APIS: an updated parentage assignment software managing triploids induced from diploid parents.

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximises the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96 to 192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low False Discovery Rate (<0.01) and excellent specificity (0.96-0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents.

Brown trout in Oder estuary tributaries: genetic structure, stocking, and admixture.

Several rivers that are tributaries of the Oder estuary are inhabited by Salmo trutta L, the most important of which are Ina, Gowienica, and Wolczenica. Both forms of the species, sea trout and resident brown trout, are present. All rivers are traditionally stocked with either sea trout from the neighboring Pomeranian river Rega basin or resident brown trout from various locations. To examine populations in these rivers in terms of genetic structure, genetic diversity, and origin, they were analyzed using 13 microsatellite loci. Relatedness was also assessed for fish stocked in the same year. The obtained genotypes were compared with breeding stocks used for stocking in Poland. The analyses revealed a significant genetic distance between adult individuals from Ina and Rega Rivers and fish caught during electrofishing. Strong kinship relationships were identified in the sampled areas, with high proportions of fish originating from stocking and their dominance in numbers over wild juveniles, primarily in smaller tributaries. Additionally, clear separation in the origin of stocked individuals was observed. Adult trout from Ina and Rega are genetically closer to northern brown trout lineages, providing crucial information for the management and biodiversity conservation of Polish Salmo trutta populations.

The Benefit of a National Genomic Testing Scheme.

Although a significant cost, genotyping an entire population offers many benefits, many of which can reduce the workload and effort in decision-making on farm. As well as providing more accurate predictions of the genetic merit of individuals (and by extension their expected performance), national genotyping strategies enable complete traceability from the cradle to the grave as well as parentage discovery. The information available per animal aids more informed breeding and management decisions, including mating advice, and determining the optimal role and eventual fate of each animal.

Genetic assessment of eight zoo populations of golden snub-nosed monkey (Rhinopithecus roxellana) implication to the conservation management of captive populations.

Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster.

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.

Revealing misattributed parentage through the integration of genetic information into the electronic health record.

The integration of genetic information (GI) into the electronic health record (EHR) seems inevitable as the mainstreaming of genomics continues. Such newly provided accessibility to GI could be beneficial for improving health care, as well as for supporting clinical decision-making and health management. Notwithstanding these promising benefits, the automatic integration of GI into the EHR, allowing unrestricted access to one's GI through patient portals, carries various knowledge-related risks for patients. This article is focused on the potential case of inadvertently revealing misattributed parentage through such practice. The article aims to identify key clinical and ethical implications of such revelation for adult patients. Clinical implications include, for example, altering the physician-patient interaction and the need to enhance physician's genetic literacy to improve genetic-information-specific communication skills. Ethical implications yield arguments supporting disclosure of MP, such as autonomy, individuals' right to know medical information pertaining to them, and the right to know one's genetic origins. Arguments opposing disclosure of MP centre on the right not to know GI and concerns for post-disclosure family relationships. Following the clinical and ethical analyses of these respective implications, we consider how such integration of GI into the EHR ought to be carried out, ethically. We therefore suggest a solution, featuring an autonomy-based approach, built around EHR users' right not to know. Our solution of nuanced consent options (including a 'genetic ignorance option') is designed to enable patients' informed exposure to GI through the EHR, allowing them some control over their self- and familial narrative.

Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas.

Premise: Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity. Methods: We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections. Results: Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual. Discussion: Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.

Establishment of Parentage Identification Method for Sea Urchin Strongylocentrotus intermedius Based on SSR-seq Technology.

To establish a parentage identification method for Strongylocentrotus intermedius, 15 microsatellite loci and simple sequence repeat sequencing (SSR-seq) technology were used to perform SSR sequencing and typing of the validation population with known pedigree information and the simulation population. Cervus v3.0 was used for gene frequency statistics, simulated analysis, and parentage identification analysis. The results showed that, in validation population, using 15 microsatellite loci, the highest success rate of parent pairs identification was 86%, the highest success rate of female parent identification was 93%, and the highest success rate of male parent identification was 90%. The simulated population was analyzed using 12-15 loci, and the identification rate was up to 90%. In cases where accurate parentage was not achieved, individuals could exhibit genetic similarities with 1-3 male or female parents. Individuals identified as lacking a genetic relationship can be selected as parents to prevent inbreeding. This study shows that parent pairs or single parents of most offspring can be identified successfully using these 15 selected loci. The results lay a foundation for the establishment of a parentage identification method for S. intermedius.

Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead.

Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.

Visual and genetic stock identification of a test fishery to forecast Columbia River spring Chinook salmon stocks 2 weeks into the future.

Modern fisheries management strives to balance opposing goals of protection for weak stocks and opportunity for harvesting healthy stocks. Test fisheries can aid management of anadromous fishes if they can forecast the strength and timing of an annual run with adequate time to allow fisheries planning. Integration of genetic stock identification (GSI) can further maximize utility of test fisheries by resolving run forecasts into weak- and healthy-stock subcomponents. Using 5 years (2017-2022) of test fishery data, our study evaluated accuracy, resolution, and lead time of predictions for stock-specific run timing and abundance of Columbia River spring Chinook salmon (Oncorhynchus tshawytscha). We determined if this test fishery (1) could use visual stock identification (VSI) to forecast at the coarse stock resolution (i.e., classification of "lower" vs. "upriver" stocks) upon which current management is based and (2) could be enhanced with GSI to forecast at higher stock resolution. VSI accurately identified coarse stocks (83.3% GSI concordance), and estimated a proxy for abundance (catch per unit effort, CPUE) of the upriver stock in the test fishery that was correlated (R 2 = 0.90) with spring Chinook salmon abundance at Bonneville dam (Rkm 235). Salmon travel rates (~8.6 Rkm/day) provided predictions with 2-week lead time prior to dam passage. Importantly, GSI resolved this predictive ability as finely as the hatchery broodstock level. Lower river stock CPUE in the test fishery was correlated with abundance at Willamette Falls (Rkm 196, R 2 = 0.62), but could not be as finely resolved as achieved for upriver stocks. We described steps to combine VSI and GSI to provide timely in-season information and with prediction accuracy of ~12.4 mean absolute percentage error and high stock resolution to help plan Columbia River mainstem fisheries.

Demographic patterns of walleye (Sander vitreus) reproductive success in a Wisconsin population.

Harvest in walleye Sander vitreus fisheries is size-selective and could influence phenotypic traits of spawners; however, contributions of individual spawners to recruitment are unknown. We used parentage analyses using single nucleotide polymorphisms to test whether parental traits were related to the probability of offspring survival in Escanaba Lake, Wisconsin. From 2017 to 2020, 1339 adults and 1138 juveniles were genotyped and 66% of the offspring were assigned to at least one parent. Logistic regression indicated the probability of reproductive success (survival of age-0 to first fall) was positively (but weakly) related to total length and growth rate in females, but not age. No traits analyzed were related to reproductive success for males. Our analysis identified the model with the predictors' growth rate and year for females and the models with year and age and year for males as the most likely models to explain variation in reproductive success. Our findings indicate that interannual variation (i.e., environmental conditions) likely plays a key role in determining the probability of reproductive success in this population and provide limited support that female age, length, and growth rate influence recruitment.

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing.

In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.

Prepartum and postpartum mothers' and fathers' feelings of frustration in response to infant crying.

In this cross-sectional study performed in Canada, we evaluated the frustration levels of prepartum and postpartum mother and father couple-pairs. Our goal was to determine if there were differences in frustration levels between mothers and fathers while listening to prolonged infant crying, and further, how frustration levels might differ between prepartum and postpartum samples. Using two discrete groups, prepartum (Sample 1; N = 48) and postpartum (Sample 2; N = 44) mother and father couple-pairs completed 600 s of listening to audio-recorded infant cry sounds. Participants continuously reported their subjective frustration using a computerized Continuous Visual Analog Scale (CVAS). There was no significant difference in frustration responses between mothers and fathers across both prepartum and postpartum samples. Postpartum mothers and fathers experienced greater frustration than their prepartum counterparts, and frustration increased faster in postpartum couples compared to prepartum couples. Informing first-time parents of the universal experiences of frustration to prolonged crying bouts that are characteristic of their infant's early weeks of life may lead to greater understanding towards their infant, and perhaps decreased instances of harmful responses.

En este estudio transeccional, evaluamos los niveles de frustración de las parejas de mamás y papás antes y después del parto. Nuestro propósito fue determinar si hay diferencias entre mamás y papás en cuanto a los niveles de frustración mientras escuchan el prolongado llanto del infante, y cómo los niveles de frustración pudieran diferir entre grupos­muestra antes y después del parto. Usando dos grupos discretos, antes del parto (grupo­muestra 1; N = 48) y después del parto (grupo­muestra 2; N = 44), las parejas de mamás y papás completaron 600 segundos escuchando sonidos grabados en audio de llanto de infante. Los participantes continuamente reportaron su frustración subjetiva usando una escala análoga visual continua computarizada (CVAS). No hubo diferencia significativa en las respuestas de frustración entre mamás y papás a lo largo de los grupos­muestra tanto antes del parto como después del parto. Las mamás y papás en el grupo­muestra después del parto experimentaron mayor frustración que sus homólogos en el grupo­muestra antes del parto, y la frustración aumentó más rápido en las parejas del grupo­muestra después del parto tal como se les comparó con las parejas del grupo­muestra antes del parto. Estos resultados sugieren que las parejas primíparas posterior al parto están más propensas a experimentar considerables cantidades de frustración como respuesta al llanto del infante después que el bebé ha nacido. Informarles a los progenitores primerizos acerca de las experiencias generales de la frustración a los prolongados ataques de llanto que son característicos de las primeras semanas de vida de su infante pudiera llevar a una mayor comprensión hacia su infante y quizás disminuir las instancias de respuestas dañinas.

Dans cette étude transversale nous avons évalué les niveaux de frustration des couples­paires mère et père avant et après la naissance. Notre but était de déterminer s'il existe des différences entres les mères et les pères dans leurs niveaux de frustration en entendant des pleurs de bébé prolongés et de quelle manière les niveaux pourraient différer entre les échantillons avant la naissance et après la naissance. En utilisant deux groupes discrets, avant la naissance (Echantillon 1; N = 48) et après la naissance (Echantillon 2; N = 44) les couples­paires mère et père ont écouté 600 seconds d'enregistrements de pleurs de bébés. Les participants ont fait état de leur frustration subjective en utilisant une échelle analogique visuelle continue informatisée (CVAS). Il s'est avéré n'y avoir aucune différence importante dans les réactions de frustration entre les mères et les pères au travers des échantillons à la fois avant l'accouchement et après l'accouchement. Ces résultats suggèrent que les coupes postpartum primipares sont plus à même de faire l'expérience de niveaux élevés de frustration en réaction aux pleurs du bébé une fois le bébé arrivé. Informer les parents qui sont parents pour la première fois des expériences universelles de frustration aux crises de pleurs prolongées qui caractérisent les premières semaines de la vie des bébés peut mener à une plus grande compréhension de leur bébé et peut­être à une baisse des case d réactions néfastes.

Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses.

The International Society for Animal Genetics (ISAG) currently advocates for a transition towards single nucleotide polymorphism (SNP) markers as a potential alternative for equine parentage verification. To ascertain the efficacy of this transition, it is imperative to evaluate the performance of parentage testing using SNPs in juxtaposition with short tandem repeats (STRs). As per ISAG's recommendation, we used an equine genotyping-by-sequencing panel with 144 SNPs for this purpose. Equine parentage is currently realized using 16 microsatellites (STRs) excluding the LEX3 marker. In this study, 1074 horses were genotyped using the 144 SNPs panel, including 432 foals, 414 mares, and 228 stallions, from five different breeds: 293 Arabians, 167 Barbs, 189 Thoroughbreds, 73 Anglo-Arabians, and 352 Arabian-Barbs. As a result, two SNPs markers were eliminated from the panel system due to inconsistent amplification across all examined individuals leaving 142 SNPs markers for analysis. A comparative analysis between SNPs and STRs markers revealed that the mean expected heterozygosity was 0.457 for SNPs and 0.76 for STRs, while the mean observed heterozygosity stood at 0.472 for SNPs and 0.72 for STRs. Furthermore, the probability of identity was calculated to be 5.722 × 10-57 for SNPs and 1.25 × 10-15 for STRs markers. In alignment with the Hardy-Weinberg equilibrium in polyploids test, 110 out of the total SNPs were consistent with the Hardy-Weinberg equilibrium in polyploids test (p > 0.05). Employing both SNPs and STRs markers, the mean polymorphic information content was discerned to be 0.351 for SNPs and 0.72 for STRs. The cumulative exclusion probabilities for SNP markers exceeded 99.99%, indicating that the 142 SNPs panel might be adequate for parentage testing. In contrast, when utilizing STRs markers, the combined average exclusion probabilities for one and both parents were determined to be 99.8% and 99.9%, respectively. Our comprehensive study underscores the potential of SNPs in equine parentage verification, especially when compared to STRs in terms of exclusion probabilities. As a corollary, the application of SNPs for parentage verification and identification can significantly contribute to the conservation initiative for the five Moroccan horse breeds. Nonetheless, further research is required to address and replace the deficient SNPs within the panel.

Hatchery supplementation provides a demographic boost but alters age composition of sockeye salmon in Auke Lake, Southeast Alaska.

Evaluating salmon hatchery supplementation programs requires assessing not only program objectives but identifying potential risks to wild populations as well. Such evaluations can be hampered by difficulty in distinguishing between hatchery- and wild-born returning adults. Here, we conducted 3 years (2011-2013) of experimental hatchery supplementation of sockeye salmon in Auke Lake, Juneau, Alaska where a permanent weir allows sampling and genotyping of every returning adult (2008-2019). We identified both hatchery- and wild-born returning adults with parentage assignment, quantified the productivity (adult offspring/spawner) of hatchery spawners relative to that of wild spawners, and compared run timing, age, and size at age between hatchery- and wild-born adults. Hatchery-spawning females produced from approximately six to 50 times more returning adults than did naturally spawning females. Supplementation had no discernable effect on run timing and limited consequences for size at age, but we observed a distinct shift to younger age at maturity in the hatchery-born individuals in all three brood years. The shift appeared to be driven by hatchery-born fish being more likely to emigrate after one, rather than two, years in the lake but the cause is unknown. In cases when spawning or incubation habitat is limiting sockeye salmon production, hatchery supplementation can be effective for enhancing the number of returning adult fish but not without the risk of phenotypic change in the recipient population, which can be an undesired outcome of hatchery supplementation. This study adds to a growing body of evidence suggesting that phenotypic change within a single generation of captive spawning might be widespread in salmon hatchery programs.

Identification of the efficacy of parentage testing based on bi-allelic autosomal single nucleotide polymorphism markers in Taiwanese population.

Parentage testing is crucial for forensic DNA analysis, using short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) with high minor allele frequency (MAF) are promising for human identification. This study aimed to develop SNP markers for parentage testing in the Taiwanese population and compare their accuracy with STRs. The TPMv1 SNP microarray (714,457 SNPs) was used to screen 180,000 Taiwanese individuals and analyze the SNP data using PLINK. After quality control, allelic distribution, and MAF considerations, a set of SNPs with significant inheritance information was selected. Parentage testing was conducted on 355 single parent-child pairs using both STRs and SNPs, employing three kinship algorithms: identity by descent, kinship-based inference for genome-wide association studies, and the combined paternity index/probability of paternity (CPI/PP). An Affymetrix signature probe for kinship testing (ASP) was also used. Based on the quality control and selection criteria, 176 SNPs with MAF > 0.4995 were selected from the Taiwanese population. The CPI/PP results calculated using SNPs were consistent with the STR results. The accuracy of the SNPs used in the single-parent-child parentage testing was > 99.99%. The set of 176 SNPs had a higher identification rate in the single parent-child parentage test than in the ASP. The CPI/PP value calculated using 176 SNPs was also more accurate than that calculated using ASP. Our findings suggest that these 176 SNPs could be used for single-parent-child parentage identification in the Taiwanese population.

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping.

Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.

Development of a coding SNP panel for tracking the origin of whole-exome sequencing samples.

Whole-exome sequencing (WES) is widely used to diagnose complex genetic diseases and rare conditions. The implementation of a robust and effective quality control system for sample identification and tracking throughout the WES process is essential. We established a multiplex panel that included 22 coding single-nucleotide polymorphism (cSNP) loci. The personal identification and paternity identification abilities of the panel were evaluated, and a preliminary validation of the practical feasibility of the panel was conducted in a clinical WES case. These results indicate that the cSNP panel could be a useful tool for sample tracking in WES.

Exploring genetic counselors' experiences with non-paternity in clinical settings.

Non-paternity (NP) is a challenging dilemma faced by genetics providers and there is little consensus on whether this finding should be disclosed. Discussions in the literature are highly theoretical, with limited research regarding how disclosure decisions are enacted in practice. We explored genetic counselors' (GCs) clinical experiences with NP to understand if, how, and why this finding is communicated. Our semi-structured interviews with genetic counselors in the United States and Canada were analyzed using reflexive thematic analysis to analyze data inductively, describe themes, and present a meaningful interpretation of the data. Eighteen participants who responded to list-serv messages were interviewed. Our framework describes five salient themes: (1) GC-lab relationship: the GCs awareness of laboratory processes such as quality control metrics that can uncover NP findings and the way in which a finding of NP was disclosed by the laboratory had an impact on disclosure decisions. This triggered a decision-making trajectory that involved (2) consultation, (3) ethical reasoning, and (4) practical constraints. GCs frequently consulted other professionals during decision-making. These conversations impacted disclosure decisions with some consultations carrying greater weight than others. GCs weighed moral concepts of patient autonomy, medical relevance, and preventing harm to rationalize decisions. Access to patients and documentation requirements often dictated how disclosure occurred. Finally, once a decision had been made and enacted, GCs used the experience to reconsider their approach to (5) consenting in future cases, with some GCs altering their pre-test counseling to always include a discussion of NP. Although NP scenarios are frequently unique in context, our findings demonstrate several common decision-making factors GCs harness to navigate the identification of NP through clinical genetic testing.

Household chaos and parenting: The effect of household chaos does not depend on sensory-processing sensitivity and self-regulation.

Previous studies have found evidence for a causal effect of household chaos on parenting and suggest that this effect may be stronger for parents with higher sensory-processing sensitivity (SPS) or lower self-regulation. This study investigates whether primary caregivers of children around age 1.5-2 years show greater improvement in parenting after a decrease in household chaos if parents have higher SPS or lower self-regulation. The study employs a randomized controlled trial (RCT) design with an intervention aimed at reducing household chaos. A total of 125 parents of toddlers participated in the study. All participants were living in the Netherlands at the time of the study, 89% identified with the Dutch ethnicity and 11% with a non-Dutch ethnicity. Self-report as well as objective measures were used, including videotaped parent-child interactions and home observations. The effect of the intervention on parenting did not depend on SPS or self-regulation. When studying the relation between change in measures of household chaos and posttest parenting, decreased self-reported household chaos was related to less harsh discipline in parents with higher self-regulation, and to more harsh discipline in parents with lower self-regulation. However, this is a tentative finding that should be further explored in future research.

Estudios anteriores han encontrado evidencia de un efecto casual del caos en el hogar sobre la crianza y sugieren que este efecto pudiera ser más fuerte para progenitores con una más alta sensibilidad del proceso sensorial (SPS) o más baja autorregulación. Este estudio investiga si quienes primariamente cuidan a los niños de alrededor de 1.5-2 años muestran un más alto nivel de mejoras en la crianza después de una disminución en el caos del hogar si los progenitores poseen un alto nivel de SPS o baja autorregulación. El estudio emplea un diseño RCT con una intervención dirigida a reducir el caos en el hogar. En el estudio participaron 125 progenitores de niños pequeñitos. Todos los participantes vivían en Holanda al momento del estudio, 89% se identificaba con la etnicidad holandesa y 11% con una etnicidad no holandesa. Se usaron auto reportes, así como medidas de objetivos, incluyendo interacciones entre progenitor y niño grabadas en video y observaciones en casa. El efecto de la intervención sobre la crianza no dependió de SPS o de la autorregulación. Cuando se estudiaba la relación entre el cambio en las medidas del caos en el hogar y la crianza posterior a la prueba, la disminución del auto reportado caos en el hogar se relacionó con menos disciplina dura en progenitores con más alta autorregulación, así como con más disciplina dura en progenitores con más baja autorregulación. Sin embargo, se trata de un resultado tentativo que se debe explorar más en la futura investigación.

Des études précédentes ont trouvé peu de preuves à un effet de cause du chaos domestique sur le parentage et suggèrent que cet effet pourrait être plus fort pour les parents avec une sensibilité du traitement sensoriel (STS) plus élevée et une auto-régulation plus faible. Cette étude évalue si les personnes prenant soin des enfants autour de l'âge de 1,5-2 ans font preuve d'une plus grande amélioration dans le parentage avec moins de chaos domestique si les parents ont une STS plus élevée ou une autorégulation plus basse. Cette étude a employé un plan ECR avec une intervention destinée à réduire le chaos domestique. 125 parents de jeunes enfants ont participé à l'étude. Tous les participants vivaient aux Pays Bas au moment de l'étude, 89% s'identifiant comme d'ethnicité hollandaise et 11% d'ethnicité non hollandaise. Des auto-évaluations ainsi que des mesures objectives ont été utilisées, en utilisant des interactions parent-enfant filmées à la vidéo et des observations à domicile. L'effet de l'intervention sur le parentage n'a pas dépendu de la STS ou de l'auto-régulation. En étudiant la relation entre le changement dans les mesures de chaos domestique et de parentage posttest, le chaos autosignalé décru à une discipline moins sévère chez les parents avec une autorégulation plus élevée, et à une discipline plus sévère chez les parents avec une autorégulation moins élevée. Cependant c'est une constatation tentative qui devrait être explorée plus profondément dans des recherches futures.