallions had been used for breeding. A tendency for an increase in inbreeding coefficients was observed. F-statistics revealed that a small effective population size majorly contributed to this increase, although non-random mating in particular regions also contributed. Because the bottlenecks are thought to have reduced the effective population size, our results imply that mitigation of bottlenecks is important for conservation. To this end, breeding should involve genetically diverse stallions. In addition, to prevent non-random mating observed in particular regions, efforts should be made to plan mating with consideration of kinships.

Pedigree and BRCA gene analysis in breast cancer patients to identify hereditary breast and ovarian cancer syndrome to prevent morbidity and mortality of disease in Indian population

Global burden of breast cancer is expected to increase to >2 million new cases every year by 2030 and 10% of these are likely to have hereditary breast and ovarian cancer syndrome. Identifying these individuals by pedigree and BRCA1/2 mutation analyses will enable us to offer targeted mutation testing and appropriate counseling. This study from a tertiary care hospital showed that of the 127 breast cancer patients on treatment during 2014-2015, 24 of them fulfilled the criteria of hereditary breast and ovarian cancer syndrome after detailed verbal autopsy and pedigree analysis, and BRCA1 and 2 next-generation sequencing done after pre-test counseling revealed mutations in 13 cases (54%), these included 9 BRCA1 mutations (69%) and 4 BRCA2 mutation (31%). Subsequent post-test counseling recommended targeted mutation analysis for 64 high-risk members in these 13 families with pathogenic mutations, which will help in surveillance for early detection, appropriate management, and prevention of the disease by decreasing the burden to both family and nation. Results from this preliminary study highlight the importance of genetic counseling, pedigree analysis, and genetic testing. It can be recommended that all oncology units should have a genetic counseling service for providing appropriate support to oncologists, patients, and families to prevent unnecessary testing; however, breast cancer screening program is incomplete without evaluating for hereditary breast and ovarian cancer syndrome.

Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N e), the effective number of founders (f e), the effective number of ancestors (f a) and the number of founder genome equivalents (f g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the mean F and AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and the f e, f a and f g were 342, 223, 40, 22 and 9.6 for the RP. The large differences observed between f e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability. N e estimated via an individual increase in inbreeding per generation ( $$ \hskip3pt{\bar{\hskip-2ptN}_{{\rm e}} } $$ ), and paired increase in coancestry $$\left(\! \hskip3pt{\bar{\hskip-2ptN}_{{ eC}} } \right)$$ , were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.

Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations

Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.

Genomics advances the study of inbreeding depression in the wild

Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.

Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs

Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84-0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (P << 0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs.

Familial dilated cardiomyopathy diagnosis is commonly overlooked at the time of transplant listing

BACKGROUND

The prevalence and clinical characteristics of familial dilated cardiomyopathy (FDCM) among patients with end stage heart failure (ESHF) has yet to be elucidated. We sought to determine the prevalence of FDCM in ESHF in the United Network for Organ Sharing (UNOS) registry and compare this with center specific data from a large tertiary teaching hospital. Patients with a banked UNOS diagnosis of dilated cardiomyopathy (DCM) whose care originated at our center then underwent detailed pedigree analysis in order to determine the true prevalence of FDCM.

METHODS AND RESULTS

A total of 16,091 patients with DCM from all centers were identified in the UNOS registry of whom 492 carried the diagnosis of FDCM (3.1%). Patients with the diagnosis of FDCM tended to be younger (42 versus 49 years old in idiopathic dilated cardiomyopathy (IDCM), p=0.001), were less likely to have diabetes (7.8% versus 16.5% in IDCM, p<0.0001), had slightly lower creatinine (1.2 versus 1.4 in IDCM, p=0.0001) and were more likely to have a panel reactive antibody level ≥ 20% (62.1% versus 44.7% in IDCM, p<0.0001). Consecutive living adult patients with ESHF were identified from the UNOS registry that had been treated at the Yale Center for Advanced Heart Failure (YCAHF). After excluding all diagnoses that did not include any form of non-ischemic DCM, 73 patients met the inclusion criteria. Center-specific UNOS data showed pre-pedigree analysis diagnosis of FDCM in 4.12% of patients (3 out of 73), consistent with that found in the UNOS database for all centers. However, after detailed family history and pedigree analysis, 19 (26%) of 73 patients were found to have FDCM, while the remaining 54 were found to have IDCM. Echocardiographic findings including mitral regurgitation, mitral valve annulus and left ventricular end diastolic dimension were not significantly different between groups when adjusting for multiple testing.

CONCLUSIONS

The diagnosis of FDCM was missed in the majority of patients with end stage heart failure enrolled in the UNOS database, as sampled from a large, tertiary care teaching hospital in the United States. Echocardiographic findings are unlikely to aid in the differentiation between DCM and FDCM. Detailed pedigree analysis can successfully identify undiagnosed FDCM and should be encouraged prior to transplant listing as it has important implications for early detection and treatment of disease in family members.

Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed

The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X-linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX  = 0.46 and 0.22 and FX  = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non-founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole-genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis: -0.20 born piglets per litter by a 10% of new inbreeding, and -0.03 and -0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in -0.91 and -0.17 piglets by a 10% of old and X-linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals.