PubMed Health⌕ Search

Biomedical subjects

Y Da

Publications and source records attributed to Y Da.

At least 19 recordsLinked to original sources
PubMed2004

Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle.

We report putative quantitative trait loci affecting female fertility and milk production traits using the merged data from two research groups that conducted independent genome scans in Dairy Bull DNA Repository grandsire families to identify quantitative trait loci (QTL) affecting economically important traits. Six families used by both groups had been genotyped for 367 microsatellite markers covering 2713.5 cM of the cattle genome (90%), with an average spacing of 7.4 cM. Phenotypic traits included PTA for pregnancy rate and daughter deviations for milk, protein and fat yields, protein and fat percentages, somatic cell score, and productive life. Analysis of the merged dataset identified putative quantitative trait loci that were not detected in the separate studies, and the pregnancy rate PTA estimates that recently became available allowed detection of pregnancy rate QTL for the first time. Sixty-one putative significant marker effects were identified within families, and 13 were identified across families. Highly significant effects were found on chromosome 3 affecting fat percentage and protein yield, on chromosome 6 affecting protein and fat percentages, on chromosome 14 affecting fat percentage, on chromosome 18 affecting pregnancy rate, and on chromosome 20 affecting protein percentage. Within-family analysis detected putative QTL associated with pregnancy rate on six chromosomes, with the effect on chromosome 18 being the most significant statistically. These findings may help identify the most useful markers available for QTL detection and, eventually, for marker-assisted selection for improvement of these economically important traits.

Animals↗
PubMed2003

Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping.

Efforts to build a comprehensive genetic linkage map for the turkey (Meleagris gallopavo) have focused on development of genetic markers and experimental resource families. In this study, PCR amplification was attempted for 772 microsatellite markers that had been previously developed for three avian species (chicken, quail and turkey). Allelic polymorphism at 410 markers (53.1% of total examined) was determined by genotyping ten individuals (six F1 parents and four grandparents) in a new resource population specifically developed for genetic linkage mapping. Of these 410 markers, 109 (26.6%) were polymorphic in the tested individuals, with an average of 2.3 alleles per marker. Higher levels of polymorphism were found for the turkey-specific markers (61.1%) than for the chicken (22.7%) or quail-specific markers (33.3%). To test the fidelity of the matings, demonstrate the power of these families for linkage analysis, and determine genetic linkage relationships, 86 polymorphic markers were genotyped for up to 224 birds including founder grandparents, parents and F2 progeny. Linkage relationships for many of the chicken markers elucidated in the turkey were comparable to those observed in the chicken. These data demonstrate that the new UMN/NTBF resource population will provide a solid foundation for constructing a comparative genetic map of the turkey.

Alleles↗
PubMed2003

Statistical analysis and experimental design for mapping genes of complex traits in domestic animals.

Gene mapping for complex traits has been an active and challenging research area in humans, agricultural and laboratory species. In domestic animals and poultry, the goal of gene mapping is to find genes associated with production, reproduction and health traits. In humans, gene mapping for complex diseases has been a significant challenge. Although gene mapping results are accumulating rapidly, confirmed results are scarce. In domestic animals, gene mapping results are also accumulating rapidly and several large scale mapping projects in chickens, swine, and dairy cattle are currently in progress. Although new and more reliable results can be expected in the near future, the precise understanding of genes underlying complex traits is still some distance away. Recently, the approach of mapping genes of complex traits has been applied to gene expression data to map transcription regulatory elements, adding a new dimension to gene mapping. Statistical analysis of gene mapping data and experimental design are critical components of a gene mapping research. The purpose of this review article is to discuss current status as well as future directions and challenges in statistical analysis and experimental design for mapping genes of complex traits in domestic animals and poultry.

Animals↗
PubMed2003

A software tool for the graphical visualization of large and complex populations.

Pedigree drawing is an essential tool in genetic and genealogical studies. A genetic analysis of a disease often starts with drawing a pedigree to show the overall population structure, the relationship among individuals, and gene flows from generation to generation. Such a graphical presentation of a pedigree is valuable for understanding the nature of the disease such as inheritance mode and familial trends and of the disease, for tracing the source of a detrimental gene, and for identifying the founders of the population. A genealogy study typically requires a pedigree drawing to show relationships among individuals. However, as the size and complexity of a pedigree increase, drawing a clear pedigree becomes a challenge. Pedigraph has been created to solve this problem. We developed a software tool named Pedigraph capable of creating artistic graphical pedigree drawings of large and complex populations with flexible options for pedigree analysis. Preliminary tests show that this software tool has great potential to be a useful tool for research in breeding, genetics and genomics in plants, animals, and zoo species, as well as a useful tool for studying history and human populations.

Computer Graphics↗
PubMed2002

Linkage analysis using direct and indirect counting and relative efficiencies for codominant and dominant loci.

A method based on direct and indirect counting is developed for rapid and accurate linkage analysis for codominant and dominant loci. Methods for estimating gender-specific recombination frequencies are available for cases where at least one of the two loci is multiallelic and for biallelic loci with mixed parental linkage phases where at least one locus is codominant. Most of the estimates of gender-average and gender-specific recombination frequencies required iterative solutions. The new method makes use of the full data set, yields exact estimates of the recombination frequencies when the observed and expected genotypic frequencies are equal, and are computationally efficient. Relative efficiency of various data types is affected by the inheritance mode and by parental linkage phases of biallelic loci, but unaffected by the locus polymorphism when using the full data set for linkage analysis. The ability to determine parental linkage phases is affected by the locus polymorphism as well as inheritance mode. Intercross (or F-2 design) is more efficient for mapping codominant loci, whereas backcross is more efficient if dominance is involved. Mixed parental linkage phases of biallelic loci are less efficient than coupling or repulsion linkage phases. Ignoring noninformative offspring results in biased estimates of recombination frequency for biallelic loci only and reduced LOD scores for all cases.

Animals↗
PubMed2001

Generation and exploration of a dense genetic map in a region of a QTL affecting corpora lutea in a Meishan x Yorkshire cross.

Previously genomic scans revealed quantitative trait loci (QTL) on porcine Chromosome 8 (SSC8) as significantly affecting the number of corpora lutea (CL) in swine. In one study, statistical evidence for the putative QTL was found in the chromosomal region defined by the microsatellites (MS) SW205, SW444, SW206, and SW29. A Yeast Artificial Chromosome library was screened by using the corresponding primers for clones containing these MS by PCR. From five positive YAC clones, 10 additional MS were isolated and mapped to SSC8 with the INRA-University of Minnesota porcine Radiation Hybrid (IMpRH) panel. The genetic map position of the QTL has been refined by addition of these 10 markers. The QTL evaluation included pedigrees of F2-intercross Meishan x Yorkshire design, with phenotypic data of 108 F2 female offspring and genotypic data for 29 MS markers on SSC8. The analysis was performed by using the least squares regression method. The calculated QTL effect for CL obtained by the multilocus least squares method showed a maximum test statistic (F value = 13.98) at position 99 cM between three MS derived from YACs containing SW205 and SW1843 spanning an interval of 7.1 cM. The point-wise (nominal) P-value was 5.21 x 10-6 corresponding to a genome-wide P-value of 0.009. The additive QTL effect explained 17.4% of the phenotypic variance.

Animals↗
PubMed2000

A new mutation in the connexin 32 gene was found in Charcot- Marie-Tooth disease in Chinese patients.

OBJECTIVE: To investigate the characteristics of gene mutations of connexin 32 exon 2 in Charcot-Marie-Tooth disease in Chinese patients. METHODS: Screening for connexin 32 gene mutation was conducted in 6 unrelated CMT1 patients without duplication and 10 unrelated CMT2 patients. Mobility shift of exon 2 was analyzed by SSCP and further confirmed by sequencing. The PCR products were cut by appropriate restricted enzyme in 50 normal controls. RESULTS: One missense mutation at nucleotides 62(G-->A) was found in a CMT1 patient. 50 normal controls were analyzed by the enzyme HaeIII and no abnormality was found. This proved that the mutation was the cause of disease. CONCLUSION: This mutation has not been reported previously. A proportion of CMTX patients may exist in the group of CMT1 patients in China.

Adolescent↗
PubMed1999

A genome scan for QTL influencing milk production and health traits in dairy cattle.

A genome scan was conducted in the North American Holstein-Friesian population for quantitative trait loci (QTL) affecting production and health traits using the granddaughter design. Resource families consisted of 1,068 sons of eight elite sires. Genome coverage was estimated to be 2,551 cM (85%) for 174 genotyped markers. Each marker was tested for effects on milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score, and productive herd life using analysis of variance. Joint analysis of all families identified marker effects on 11 chromosomes that exceeded the genomewide, suggestive, or nominal significance threshold for QTL effects. Large marker effects on fat percentage were found on chromosomes 3 and 14, and multimarker regression analysis was used to refine the position of these QTL. Half-sibling families from Israeli Holstein dairy herds were used in a daughter design to confirm the presence of the QTL for fat percentage on chromosome 14. The QTL identified in this study may be useful for marker-assisted selection and for selection of a refined set of candidate genes affecting these traits.

Animals↗
PubMed1999

Standardization and conversion of marker polymorphism measures.

Large scale gene mapping efforts in domestic animals have generated and mapped a large number of genetic markers that are useful for mapping quantitative trait and disease loci and for DNA diagnostic purposes such as parentage testing. Marker polymorphism is an important criterion for selecting genetic markers in planning experiment for mapping quantitative trait loci or for DNA diagnostic purposes. Current formulations of marker polymorphism measures are functions of marker allele frequencies. In this study, two measures of marker polymorphism that are available from gene mapping studies and do not require allele frequencies were proposed and analyzed: the observed polymorphic information content (PIC) and the observed family information content (FIC). The observed FIC was more stable than the observed PIC because the observed FIC is unaffected by the variation in the frequency of heterozygous parents. However, both FIC and PIC are dependent on the gene mapping design. The effective number of alleles is recommended as a tool to standardize marker polymorphism measures so that polymorphism of different markers can be compared on an equal basis, and to obtain a new polymorphism measure (such an exclusion probability) from an existing measure (such as FIC). The usage of the effective number of alleles to standardize FIC, PIC and exclusion probabilities is illustrated using genetic markers in a published linkage map.

Animals↗
PubMed1998

Reduced bovine leukaemia virus proviral load in genetically resistant cattle.

The bovine leukaemia virus (BLV) is an exogenous retrovirus that is closely related to the human T cell leukaemia viruses. Genetic resistance and susceptibility to persistent lymphocytosis (PL), an advanced subclinical stage of infection characterized by a polyclonal expansion of the infected B cell population, have been mapped to structural motifs in bovine MHC DRB3 (class II) alleles. To determine whether alleles of DRB3 influence the number of BLV-infected B cells in peripheral blood, seven pairs of Holstein cows naturally infected with BLV were matched on the basis of DRB3 genotype (resistance or susceptibility to PL), age, and year of seroconversion. Flow cytometry was used to separate B cell populations that then were tested for the presence of provirus by a single-cell PCR methodology. Animals with the PL-resistance associated DRB3.2*11 allele had significantly fewer BLV-infected B cells than did age- and seroconversion-matched cows with DRB3 alleles associated with susceptibility to PL. Our results demonstrate that DRB3 or a closely linked gene may play a direct role in controlling the number of BLV-infected peripheral B cells in vivo. Association of MHC class II alleles with resistance to disease progression in cattle naturally infected with BLV provides a unique immunogenetic model for the study of host resistance to human and other animal retroviral infections.

Aging↗
PubMed1998

Designs of reference families for the construction of genetic linkage maps.

The reference family panel is the foundation of a gene mapping program because it affects the cost and quality of the genetic linkage maps, and should be designed to yield reliable linkage detection and locus ordering at minimal gene mapping cost. A map cost function was defined as the number of genotypes required per marker per unit of genome coverage and was used to obtain optimal designs with respect to linkage detection. An ordering reliability function was defined as the likelihood ratio of the most likely order to the second most likely order of genetic markers and was used to find optimal designs with respect to locus ordering. Optimum levels of recombination frequency were found to be in the neighborhood of 0.11-0.15 for linkage detection and were in the region of 0.05-0.20 for locus ordering. Therefore, recombination frequencies optimal for linkage detection are also optimal for locus ordering. Based on the optimal detection levels, sample size (number of offspring) and map cost requirements were derived for six representative designs, assuming gender-specific linkage maps and two alleles with equal frequency for each marker. The sample size required for linkage detection ranged from 168 to 432 offspring for full-sib designs and ranged from 350 to 600 offspring for half-sib designs depending on the family size and the target LOD score, with corresponding minimal map costs of 10-20 genotypes per marker per centiMorgan map coverage. Locus ordering generally requires more genotypes than linkage detection. For full-sib designs, meioses from both genders should be used for locus ordering even when the maps are gender-specific. For half-sib designs, additional families may be needed for locus ordering. Sample size for ordering closely linked loci as required by positional cloning were provided. Effects of family size, grandparents, and marker polymorphism on design efficiency were analyzed.

Chromosome Mapping↗
PubMed1998

Detection of putative loci affecting conformational type traits in an elite population of United States Holsteins using microsatellite markers.

Quantitative trait loci affecting conformational type traits were studied in seven large grandsire families of US Holsteins using the granddaughter design and 16 microsatellite markers on 10 chromosomes. The most significant marker effect was marker BM203 (chromosome 27) for dairy form in a single grandsire family. A multivariate analysis for dairy form and milk yield was also conducted, and the result was highly significant, indicating that a segregating quantitative trait locus or loci affecting dairy form and milk yield could exist near BM203 on chromosome 27. Marker BM1258 (chromosome 23) had a significant effect on udder depth. A multivariate analysis on udder depth and somatic cell score was conducted for markers 513 and BM1258, and both markers showed significant effects on these two traits, indicating that one or several quantitative trait loci affecting udder depth and mastitis might exist on chromosome 23. Marker BM4204 (chromosome 9) had a significant effect on foot angle and on the composite index of traits pertaining to feet and legs, indicating that one or several quantitative trait loci affecting traits pertaining to feet and legs might exist on chromosome 9. Selection on these markers could increase genetic progress within these families.

Animals↗
PubMed1998

Detection of putative loci affecting milk production and composition, health, and type traits in a United States Holstein population.

Quantitative trait loci affecting milk yield and composition, health, and type traits were studied for seven large grandsire families of US Holstein using the granddaughter design. The families were genotyped at 20 microsatellite markers on 15 chromosomes, and the effects of the marker alleles were analyzed for 28 traits (21 type traits, 5 milk yield and composition traits, somatic cell score, and productive herd life). Markers BM415 on chromosome 6 and BM6425 on chromosome 14 were associated with effects on protein percentage in a single grandsire family. The latter marker had a lower probability of being associated with changes in milk yield and fat percentage in the same family. Increases in productive herd life were associated with an allele at marker BM719 on chromosome 16 in one grandsire family.

Animals↗
PubMed1997

Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing.

Six multiplexes developed for semiautomated fluorescence genotyping were evaluated for parentage testing. These multiplexes contained primer pairs for the amplification of 22 microsatellites on 17 bovine autosomes. Exclusion probabilities were determined from genotypes of 1022 Holstein cattle and 311 beef cattle belonging to five breeds. Two cases were considered: case 1, genotypes are known for an alleged parent and an offspring but genotypes of a confirmed parent are unknown; and case 2, genotypes are known for an alleged parent, a confirmed parent and an offspring. If the alleged parent is not the true parent, then the 22 markers will exclude the alleged parent with a probability of > 0.9986 for case 1 and with a probability of > 0.99999 for case 2. On the basis of these exclusion probabilities, the probability that an alleged parent will be falsely included as a parent is in the range of 1/716 to 1/2845 for case 1 and 1/1.2 million to 1/159753 for case 2. In addition to these results, a rapid and efficient non-organic method for extraction of DNA from semen is described.

Animals↗
PubMed1996

The prevalence of proviral bovine leukemia virus in peripheral blood mononuclear cells at two subclinical stages of infection.

The bovine leukemia virus (BLV) is an oncogenic retrovirus that is associated with the development of persistent lymphocytosis (PL) and lymphoma in cattle. While B lymphocytes have been shown to be the primary cellular target of BLV, recent studies suggest that some T lymphocytes and monocytes may be infected by the virus. Because virally altered functions of monocytes and/or T cells could contribute to the development of lymphoproliferative disease, we sought to clarify the distribution of the BLV provirus in subpopulations of peripheral blood mononuclear cells in seropositive cows with and without PL. CD2+ T cells, monocytes, and CD5+ and CD5- B cells were sorted by flow cytometry and tested for the presence of BLV by single-cell PCR. We did not obtain convincing evidence that peripheral blood monocytes or T lymphocytes contain the BLV provirus in seropositive cows with or without PL. In seropositive cows without PL (n=14), BLV-infected CD5+ and CD5- B cells accounted for 9.2% +/- 19% and 0.1% +/- 1.8% of circulating B lymphocytes, respectively. In cows with PL (n=5), BLV-infected CD5+ and CD5- B cells accounted for 66% +/- 4.8% and 13.9% +/- 6.6% of circulating B lymphocytes, respectively. The increase in lymphocyte numbers in cows with PL was entirely attributable to the 45-fold and 99-fold expansions of infected CD5+ and CD5- B-cell populations, respectively. Our results demonstrate that B cells are the only mononuclear cells in peripheral blood that are significantly infected with BLV. On the basis of the absolute numbers of infected cells in seropositive, hematologically normal animals, there appear to be differences in susceptibility to viral spread in vivo that may be under the genetic control of the host.

Age Factors↗
PubMed1995

Gene-centromere mapping of bovine DYA, DRB3, and PRL using secondary oocytes and first polar bodies: evidence for four-strand double crossovers between DYA and DRB3.

A genetic map consisting of three loci anchored at the centromere of bovine chromosome 23 was constructed by genotyping secondary oocytes (SO) and first polar bodies (PB1) using a polymerase chain reaction (PCR)-based approach. Primary oocytes arrested in prophase of meiosis I were stimulated in vitro to resume division and extrude PB1. Sixty SO and their matched PB1 were collected from 14 cows by micro-manipulation, subjected to amplification of the whole genome by primer extension preamplification, and genotyped independently for the linked genes PRL, DRB3, and DYA by PCR-RFLP analysis. Single-locus analysis of gene-centromere recombination rates were theta cen-DYA = 0.042, theta cen-DRB3 = 0.113, and theta cen-PRL = 0.166. The most likely order is cen-DYA-DRB3-PRL. Analysis of typing data from 3 cows revealed three meiotic divisions consistent with "linkage phase exchange" between DYA and DRB3 or PRL. One of the three linkage phase exchanges was confirmed by complementary genotypes in a matched secondary oocyte-first polar body pair. Such linkage phase exchanges could result from four-strand double crossovers between homologous chromosomes. Because all four gametes produced by four-strand double crossovers will be recombinant, more frequent occurrence of such events in females may explain the sexual dimorphism in genetic maps. Alternatively, four-strand crossovers could represent a type of recombination hotspot between DYA and DRB3, suggesting a mechanism for the high recombination frequency (15%) between these two class II genes of the bovine major histocompatibility complex.

Animals↗
PubMed1995

Genetic mapping of F13A to BTA23 by sperm typing: difference in recombination rate between bulls in the DYA-PRL interval.

Our objective was to extend the linkage and comparative maps of BTA23 by determining whether the structural gene for the A subunit of blood coagulation factor XIII (F13A) is linked to BoLA-DYA, a centromeric marker, or the distally located gene encoding prolactin (PRL). Bovine F13A was mapped relative to DYA and PRL in an experiment that examined segregation of alleles in 176 sperm. Genotyping was performed by PCR-RFLP for all loci, following amplification of the haploid genome by primer extension preamplification. F13A was found to be linked to PRL (theta = 0.314 +/- 0.038). The most likely order is DYA-PRL-F13A (odds > 10(4):1). This result demonstrates conservation of synteny between BTA23 and most of HSA6p. Surprisingly, theta DYA-PRL was 0.310 +/- 0.039, 83.4% greater (P < 0.02) than we found for another bull (Van Eijk et al., Mamm. Genome 4: 113, 1993). The difference in recombination rate in the DYA-PRL interval provides further evidence for an unusual recombination hot spot between the bovine Mhc class IIa and class IIb subregions and suggests that bull-specific maps may be necessary for marker-assisted selection.

Animals↗