The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within ...its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (F
), genomic relationship matrix (F
), and pedigree-based coefficient (F
).
The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of F
and F
, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between F
-F
was zero, while the correlation (- 0.01 to - 0.07) between F
-F
decreased as a function of ROH length, except for F
(- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands.
Low F
F
correlation estimates indicate that F
is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and F
should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 ...with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases.
In this study using the high density BovineHD SNP array, we performed high resolution CNV analyses on both Btau_4.0 and UMD3.1 with 674 animals of 27 cattle breeds. We first compared CNV results derived from these two different SNP array platforms on Btau_4.0. With two thirds of the animals shared between studies, on Btau_4.0 we identified 3,346 candidate CNV regions representing 142.7 megabases (~4.70%) of the genome. With a similar total length but 5 times more event counts, the average CNVR length of current Btau_4.0 dataset is significantly shorter than the previous one (42.7 kb vs. 205 kb). Although subsets of these two results overlapped, 64% (91.6 megabases) of current dataset was not present in the previous study. We also performed similar analyses on UMD3.1 using these BovineHD SNP array results. Approximately 50% more and 20% longer CNVs were called on UMD3.1 as compared to those on Btau_4.0. However, a comparable result of CNVRs (3,438 regions with a total length 146.9 megabases) was obtained. We suspect that these results are due to the UMD3.1 assembly's efforts of placing unplaced contigs and removing unmerged alleles. Selected CNVs were further experimentally validated, achieving a 73% PCR validation rate, which is considerably higher than the previous validation rate. About 20-45% of CNV regions overlapped with cattle RefSeq genes and Ensembl genes. Panther and IPA analyses indicated that these genes provide a wide spectrum of biological processes involving immune system, lipid metabolism, cell, organism and system development.
We present a comprehensive result of cattle CNVs at a higher resolution and sensitivity. We identified over 3,000 candidate CNV regions on both Btau_4.0 and UMD3.1, further compared current datasets with previous results, and examined the impacts of genome assemblies on CNV calling.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
: Canine biological specimens are often part of the physical evidence from crime scenes. Until now, there have been no validated canine‐specific forensic reagent kits available. A multiplex ...genotyping system, comprising 18 short tandem repeats (STRs) and a sex‐linked zinc finger locus for gender determination, was developed for generating population genetic data assessing the weight of canine forensic DNA profiles. Allele frequencies were estimated for 236 pedigreed and 431 mixed breed dogs residing in the U.S. Average random match probability is 1 in 2 × 1033 using the regional database and 1 in 4 × 1039 using the breed dataset. Each pedigreed population was genetically distinct and could be differentiated from the mixed breed dog population but genetic variation was not significantly correlated with geographic transition. Results herein support the use of the allele frequency data with the canine STR multiplex for conveying the significance of identity testing for forensic casework, parentage testing, and breed assignments.
: Despite the popularity of dogs in US households, canine DNA evidence remains largely untapped in forensic investigations partially because of the absence of well‐defined forensic short tandem ...repeats (STRs), lack of standardized and validated PCR protocols, STR reagent kits, and poorly developed nomenclature. A nomenclature system was established based on internationally recognized recommendations for human forensic STRs for a recently developed canine STR reagent kit. Representative alleles were sequenced from each of the 18 STRs and the sex‐typing marker included in the kit. This study also reflects on the impact of point mutations, insertions, and deletions within and outside the STR core repeat structures. An understanding of the STRs’ sequence and repeat structures will enable development of a robust and reliable allele nomenclature and improve the accuracy and precision of allele fragment sizing in canine forensic profiling. The expected allele sizes have been calculated, and their repeat stuctures defined based on sequence information.
Prediction of complex trait phenotypes in the presence of unknown gene action is an ongoing challenge in animals, plants, and humans. Development of flexible predictive models that perform well ...irrespective of genetic and environmental architectures is desirable. Methods that can address non-additive variation in a non-explicit manner are gaining attention for this purpose and, in particular, semi-parametric kernel-based methods have been applied to diverse datasets, mostly providing encouraging results. On the other hand, the gains obtained from these methods have been smaller when smoothed values such as estimated breeding value (EBV) have been used as response variables. However, less emphasis has been placed on the choice of phenotypes to be used in kernel-based whole-genome prediction. This study aimed to evaluate differences between semi-parametric and parametric approaches using two types of response variables and molecular markers as inputs. Pre-corrected phenotypes (PCP) and EBV obtained for dairy cow health traits were used for this comparison. We observed that non-additive genetic variances were major contributors to total genetic variances in PCP, whereas additivity was the largest contributor to variability of EBV, as expected. Within the kernels evaluated, non-parametric methods yielded slightly better predictive performance across traits relative to their additive counterparts regardless of the type of response variable used. This reinforces the view that non-parametric kernels aiming to capture non-linear relationships between a panel of SNPs and phenotypes are appealing for complex trait prediction. However, like past studies, the gain in predictive correlation was not large for either PCP or EBV. We conclude that capturing non-additive genetic variation, especially epistatic variation, in a cross-validation framework remains a significant challenge even when it is important, as seems to be the case for health traits in dairy cows.
In cases of child abuse, including child sexual abuse, children are often told to keep the maltreatment secret. When mothers suspect something is wrong, they may question their children and obtain a ...disclosure of abuse. In many cases, when children disclose, they do so to their own mothers first. Initial disclosures like these are then questioned during legal proceedings due to concerns about children’s suggestibility. The current study assessed secret-keeping and suggestibility of children ages 36- to 72-months-old ( N = 62) when they were interviewed by their own mothers versus when they were interviewed by strangers who were mothers of other children. In the study, children participated in a scripted novel activity with a research assistant called a “babysitter”. All of the children (and their babysitters) were told not to play with certain toys, but the babysitter played with them anyway and encouraged the children to do the same. All of the children were urged by the babysitter not to tell anyone that they played with the forbidden toys. After a short time delay (approximately 15 minutes), children were interviewed by their own mothers or by strangers. Interviews were scripted, and children were asked questions about the forbidden toys to assess secret-keeping and asked misleading questions to assess suggestibility. Mothers’ self-reported attachment orientations were measured as possible predictors of children’s secret-keeping and suggestibility. Interviewer identity and child gender emerged as predictors of children’s secret-keeping. Increased age and cognitive abilities were associated with decreased suggestibility. Implications for developmental theory are addressed. The findings have forensic relevance in court cases when children have been told to keep abuse a secret and mothers have then questioned their children about the abuse.
Thirty-seven Holstein and 26 Brown Swiss dairy cows were used to evaluate the effect of two different cooling systems on physiological and hormonal responses during the summer. A control group of ...cows had access only to shade (C). A second group was cooled with spray and fans (S/F) and the third group was under an evaporative cooling system called Korral Kool (KK). The maximum temperature humidity index during the trial was from 73 to 85. Rectal temperatures and respiration rates of the C group were higher (P<0.05) than those of the S/F and KK groups in both Holstein and Brown Swiss cows. Triiodothyronine levels in milk were higher (P<0.05) in the KK group than in the S/F and C groups, while cortisol levels were lower (P<0.05) in the C group than in S/F and KK. There was no significant difference in the hormonal response of the two breeds. These results demonstrate that both cooling systems may be used increase the comfort of Holstein and Brown Swiss cows during summer in hot, dry climates.
To develop a reagent kit that enables multiplex polymerase chain reaction (PCR) amplification of 18 short tandem repeats (STR) and the canine sex-determining Zinc Finger marker.
Validation studies to ...determine the robustness and reliability in forensic DNA typing of this multiplex assay included sensitivity testing, reproducibility studies, intra- and inter-locus color balance studies, annealing temperature and cycle number studies, peak height ratio determination, characterization of artifacts such as stutter percentages and dye blobs, mixture analyses, species-specificity, case type samples analyses and population studies.
The kit robustly amplified domesticated dog samples and consistently generated full 19-locus profiles from as little as 125 pg of dog DNA. In addition, wolf DNA samples could be analyzed with the kit.
The kit, which produces robust, reliable, and reproducible results, will be made available for the forensic research community after modifications based on this study's evaluation to comply with the quality standards expected for forensic casework.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Enrollment in Seventh-day Adventist (SDA) schools is declining as is the number of schools and teachers. While there could be many reasons for this, one perception of SDA schools, held by parents, ...teachers, pastors, and school board members, is that students enrolled in schools with one, two, or three teachers do not achieve at the same rate as those in schools with four or more teachers. This study compares the academic achievement of students in grades three through eight in different types of schools (designated by number of teachers) and the interaction of teacher, student, parent, and school variables with school type. Data from the CognitiveGenesis research study, including student, parent, teacher, and administrator surveys and Iowa Test of Basic Skills (ITBS) test results, were used in this analysis. Results indicated that there were no significant differences in student achievement in reading, science, and social studies among the school types. Students in one-teacher schools had significantly higher achievement than did students in the other three school types in the following areas: language arts, mathematics, sources of information, and the composite score and the effects were consistent across grades three through eight. The differences were small. There were nine significant interactions between school type and student, parent, teacher, and school characteristics on achievement. In the few areas where there was interaction between school type and student and teacher characteristics, the interaction was relatively small. Seventh-day Adventist educators are encouraged to share the finding that while there were differences in achievement among the four school types, and small schools do as well or better academically than larger schools, these differences were small. The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.
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