-
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 -
Experimental Biology and Medicine... Jun 2022To describe clinical and genetic characteristics in a series of Chinese patients with non-syndromic retinitis pigmentosa, a total of 20 unrelated Chinese pedigrees with...
To describe clinical and genetic characteristics in a series of Chinese patients with non-syndromic retinitis pigmentosa, a total of 20 unrelated Chinese pedigrees with non-syndromic retinitis pigmentosa were evaluated. Complete ophthalmic examinations data including the Humphrey visual field, spectral domain-optical coherence tomography, full-field electroretinography, and fundus fluorescence were collected and analyzed. Targeted exome sequencing was utilized to investigate variations in 260 known genes of inherited retinal disease, including the 90 known causative retinitis pigmentosa genes. We initially identified the potential candidate variants in the pedigrees, then validated the variants using the Sanger sequencing and performed segregation analysis to verify that the variants constituted disease-causing mutations in these pedigrees. We detected three novel (likely) pathogenic and eight previously reported (likely) pathogenic variations in nine genes reported to be related to non-syndromic retinitis pigmentosa in nine of the pedigrees. We report clinical characteristics of Chinese patients with retinitis pigmentosa and novel mutations responsible for non-syndromic retinitis pigmentosa in Chinese pedigrees, expanding the number of gene mutations associated with this disorder and clarifying its genetic basis in the Chinese population. These data will help with rapid and efficient molecular diagnosis and the study of targeted treatment for retinitis pigmentosa in this population.
Topics: Asian People; China; DNA Mutational Analysis; Electroretinography; Humans; Mutation; Pedigree; Retinitis Pigmentosa
PubMed: 35410501
DOI: 10.1177/15353702221085711 -
Scientific Reports Jun 2022Mutations in the FERM domain containing 7 (FRMD7) gene have been proven to be responsible for infantile nystagmus (IN). The purpose of this study is to investigate FRMD7...
Mutations in the FERM domain containing 7 (FRMD7) gene have been proven to be responsible for infantile nystagmus (IN). The purpose of this study is to investigate FRMD7 gene mutations in patients with IN, and to evaluate the nystagmus intensity among patients with and without FRMD7 mutations. The affected males were subdivided into three groups according to whether or not having FRMD7 mutations and the types of mutations. Fifty-two mutations were detected in FRMD7 in 56 pedigrees and 34 sporadic patients with IN, including 28 novel and 24 previous reported mutations. The novel identified mutations further expand the spectrum of FRMD7 mutations. The parameters of nystagmus intensity and the patients' best corrected visual acuity were not statistically different among the patients with and without identified FRMD7 mutations, and also not different among patients with different mutant types. The FERM-C domain, whose amino acids are encoded by exons 7, 8 and 9, could be the harbor region for most mutations. Loss-of-function is suggested to be the common molecular mechanism for the X-linked infantile nystagmus.
Topics: Cytoskeletal Proteins; DNA Mutational Analysis; Genetic Diseases, X-Linked; Humans; Male; Membrane Proteins; Mutation; Nystagmus, Congenital; Pedigree
PubMed: 35705619
DOI: 10.1038/s41598-022-14144-7 -
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 -
Disease Models & Mechanisms Jun 2022DMM is launching a new Subject Focus on genetic variance in human disease. Here, we discuss this ongoing series of invited articles and reflect on advances in...
DMM is launching a new Subject Focus on genetic variance in human disease. Here, we discuss this ongoing series of invited articles and reflect on advances in understanding the genotype–phenotype complexities in disease.
Topics: Breeding; Genomic Medicine; Humans; Models, Genetic; Pedigree
PubMed: 35771631
DOI: 10.1242/dmm.049700 -
Genes Aug 2022Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has... (Review)
Review
Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads and identify unknown individuals. Consumer DNA testing and the public's increased curiosity about their own DNA and genetic ancestry, have greatly contributed to the availability of human genetic data. Genetic genealogy has been a field of study/interest for many years as both amateur and professional genetic genealogists use consumer DNA data to explore genetic connections in family trees. FGG encompasses this knowledge by applying advanced sequencing technologies to forensic DNA evidence samples and by performing genetic genealogy methods and genealogical research, to produce possible identities of unknown perpetrators of violent crimes and unidentified human remains. This combination of forensic genetics, genetic genealogy, and genealogical research has formed a new subdiscipline within the forensic sciences. This paper will summarize the individual disciplines that led to the emergence of FGG, its practice in forensic investigations, and current/future considerations for its use.
Topics: DNA; Forensic Genetics; Humans; Pedigree; United States
PubMed: 36011291
DOI: 10.3390/genes13081381 -
Journal of Dairy Science Jul 2020Single-step genomic BLUP (ssGBLUP) is a powerful approach for breeding value prediction in populations with a limited number of genotyped animals. However, conflicting...
Single-step genomic BLUP (ssGBLUP) is a powerful approach for breeding value prediction in populations with a limited number of genotyped animals. However, conflicting genomic (G) and pedigree (A) relationship matrices complicate the implementation of ssGBLUP into practice. The metafounder (MF) approach is a recently proposed solution for this problem and has been successfully used on simulated and real multi-breed pig data. Advantages of the method are easily seen across breed evaluations, where pedigrees are traced to several pure breeds, which are thereafter used as MF. Application of the MF method to ruminants is complicated due to multi-breed pedigree structures and the inability to transmit existing unknown parent groups (UPG) to MF. In this study, we apply the MF approach for ssGBLUP evaluation of Finnish Red Dairy cattle treated as a single breed. Relationships among MF were accounted for by a (co)variance matrix (Γ) computed using estimated base population allele frequencies. The attained Γ was used to calculate a relationship matrix A for the genotyped animals. We tested the influence of SNP selection on the Γ matrix by applying a minor allele frequency (MAF) threshold (Γ) where accepted markers had an MAF ≥0.05. Elements in the Γ matrix were slightly lower than in the Γ matrix. Correlation between diagonal elements of the genomic and pedigree relationship matrices increased from 0.53 (A) to 0.76 ( A and [Formula: see text] ). Average diagonal elements of A and [Formula: see text] matrices increased to the same level as in the G matrix. The ssGBLUP breeding values (GEBV) were solved using either the original 236 or redefined 8 UPG, or 8 MF computed with or without the MAF threshold. For bulls, the GEBV validation test results for the 8 UPG and 8 MF gave the same validation reliability (R; 0.31) and over-dispersion (0.73, measured by regression coefficient b). No significant R increase was observed in cows. Thus, the MF greatly influenced the pedigree relationship matrices but not the GEBV. Selection of SNP according to MAF had a notable effect on the Γ matrix and made the A and G matrices more similar.
Topics: Animals; Cattle; Female; Food, Formulated; Gene Frequency; Genome; Genomics; Genotype; Male; Models, Genetic; Pedigree; Reproducibility of Results; Selective Breeding
PubMed: 32418688
DOI: 10.3168/jds.2019-17483 -
Scientific Reports Jan 2020Local ancestry, defined as the genetic ancestry at a genomic location of an admixed individual, is widely used as a genetic marker in genetic association and...
Local ancestry, defined as the genetic ancestry at a genomic location of an admixed individual, is widely used as a genetic marker in genetic association and evolutionary genetics studies. Many methods have been developed to infer the local ancestries in a set of unrelated individuals, a few of them have been extended to small nuclear families, but none can be applied to large (e.g. three-generation) pedigrees. In this study, we developed a method, FamANC, that can improve the accuracy of local ancestry inference in large pedigrees by: (1) using an existing algorithm to infer local ancestries for all individuals in a family, assuming (contrary to fact) they are unrelated, and (2) improving its accuracy by correcting inference errors using pedigree structure. Applied on African-American pedigrees from the Cleveland Family Study, FamANC was able to correct all identified Mendelian errors and most of double crossovers.
Topics: Algorithms; Computer Simulation; Ethnicity; Genetics, Population; Genotype; Haplotypes; Humans; Models, Genetic; Models, Statistical; Pedigree; Polymorphism, Single Nucleotide
PubMed: 31932708
DOI: 10.1038/s41598-019-57039-w -
Journal of Dairy Science Feb 2021Single-step genomic BLUP (ssGBLUP) requires compatibility between genomic and pedigree relationships for unbiased and accurate predictions. Scaling the genomic...
Single-step genomic BLUP (ssGBLUP) requires compatibility between genomic and pedigree relationships for unbiased and accurate predictions. Scaling the genomic relationship matrix (G) to have the same averages as the pedigree relationship matrix (i.e., scaling by averages) is one way to ensure compatibility. This requires computing both relationship matrices, calculating averages, and changing G, whereas only the inverses of those matrices are needed in the mixed model equations. Therefore, the compatibility process can add extra computing burden. In the single-step Bayesian regression, the scaling is done by including a mean (μ) as a fixed effect in the model. The parameter μ can be interpreted as the average of the breeding values of the genotyped animals. In this study, such scaling, called automatic, was implemented in ssGBLUP via Quaas-Pollak transformation of the inverse of the relationship matrix used in ssGBLUP (H), which combines the inverses of the pedigree and genomic relationship matrices. Comparisons involved a simulated data set, and the genomic relationship matrix was computed using different allele frequencies either from the current population (i.e., realized allele frequencies), equal among all the loci, or from the base population. For all of the scenarios, we computed bias [defined as the average difference between true breeding values (TBV) and genomic estimated breeding values (GEBV)], accuracy (defined as the correlation between TBV and GEBV), and dispersion (defined as the regression coefficient of GEBV on TBV). With no scaling, the bias expressed in terms of genetic standard deviations was 0.86, 0.64, and 0.58 with realized, equal, and base population allele frequencies, respectively. With scaling by averages, which is currently used in ssGBLUP, bias was 0.07, 0.08, and 0.03, respectively. With automatic scaling, bias was 0.18 regardless of allele frequencies. Accuracies were similar among scaling methods, but about 0.1 lower in the scenario without scaling. The GEBV were more inflated without any scaling, whereas the automatic scaling performed similarly to the scaling by averages. The average dispersion for those methods was 0.94. When μ was treated as random, with the variance equal to differences between pedigree and genomic relationships, the bias was the same as with the scaling by averages. The automatic scaling is biased, especially when μ is treated as a fixed effect. The bias may be small in real data with fewer generations, when traits are undergoing weak selection, or when the number of genotyped animals is large.
Topics: Animals; Bayes Theorem; Gene Frequency; Genome; Genomics; Genotype; Models, Genetic; Models, Statistical; Pedigree; Phenotype
PubMed: 33309381
DOI: 10.3168/jds.2020-18969 -
Journal of Thrombosis and Haemostasis :... Mar 2024Most family studies on venous thromboembolism (VTE) have focused on first-degree relatives.
BACKGROUND
Most family studies on venous thromboembolism (VTE) have focused on first-degree relatives.
OBJECTIVES
We took a pedigree-based approach and examined the risk of VTE and cardiometabolic disorders in offspring from extended pedigrees according to the densities of VTE in pedigrees.
METHODS
From the Swedish population, we identified a total of 482 185 pedigrees containing a mean of 14.2 parents, aunts/uncles, grandparents, and cousins of a core full sibship that we termed the pedigree offspring (n = 751 060). We then derived 8 empirical classes of these pedigrees based on the density of cases of VTE. The risk was determined in offspring for VTE and cardiometabolic disorders as a function of VTE density in their pedigrees. Bonferroni correction for multiple comparisons was performed.
RESULTS
VTE was unevenly distributed in the population; the Gini coefficient was 0.59. Higher VTE density in pedigrees was associated in the offspring with a higher risk of different VTE manifestations (deep venous thrombosis, pulmonary embolism, pregnancy-related VTE, unusual thrombosis, and superficial thrombophlebitis), thrombophilia, and lower age of first VTE event. Moreover, VTE density in pedigrees was significantly associated in the offspring with obesity, diabetes, gout, varicose veins, and arterial embolism and thrombosis (excluding brain and heart). No significant associations were observed for retinal vein occlusion, hypercholesterolemia, hypertension, coronary heart disease, myocardial infarction, ischemic stroke, atrial fibrillation, heart failure, primary pulmonary hypertension, cerebral hemorrhage, aortic aneurysm, peripheral artery disease, and overall mortality.
CONCLUSION
Offspring of pedigrees with a high density of VTE are disadvantaged regarding VTE manifestations and certain cardiometabolic disorders.
Topics: Humans; Venous Thromboembolism; Pedigree; Risk Factors; Thrombophlebitis; Pulmonary Embolism
PubMed: 38072377
DOI: 10.1016/j.jtha.2023.11.024