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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 -
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 -
Heart Rhythm Oct 2022
Topics: Exome; Heart; Mitochondrial Proteins; Pedigree
PubMed: 35640786
DOI: 10.1016/j.hrthm.2022.05.030 -
Nucleic Acids Research Feb 2021The maternal mode of mitochondrial DNA (mtDNA) inheritance is central to human genetics. Recently, evidence for bi-parental inheritance of mtDNA was claimed for...
The maternal mode of mitochondrial DNA (mtDNA) inheritance is central to human genetics. Recently, evidence for bi-parental inheritance of mtDNA was claimed for individuals of three pedigrees that suffered mitochondrial disorders. We sequenced mtDNA using both direct Sanger and Massively Parallel Sequencing in several tissues of eleven maternally related and other affiliated healthy individuals of a family pedigree and observed mixed mitotypes in eight individuals. Cells without nuclear DNA, i.e. thrombocytes and hair shafts, only showed the mitotype of haplogroup (hg) V. Skin biopsies were prepared to generate ρ° cells void of mtDNA, sequencing of which resulted in a hg U4c1 mitotype. The position of the Mega-NUMT sequence was determined by fluorescence in situ hybridization and two different quantitative PCR assays were used to determine the number of contributing mtDNA copies. Thus, evidence for the presence of repetitive, full mitogenome Mega-NUMTs matching haplogroup U4c1 in various tissues of eight maternally related individuals was provided. Multi-copy Mega-NUMTs mimic mixtures of mtDNA that cannot be experimentally avoided and thus may appear in diverse fields of mtDNA research and diagnostics. We demonstrate that hair shaft mtDNA sequencing provides a simple but reliable approach to exclude NUMTs as source of misleading results.
Topics: Cell Nucleus; DNA Copy Number Variations; DNA, Mitochondrial; Female; Genome, Human; Humans; Male; Pedigree; Sequence Analysis, DNA
PubMed: 33450006
DOI: 10.1093/nar/gkaa1271 -
Radiation Research Jul 2022Previous epidemiological studies have demonstrated elevated susceptibility to ionizing radiation in some families, thus suggesting the presence of genetic components...
Previous epidemiological studies have demonstrated elevated susceptibility to ionizing radiation in some families, thus suggesting the presence of genetic components that conferred increased rate of radiation-associated meningioma (RAM). In this study, we exome-sequenced and investigated the segregation pattern of rare deleterious variants in 11 RAM pedigrees. In addition, we performed a rare-variant association analysis in 92 unrelated familial cases of RAM that were ancestry-matched with 88 meningioma-free controls. In the pedigree analysis, we found that each family carried mostly a unique set of rare deleterious variants. A follow-up pathway analysis of the union of the genes that segregated within each of the 11 pedigrees identified a single statistically significant (q value = 7.90E-04) "ECM receptor interaction" set. In the case-control association analysis, we observed no statistically significant variants or genes after multiple testing correction; however, examination of ontological categories of the genes that associated with RAM at nominal P values <0.01 identified biologically relevant pathways such as DNA repair, cell cycle and apoptosis. These results suggest that it is unlikely that a small number of highly penetrant genes are involved in the pathogenesis of RAM. Substantially larger studies are needed to identify genetic risk variants and genes in RAM.
Topics: Case-Control Studies; Exome; Genetic Predisposition to Disease; Humans; Pedigree; Radiation, Ionizing
PubMed: 35405740
DOI: 10.1667/RADE-21-00035.1 -
Bioinformatics (Oxford, England) Oct 2019Plant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a...
MOTIVATION
Plant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data.
RESULTS
As a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships.
AVAILABILITY AND IMPLEMENTATION
PedigreeNet is accessible at https://www.maizegdb.org/breeders_toolbox. The open source code is publically and freely available at GitHub: https://github.com/Maize-Genetics-and-Genomics-Database/PedigreeNet.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Databases, Factual; Databases, Genetic; Internet; Pedigree; Software; Zea mays
PubMed: 30903182
DOI: 10.1093/bioinformatics/btz208 -
Amyotrophic Lateral Sclerosis &... Nov 2020With the exception of rare, juvenile-onset, autosomal recessive cases, primary lateral sclerosis (PLS) has long been considered an exclusively sporadic motor neuron...
With the exception of rare, juvenile-onset, autosomal recessive cases, primary lateral sclerosis (PLS) has long been considered an exclusively sporadic motor neuron disease. However, the identification of PLS cases within pedigrees with familial amyotrophic lateral sclerosis (ALS), together with the clinical and neuropathological overlap with other neurodegenerative disease with strong genetic component such as ALS and hereditary spastic paraparesis (HSP), suggest the existence of a genetic component in PLS as well. Here we will review the genetics of juvenile PLS-like syndromes and the contribution of mutations in ALS and HSP-associated genes to PLS pathogenesis.
Topics: Amyotrophic Lateral Sclerosis; Humans; Motor Neuron Disease; Neurodegenerative Diseases; Pedigree; Spastic Paraplegia, Hereditary
PubMed: 33602012
DOI: 10.1080/21678421.2020.1837177 -
Journal of Health Communication Apr 2015Family history is important for assessing risk of cancer. This study aimed to improve cancer family history communication and collection by training and motivating lay...
Family history is important for assessing risk of cancer. This study aimed to improve cancer family history communication and collection by training and motivating lay individuals to construct pedigrees. The authors' ultimate goal is to improve identification of familial cancer. Participants (n = 200) completed preintervention, postintervention, and 1-week follow-up surveys to assess pedigree construction. The intervention reviewed basic construction and interpretation of a pedigree for familial cancer. As a result of intervention, individuals reported more positive attitudes about collecting family history, were more likely to intend to speak to family and physicians about cancer risk, better understood a sample pedigree, and constructed more detailed pedigrees of their family history. At follow-up, 25% of the sample had spoken with their families about cancer risk. For those individuals who had not spoken with family, higher postintervention pedigree knowledge was associated with greater intentions to speak with family in the future. The intervention improved the communication and collection of pedigrees and communication about cancer risk, which could be used to improve the identification of individuals with familial cancers and awareness of family cancer risk.
Topics: Adolescent; Adult; Attitude to Health; Communication; Family; Female; Follow-Up Studies; Humans; Intention; Male; Medical History Taking; Neoplasms; Pedigree; Physician-Patient Relations; Risk Assessment; Young Adult
PubMed: 25763471
DOI: 10.1080/10810730.2014.977470 -
BMC Genomics Mar 2021Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a...
BACKGROUND
Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.
RESULTS
Phenotypic data of seven F low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172-182 cM), LG4 (48-54 cM), and LG7 (62-70 cM), explaining 17-54%, 11-55%, and 11-18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40-46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.
CONCLUSIONS
A multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.
Topics: Pedigree; Plant Breeding; Polymorphism, Single Nucleotide; Prunus persica; Quantitative Trait Loci
PubMed: 33726679
DOI: 10.1186/s12864-021-07483-8 -
Journal of Feline Medicine and Surgery Dec 2018The purpose of this study was to investigate the prevalence of cataracts in the Russian Blue breed of cats in Sweden, and to describe the clinical appearance of this...
OBJECTIVES
The purpose of this study was to investigate the prevalence of cataracts in the Russian Blue breed of cats in Sweden, and to describe the clinical appearance of this presumed inherited form of cataract.
METHODS
A total of 66 Russian Blue cats were examined in Sweden, between March and October 2014, using standard examination techniques. The examined cats were between 3 months and 14 years of age. Pedigrees were collected from all examined cats for genetic studies.
RESULTS
Mild-to-severe forms of mainly bilateral cataracts were observed in 22/66 examined Russian Blue cats of both sexes. Two affected cats were <1 year of age. The most frequently observed appearance of a cataract was a small triangular, Y-shaped or circular opacity at the border of the posterior nucleus and the anterior part of the posterior cortex, which caused no observable visual impairment. More extended forms were observed in 6/22 cats, with involvement of both the nucleus and either the entire cortex or parts of the posterior and/or anterior cortex. Visual impairment or blindness was observed in the latter six cases. Pedigree analyses indicated a simple autosomal recessive mode of inheritance for the defect, although a dominant mode with incomplete penetrance could not be excluded.
CONCLUSIONS AND RELEVANCE
This study indicates that the Russian Blue breed of cat is affected by hereditary cataracts. The high prevalence in young cats and the characteristic location of the most frequently observed defect in the study suggest an early onset type of cataract. The breeders should be aware of this defect and have their cats examined by a veterinary ophthalmologist before breeding of an individual Russian Blue cat is considered.
Topics: Animals; Breeding; Cat Diseases; Cataract; Cats; Diagnostic Techniques, Ophthalmological; Female; Male; Pedigree; Prevalence; Retinal Diseases; Sweden
PubMed: 29364031
DOI: 10.1177/1098612X17752197