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Yi Chuan = Hereditas Apr 2021The accuracy of genetic evaluations in different herds is affected by the degree of genetic connectedness among herds. In this study, we explored the application of high...
The accuracy of genetic evaluations in different herds is affected by the degree of genetic connectedness among herds. In this study, we explored the application of high density SNP markers in the assessment of genetic connectedness by comparing the genetic connectedness based on pedigree data and genomic data. Six methods, including PEVD (prediction error variance of differences between estimated breeding values), PEVD (x), VED (variance of estimated difference between the herd effects), CD (generalized coefficient of determination), r (prediction error correlation) and CR (connectedness rating), were implemented to measure the genetic connectedness based on different relationship matrices (A, G, G, G and H). Our results from both simulated data and SNP chip data indicated that, except for the PEVD (x) and VED methods, the genetic connectedness obtained by PEVD, CD, r and CR based on G. G and G matrices (using genome information only) were superior to those based on A matrix (using pedigree information only). Generally, for most approaches, the genetic connectedness based on H matrix (using both pedigree and genome information) was somewhere between A matrix and G matrices. CD could overestimate the degree of genetic connectedness as it was still very high when CR and r were close to 0. The method r could not accurately reflect the true genetic connectedness of the populations. It generated 0.01 of genetic connectedness for all three pig breeding farms, which were actually genetically different with each other. With increasing of heritability, the degree of genetic connectedness obtained by all methods were increased as well. However, in the case of heritability 0.1, PEVD based on A matrix performed better than based on G matrix, suggesting that traits with medium and high heritability are more suitable for the assessment of genetic connectedness compared to traits with low heritability. Our findings indicated that high-density SNP markers have advantages over pedigree analysis for the measurement of genetic connectedness, and CR is a robust and reliable method to assess genetic connectedness. Further, CR is easily calculated and less affected by heritability of trait. PEVD is good supplement to quantify the prediction errors of estimated breeding values under the specific genetic connectedness. In comparison, G matrix can reflect genetic connectedness better than its extensions G and G matrix.
Topics: Animals; Genome; Genomics; Genotype; Models, Genetic; Pedigree; Phenotype; Polymorphism, Single Nucleotide; Swine
PubMed: 33972208
DOI: 10.16288/j.yczz.20-351 -
Molecular Ecology Jan 2022Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage...
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics-the pedigree-has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well-informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
Topics: Conservation of Natural Resources; Genetics, Population; Genome; Genomics; Inbreeding; Pedigree
PubMed: 34553796
DOI: 10.1111/mec.16192 -
American Journal of Medical Genetics.... Nov 2022
Topics: Humans; Pedigree; Exome Sequencing
PubMed: 36209347
DOI: 10.1002/ajmg.a.62935 -
Indian Journal of Dermatology,... 2022
Topics: Humans; Keratoderma, Palmoplantar; Pedigree
PubMed: 33871192
DOI: 10.25259/IJDVL_759_20 -
Polish Journal of Veterinary Sciences Mar 2022Information regarding the correct pedigree of and relationship between animals is useful for managing dairy breeding, reducing inbreeding, estimating breeding value, and...
Information regarding the correct pedigree of and relationship between animals is useful for managing dairy breeding, reducing inbreeding, estimating breeding value, and establishing correct breeding programs. Additionally, the successful implementation of progeny testing is crucial for improving the genetics of dairy cattle, which depends on the availability of correct pedigree information. Incorrect pedigree information leads to bias in bull evaluation. In this study, Neogen GeneSeek Genomic Profiler (GGP) 50K SNP chips were used to identify and verify the sire of Taiwanese Holstein dairy cattle and analyze the reasons that lead to incorrect sire records. Samples were collected from 2,059 cows of 36 dairy farms, and the pedigree information was provided by breeders. The results of sire verification can be divided into three categories: submitted unconfirmed sire, submitted confirmed sire, and incorrectly submitted verified sire. Data on the sires of 1,323 (64.25%) and 572 (27.78%) dairy cows were verified and discovered, respectively. Sires of 1,895 (92.03%) dairy cattle were identified, which showed that the paternal pedigree of dairy cattle could be discovered and verified through genetic testing. An error-like analysis revealed that the data of 37 sires were incorrectly recorded because the bull's NAAB code number was incorrectly entered into the insemination records: for 19 sires, the wrong bull was recorded because the frozen semen of a bull placed in the wrong storage tank was used, 6 had no sire records, and for 12 sires, the NAAB code of the correct bull was recorded but with a wrong stud code, marketing code, or unique number for the stud or breed. To reduce recorded sire error rates by at least 27.78%, automated identification of the mated bull must be adopted to reduce human error and improve dairy breeding management on dairy farms.
Topics: Animals; Cattle; Female; Genome; Genomics; Inbreeding; Male; Pedigree; Taiwan
PubMed: 35575992
DOI: 10.24425/pjvs.2022.140841 -
Journal of Equine Veterinary Science May 2021The sheer diversity of heritable physiological traits, and the ingenuity of genome derived research technologies, extends the study of genetics to impact diverse... (Review)
Review
The sheer diversity of heritable physiological traits, and the ingenuity of genome derived research technologies, extends the study of genetics to impact diverse scientific fields. Equine science is no exception, experiencing a number of genome-enabled discoveries that spur further research in areas like nutrition, reproduction, and exercise physiology. Yet unexpected findings, especially those that over-turn commonly held beliefs in the horse industry, can create challenges in outreach, education and communication with stakeholders. For example, studies of ancient DNA revealed that the oldest domesticated equids in the archeological record were in fact another species, the Przewalski's horse, leaving the origins of our modern horses a mystery yet to be solved. Genomic analysis of ancestry can illuminate relationships older than our prized pedigree records, and in some cases, identify unexpected inconsistencies in those pedigrees. Even our interpretation of what constitutes a genetic disease is changing, as we re-examine common disease alleles; how these alleles impact equine physiology, and how they are perceived by breeders and professionals in the industry. Effectively translating genetic tools for utilization in horse management and preparing our community for the debate surrounding ethical questions that may arise from genomic studies, may be the next great challenges we face as scientists and educators.
Topics: Animals; DNA, Ancient; Genome; Genomics; Horses; Pedigree
PubMed: 34030792
DOI: 10.1016/j.jevs.2021.103456 -
Otolaryngology--head and Neck Surgery :... Nov 2020To evaluate inheritance patterns and define the familial clustering rate of idiopathic subglottic stenosis (iSGS). (Observational Study)
Observational Study
OBJECTIVE
To evaluate inheritance patterns and define the familial clustering rate of idiopathic subglottic stenosis (iSGS).
STUDY DESIGN
Retrospective observational study.
SETTING
International multicenter collaborative of >30 tertiary care centers.
METHODS
Patients with a clinically confirmed iSGS diagnosis within the North American Airway Collaborative's iSGS cohort consented between 2014 and 2018 were eligible for enrollment. Patient demographics and disease severity were abstracted from the collaborative's iSGS longitudinal registry. Pedigrees of affected families were created.
RESULTS
A total of 810 patients with iSGS were identified. Positive family history for iSGS was reported in 44 patients in 20 families. The rate of familial clustering in iSGS is 2.5%. Mean age of disease onset is 42.6 years. Of the 44 patients with familial aggregation of iSGS, 42 were female and 2 were male; 13 were mother-daughter pairs and 2 were father-daughter pairs. There were 3 sister-sister pairs. There was 1 niece-aunt pair and 2 groups of 3 family members. One pedigree demonstrated 2 affected mother-daughter pairs, with the mothers being first-degree paternal cousins. Inheritance is non-Mendelian, and anticipation is present in 11 of 13 (84%) parent-offspring pairs. The mean age of onset between parents (48.4 years) and offspring (36.1 years) was significantly different ( = .016).
CONCLUSION
This study quantifies the rate of familial clustering of iSGS at 2.5%. Inheritance is non-Mendelian, and disease demonstrates anticipation. These data suggest that there may be a genetic contribution in iSGS.
Topics: Adult; Age of Onset; Family; Female; Humans; Inheritance Patterns; Laryngostenosis; Male; Middle Aged; Patient Acuity; Pedigree; Retrospective Studies
PubMed: 32600122
DOI: 10.1177/0194599820935402 -
Tropical Animal Health and Production Oct 2022In unstructured dairy programs, pedigree is usually shallow, which leads to biased prediction of breeding values using best linear unbiased prediction (BLUP). The...
In unstructured dairy programs, pedigree is usually shallow, which leads to biased prediction of breeding values using best linear unbiased prediction (BLUP). The objective of this study was to come out with a genomic prediction strategy that can utilize shallow pedigree information and predict unbiased and more accurate GEBV for sex-limited traits in a small population using single-step GBLUP (ssGBLUP). The data and models for a population under selection were simulated. Out of current 10 generations, 10th generation with 1000 candidates served as validation population. For the complete pedigree scenario, pedigree (P)BLUP estimated breeding values (EBV) were unbiased with accuracy (r) of 0.35 ± 0.02 and 0.26 ± 0.01 for 0.3 and 0.1 h scenario, respectively. For the shallow pedigree, biased prediction of breeding values and low accuracies were obtained with linear decline in the accuracy of EBV for removal of information on more distant pedigree. Accuracy and bias (ρ) for scenario with removing 4 distant generations from pedigree were 0.30 ± 0.02 and 0.55 ± 0.03, respectively, in moderate h scenario. Use of Genomic (G)BLUP, especially with "extreme phenotypic contrast selective genotyping," (TB) resulted in higher accuracy for a small reference of females; however, GEBV were highly biased. We observed that ssGBLUPF, where the numerator relationship matrix is corrected for inbreeding, resulted in more accurate and unbiased estimates of GEBV across shallow pedigree scenario, with TB all female reference (missing 4 distant generations: r = 0.50 ± 0.02; ρ = 0.96 ± 0.02). We recommend use of ssGBLUPF with two tailed selectively genotyped all female reference in shallow pedigree scenarios, to obtain unbiased and accurate GEBV for sex-limited traits, when resources are limited.
Topics: Animals; Female; Genome; Genomics; Genotype; Models, Genetic; Pedigree; Phenotype
PubMed: 36210357
DOI: 10.1007/s11250-022-03340-2 -
Annual Review of Genomics and Human... Aug 2020In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism... (Review)
Review
In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism data with private and public genomic databases. Using a combination of genome comparisons and traditional genealogical research, investigators can triangulate distant relatives to the contributor of DNA data from a crime scene, ultimately identifying perpetrators of violent crimes. This approach has also been successful in identifying unknown deceased persons and perpetrators of lesser crimes. Such advances are bringing into focus ethical questions on how much access to DNA databases should be granted to law enforcement and how best to empower public genome contributors with control over their data. The necessary policies will take time to develop but can be informed by reflection on the familial searching policies developed for searches of the federal DNA database and considerations of the anonymity and privacy interests of civilians.
Topics: Crime; DNA; DNA Fingerprinting; Databases, Nucleic Acid; Forensic Genetics; Humans; Pedigree
PubMed: 32289230
DOI: 10.1146/annurev-genom-111819-084213 -
Journal of Animal Breeding and Genetics... May 2024The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of...
The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (N) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the N is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current N suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.
Topics: Sheep; Animals; Genetic Variation; Pedigree; Inbreeding; Population Density; Selection, Genetic
PubMed: 38108572
DOI: 10.1111/jbg.12842