En especies pecuarias, la consecuencia observada más importante de la consanguinidad acumulada por selección es la reducción del valor fenotípico medio de los caracteres de interés, fenómeno conocido ...como depresión consanguínea. El objetivo de este trabajo fue estimar el nivel de consanguinidad y la depresión consanguínea en caracteres de crecimiento y reproducción en bovinos Brangus de Argentina, con el fin de obtener un diagnóstico y monitorear el manejo de la raza. Los datos correspondieron a 359.257 animales (de los cuales 1.990 tenían genotipo para 40.678 SNP) con fenotipo para al menos uno de tres caracteres de crecimiento: peso al nacer (PN), peso al destete (PD) y peso final (PF). Para la circunferencia escrotal (CE), había 52.399 fenotipos disponibles, de los cuales 256 habían sido genotipificados. Había 530.938 animales en el pedigree. Los coeficientes de consanguinidad se estimaron mediante tres métodos. El primero se basó en el pedigree y consideró los padres faltantes. El segundo combinó la información de animales genotipificados y no genotipificados a partir de la matriz H del enfoque Single-Step. El tercero se basó en los genotipos e identificó segmentos homocigóticos mediante un modelo oculto de Markov. La depresión consanguínea se estimó a partir de la regresión del fenotipo en los coeficientes de consanguinidad utilizando un modelo animal multicarácter, ya sea para el conjunto total de datos o para los animales genotipificados. Todos los caracteres se vieron afectados negativamente por la depresión consanguínea. Un aumento del 10% en la consanguinidad basada en el pedigree o combinada daría como resultado una reducción de 0,34–0,39 kg en el PN, de 2,77–3,28 kg en el PD y 0,23 cm en la CE. Para el PF, un aumento del 10% en la consanguinidad basada en el pedigree, genómica o combinada resultaría en una reducción de 8,05–11,57 kg. Aún si el genotipificado tiene un costo, los programas de mejora deberían considerar el costo financiero de las pérdidas debidas a la consanguinidad.
Crop pedigrees incorporate information on the kinship and genetic evolutionary history of breeding materials. Complete and accurate pedigree information is vital for effective genetic improvement of ...crops and maximal exploitation of heterosis in crop production. It is difficult for breeders to accurately extrapolate the selection of germplasm resources with missing genealogical information based on breeding experience. In this study, an algorithm called PidTools was developed, consisting of five sets of algorithms from three core modules, for accurate pedigree identification analysis. The algorithms and associated tools are suitable for all crops, for the reconstruction and visualization of a complete pedigree for breeding materials. The algorithm and tools were validated with the model crop maize. A genotype database was constructed using Maize6H-60K array data from 5791 maize inbred lines. The pedigree of the maize inbred line Jing72464 was identified without prior provision of any parental information. The pedigree information for Zheng58 was fully identified at the genome-wide scale. With regard to group identification, the parents of a doubled-haploid group were identified based on the genotyping data. The pedigree of 21 Dan340 derived lines were visualized using PidTools. The algorithms are incorporated into a user-friendly online analytical platform, PidTools-WS, with an associated customizable toolkit program, PidTools-CLI. These analytical tools and the present results provide useful information for future maize breeding. The PidTools online analysis platform is available at https://PidTools.plantdna.site/.
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Germline mutations are the raw material for natural selection, driving species evolution and the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth would ...stagnate. Yet, it is a double‐edged sword. An excess of mutations can have devastating effects on fitness and population viability. It is therefore one of the great challenges of molecular ecology to determine the rate and mechanisms by which these mutations accrue across the tree of life. Advances in high‐throughput sequencing technologies are providing new opportunities for characterizing the rates and mutational spectra within species and populations thus informing essential evolutionary parameters such as the timing of speciation events, the intricacies of historical demography, and the degree to which lineages are subject to the burdens of mutational load. Here, we will focus on both the challenge and promise of whole‐genome comparisons among parents and their offspring from known pedigrees for the detection of germline mutations as they arise in a single generation. The potential of these studies is high, but the field is still in its infancy and much uncertainty remains. Namely, the technical challenges are daunting given that pedigree‐based genome comparisons are essentially searching for needles in a haystack given the very low signal to noise ratio. Despite the challenges, we predict that rapidly developing methods for whole‐genome comparisons hold great promise for integrating empirically derived estimates of de novo mutation rates and mutation spectra across many molecular ecological applications.
Morada Nova breed has a low effective herd, and its white variety is in risk of extinction in Brazilian semi-arid region. This study aimed to evaluate white Morada Nova sheep’s genetic variability ...and population structure in four flocks. These are the only flocks in the world. The assessed parameters of pedigree integrity and a genealogy record of 219 animals. 44.74 % did not have pedigree information on their mother or father, and 50.47 % did not have available information on their grandparents. 52.97 % had a pedigree in their first ancestry (obtained through the average of known parents), 23.74 % in the second, 13.58 % in the third, and 5.33 % in the fourth. The effective size was 10.7, considering the complete equivalent generation. The effective number of founding animals (fe) and ancestors (fa) was 10, indicating the effective participation of all founding animals in the population over the generations, reducing losses of genetic variability. Out of all the ancestors, only 3 explained 50 % of the population’s genetic variability, reflecting the low values of fa and fe. The population’s average inbreeding and kinship coefficients were 2.61 and 4.54. The F statistics of Wright, Fis, Fst, and Fit, were −0.012, 0.016, and 0.003. The genetic conservation index (GCI) had an average of 2.01 ± 1.29, with minimum and maximum values of 1.0 and 6.38, respectively. Approximately, 71 % of the population had GCI below 2.0, while only 5.9 % of sheep had an GCI bigger than 5.0. This indicates the absence of sub-structures inf the population. There is no population subdivision, considering the genealogical structure of the evaluated flocks. The inbreeding and kinship coefficient values are controlled and serve as a starting point for establishing a future management plan for the genetic variability of the flock. It is recommended to use strategies to increase the effective population size, to meet the minimum number recommended by FAO and to promote the conservation and genetic improvement of the breed.
Genome-enabled prediction plays an essential role in wheat breeding because it has the potential to increase the rate of genetic gain relative to traditional phenotypic and pedigree-based selection. ...Since the performance of wheat lines is highly influenced by environmental stimuli, it is important to accurately model the environment and its interaction with genetic factors in prediction models. Arguably, multi-environmental best linear unbiased prediction (BLUP) may deliver better prediction performance than single-environment genomic BLUP. We evaluated pedigree and genome-based prediction using 35,403 wheat lines from the Global Wheat Breeding Program of the International Maize and Wheat Improvement Center (CIMMYT). We implemented eight statistical models that included genome-wide molecular marker and pedigree information as prediction inputs in two different validation schemes. All models included main effects, but some considered interactions between the different types of pedigree and genomic covariates via Hadamard products of similarity kernels. Pedigree models always gave better prediction of new lines in observed environments than genome-based models when only main effects were fitted. However, for all traits, the highest predictive abilities were obtained when interactions between pedigree, genomes, and environments were included. When new lines were predicted in unobserved environments, in almost all trait/year combinations, the marker main-effects model was the best. These results provide strong evidence that the different sources of genetic information (molecular markers and pedigree) are not equally useful at different stages of the breeding pipelines, and can be employed differentially to improve the design and prediction of the outcome of future breeding programs.
Aggression is a rising issue in many dog breeds and is an obstacle in proper dog-human interactions. However, the aggressive behaviour can also disturb the welfare of the dog. Aggression is ...particularly common in English Cocker Spaniels. Thus, the aim of this study was to examine factor associated with aggression of English Cocker Spaniels using an owner-completed survey. Information on aggressive behaviour was collected from 503 dogs by electronic surveys distributed and collected in November 2022 in Poland. We investigated whether the occurrence of aggression towards people and animals was affected by age, sex, adoption from a shelter, contact with children and other animals, whether the dog has a pedigree or by other behavioural disorders (jumping on people, pulling on leash, digging holes, destroying objects, disobedience, vagrancy, inappropriate urination and defecation, begging for food). We have showed that the dogs aggressive towards other animals are significantly more likely to be aggressive towards humans. Also the age of a dog, a pedigree and inappropriate urination and defecation, significantly affect which type of the animals the dog will be aggressive towards. The logistic regression was used to test the effect of different factors on aggression towards human and animals. Our results showed that aggressive behaviour toward humans is particularly exhibited by males and it increased with age. Also, dogs that do not have an official pedigree showed aggression much more frequently toward people and other animals. In addition, dogs adopted from a shelter were often more aggressive towards people. It was also found that dogs that jump on people are significantly more likely to be aggressive toward a human. Other behavioural disorders had no effect on the occurrence of aggression. Analysis of collected data provides knowledge on the factors that affect the occurrence of undesirable behaviour in English Cocker Spaniel dogs. Understanding the causes of aggression can significantly improve the relationship between owner and dog. Our findings should not necessarily preclude people from wanting to own an English Cocker Spaniels breed, rather to be prepared for a need of a proper training.
•Aggression in English Cocker Spaniels is a common occurrence.•Aggression towards people in Cocker Spaniels is more often observed in males than in females.•Lack of pedigree or Kennel Club certification resulted in a higher incidence of aggression.•Adoption from shelter increased risk of aggression towards people whereas contact with other animals increased aggression towards other animals.•Aggression in English Cocker Spaniels increases with age towards people and towards animals.
The ubiquity of pedigrees in many scientific areas calls for versatile and user-friendly software. Previously published online pedigree tools have limited support for complex pedigrees and do not ...provide analysis of relatedness between pedigree members.
We introduce QuickPed, a web application for interactive pedigree creation and analysis. It supports complex inbreeding and comes with a rich built-in library of common and interesting pedigrees. The program calculates all standard coefficients of relatedness, including inbreeding, kinship and identity coefficients, and offers specialised plots for visualising relatedness. It also implements a novel algorithm for describing pairwise relationships in words.
QuickPed is a user-friendly pedigree tool aimed at researchers, case workers and teachers. It contains a number of features not found in other similar tools, and represents a significant addition to the body of pedigree software by making advanced relatedness analyses available for non-bioinformaticians.
Applications of genetic‐based estimates of population size are expanding, especially for species for which traditional demographic estimation methods are intractable due to the rarity of adult ...encounters. Estimates of breeding population size (NS) are particularly amenable to genetic‐based approaches as the parameter can be estimated using pedigrees reconstructed from genetic data gathered from discrete juvenile cohorts, therefore eliminating the need to sample adults in the population. However, a critical evaluation of how genotyping and sampling effort influence bias in pedigree reconstruction, and how these biases subsequently influence estimates of NS, is needed to evaluate the efficacy of the approach under a range of scenarios. We simulated a model system to understand the interactive effects of genotyping and sampling effort on error in genetic pedigrees reconstructed from the program COLONY. We then evaluated how errors in pedigree reconstruction influenced bias and precision in estimates of NS using three different rarefaction estimators. Results indicated that pedigree error can be minimal when adequate genetic data are available, such as when juvenile sample sizes are large and/or individuals are genotyped at many informative loci. However, even in cases for which data are limited, using results of the simulation analysis to understand the magnitude and sources of bias in reconstructed pedigrees can still be informative when estimating NS. We applied results of the simulation analysis to evaluate N̂$$ \hat{N} $$S for a population of federally endangered Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Delaware River, USA. Our results indicated that NS is likely to be three orders of magnitude lower compared with historic breeding population sizes, which is a considerable advancement in our understanding of the population status of Atlantic sturgeon in the Delaware River. Our analyses are broadly applicable in the design and interpretation of studies seeking to estimate NS and can help to guide conservation decisions when ecological uncertainty is high. The utility of these results is expected to grow as rapid advances in genetic technologies increase the popularity of genetic population monitoring and estimation.
Pedigree inference, for example determining whether two persons are second cousins or unrelated, can be done by comparing their genotypes at a selection of genetic markers. When the data for one or ...more of the persons is from low-coverage next generation sequencing (lcNGS), currently available computational methods either ignore genetic linkage or do not take advantage of the probabilistic nature of lcNGS data, relying instead on first estimating the genotype. We provide a method and software (see familias.name/lcNGS) bridging the above gap. Simulations indicate how our results are considerably more accurate compared to some previously available alternatives. Our method, utilizing a version of the Lander-Green algorithm, uses a group of symmetries to speed up calculations. This group may be of further interest in other calculations involving linked loci.
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