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PubMed1995

Multiple trait analysis of genetic mapping for quantitative trait loci.

We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis provides formal procedures to test a number of biologically interesting hypotheses concerning the nature of genetic correlations between different traits. Among the testing procedures considered are those for joint mapping, pleiotropy, QTL by environment interaction, and pleiotropy vs. close linkage. The test of pleiotropy (one pleiotropic QTL at a genome position) vs. close linkage (multiple nearby nonpleiotropic QTL) can have important implications for our understanding of the nature of genetic correlations between different traits in certain regions of a genome and also for practical applications in animal and plant breeding because one of the major goals in breeding is to break unfavorable linkage. Results of extensive simulation studies are presented to illustrate various properties of the analyses.

Algorithms↗
PubMed2026

Site-Specific Measurement of Meiotic Crossing-Over Rate with Droplet Digital PCR.

Understanding the frequency and distribution of meiotic crossovers (COs) is critical for both fundamental studies on meiosis and for practical applications in plant breeding, where controlling recombination can accelerate crop improvement. Determining CO rates at specific genomic loci has traditionally relied on labor-intensive methods that require the production and genotyping of large progenies. Here, we present a high-throughput protocol for site-specific quantification of meiotic COs in maize using droplet digital PCR (ddPCR). The method is based on genotyping individual pollen nuclei from hybrid plants to detect recombinant and nonrecombinant alleles at defined chromosomal intervals. By distributing several thousands of pollen nuclei into nanoliter-sized droplets and performing PCR with allele-specific fluorescent probes, this method allows precise quantification of CO frequency with high sensitivity. The protocol provides detailed guidance for nuclei isolation, probe master mix preparation, droplet generation, and data interpretation. This method can be easily adapted for use in other plants.

Journal Article↗
PubMed1992

Annual changes in levels of plasma LH and size of cloacal protrusion in Japanese quail (Coturnix coturnix japonica) housed in outdoor cages under natural conditions.

Japanese quail of the strain used in our laboratory do not show a complete decrease in levels of circulating luteinizing hormone (LH) concentrations and show no collapse of the testes following their transfer from long to short days under laboratory conditions. Thus, merely manipulating photoperiods in the laboratory does not simulate an annual breeding cycle. To see whether an annual breeding cycle does exist in "our" quail under natural conditions, mature male birds were housed in individual cages and placed on the roof of a building at 35 degrees 45'N, 139 degrees 53'E; day length and ambient temperature were not controlled at all though food and water were continuously supplied. For 16 months blood was collected every week and the area of the cloacal protrusion measured at the time of each blood collection. The results showed that levels of plasma LH and the area of the cloacal protrusion had a clear annual cycle under the natural conditions. To detect more precisely the changes in circulating LH concentrations during spring and autumn, samples were collected every other day. The first significant increase in levels of plasma LH was found when the day length exceeded 12-12.5 hr, though the increase was sporadic and not synchronized among individuals. The results also showed that circulating levels of LH declined significantly in early September starting when the day length was still about 14 hr; this downward trend continued rather steadily to nonbreeding levels.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of Variance↗
PubMed2006

Statistical analysis of test-day milk yields using random regression models for the comparison of feeding groups during the lactation period.

Random regression models are widely used in the field of animal breeding for the genetic evaluation of daily milk yields from different test days. These models are capable of handling different environmental effects on the respective test day, and they describe the characteristics of the course of the lactation period by using suitable covariates with fixed and random regression coefficients. As the numerically expensive estimation of parameters is already part of advanced computer software, modifications of random regression models will considerably grow in importance for statistical evaluations of nutrition and behaviour experiments with animals. Random regression models belong to the large class of linear mixed models. Thus, when choosing a model, or more precisely, when selecting a suitable covariance structure of the random effects, the information criteria of Akaike and Schwarz can be used. In this study, the fitting of random regression models for a statistical analysis of a feeding experiment with dairy cows is illustrated under application of the program package SAS. For each of the feeding groups, lactation curves modelled by covariates with fixed regression coefficients are estimated simultaneously. With the help of the fixed regression coefficients, differences between the groups are estimated and then tested for significance. The covariance structure of the random and subject-specific effects and the serial correlation matrix are selected by using information criteria and by estimating correlations between repeated measurements. For the verification of the selected model and the alternative models, mean values and standard deviations estimated with ordinary least square residuals are used.

Animal Feed↗
PubMedDate not supplied

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis.

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

Algorithms↗
PubMed2000

Crop improvement in the 21st century.

Crop yields increased dramatically in the 20th century as recorded on Broadbalk or in world averages. The vast majority of that increase has occurred since the last world war and has been powered by changes in the genetic potential of the crop and in the way in which it has been managed. Nevertheless, the challenge to feed a world population that is likely to rise to 8 billion is formidable, particularly since recent analyses suggest that the rate of increase in yields of several crops may have dropped over the last decade. What are the opportunities to meet this challenge and to continue to improve the yields of our crops? Improvements in agronomy are likely to be more concerned with efficiency and elegance rather than in major breakthroughs. More sophisticated crop protection chemicals designed on the basis of vastly increased screening potentials and (at last?) possibilities of rational design will be supplemented by a battery of decision support systems to aid management choices which can be precisely implemented. Genetic improvement is the area in which to-look for the major breakthroughs. The broad potential of recombinant DNA technology will provide the possibility of both molecular analyses of crop productivity and ways in which it may be possible to improve that productivity. The goal of analysis may be approached in three ways: starting at the beginning by generating complete sequences of the plant genome; starting at the end by genetic analysis of phenotypes using genetic marker technology; or, starting in the middle, by metabolic analysis. Improvements may be obtained by re-assorting what has been achieved through enhanced breeding technologies, by randomly induced change, and by generation of totally new possibilities through biochemical engineering. Examples of all approaches will be given. The onset of genomics will provide massive amounts of information, but the success will depend on using that to improve crop phenotypes. The ability to meet the challenges of the 21st century will depend on the ability to close that 'phenotype gap'.

Biotechnology↗
PubMed2000

Extraction and quantification by ELISA of eggshell organic matrix proteins (ovocleidin-17, ovalbumin, ovotransferrin) in shell from young and old hens.

The eggshell matrix is mainly composed of proteins that are thought to influence shell formation and calcification and, thus, modify the resulting properties of the shell. We investigated the potential of some of these proteins as biomarkers of eggshell quality by developing a competitive indirect ELISA for quantifying ovotransferrin, ovalbumin, and ovocleidin-17 in eggshell extract. Eggshell fragments were demineralized in acetic acid (20%) and freeze-dried. The micro-extraction yield was markedly increased (>50%) when Tween 20 was added to the subsequent extraction and dialysis milieus. Microplates were coated with ovotransferrin and ovalbumin in a 0.1M carbonate-bicarbonate buffer, but ovocleidin-17 was fixed with acetone (-20 C, 20 min). Optimal dilutions of the monoclonal (ovotransferrin) and polyclonal (ovalbumin and ovocleidin-17) antibodies were 1/3,000, 1/25,000 and 1/4,000, respectively. The inhibition curves were optimized by preincubating the antibodies and proteins overnight. The intraassay coefficient (<5%), parallelism of the standards and samples curves, and recovery (101%) were satisfactory for ovotransferrin. Measurements of ovalbumin were less precise because of higher interassay variation and differences between the slopes of standard and sample inhibition curves. Ovocleidin-17 assays showed similar slopes for standard and eggshell extracts. Although the total protein in soluble matrix extracts was not affected by age, the concentrations of these proteins were higher in eggshell extracts from older hens compared with those from young hens: 1.98x for ovotransferrin, 1.86x for ovalbumin, and 1.58x for ovocleidin-17. The quantification of specific eggshell matrix proteins in shell of differing quality is, therefore, a promising tool for analyzing the origin of eggshell faults and may provide useful information for breeding programs.

Aging↗
PubMed2001

Chromosomal organization of candidate genes involved in cholesterol gallstone formation: a murine gallstone map.

Epidemiologic and family studies indicate that cholesterol gallstone formation is in part genetically determined. The major contribution to our current understanding of gallstone genes derives from animal studies, particularly cross-breeding experiments in inbred mouse strains that differ in genetic susceptibility to cholesterol gallstone formation (quantitative trait loci mapping). In this review we summarize how the combined use of genomic strategies and phenotypic studies in inbred mice has proven to be a powerful means of dissecting the complex pathophysiology of this common disease. We present a "gallstone map" for the mouse, consisting of all genetic loci that have been identified to confer gallstone susceptibility as well as putative candidate genes. Translation of the genetic loci and genes between mouse and human predicts chromosomal regions in the human genome that are likely to harbor gallstone genes. Both the number and the precise understanding of gallstone genes are expected to further increase with rapid progress of the genome projects, and multiple new targets for early diagnosis and prevention of gallstone disease should become possible.

Animals↗
PubMed1999

Analysis of allele segregation distortion in a swine resource family.

Segregation distortion of alleles was found in several regions of the genome in allele type analyses of genetic markers for a swine resource family that had been constructed by crossing Göttingen miniature pig and Meishan breeds. From these regions, a region on chromosome 6 presented a distortion over several consecutive markers. This chromosome 6 region was subsequently further investigated to reveal that alleles of a chromosome 6 homologue of the Gottingen miniature pig were not found in a homozygous family member. The litter size of F1-crosses which were able to produce homozygotes in this region were 24% smaller, on average, than F1-crosses which were unable to produce homozygotes. This indicated that this region of the chromosome 6 homologue contained a recessive gene or genes which could terminate fetal development. An additional 10 markers were subsequently used to investigate the region more precisely. These studies revealed that this region spans 7 cM and is located between markers Sw855 and Sw122. Since current comparative maps show that this region corresponds to the human chromosome 19 q-arm, genes positioned on the human chromosome 19 q-arm were screened to select 20 candidate genes. These included the pregnancy-specific beta-1-glycoprotein gene.

Alleles↗
PubMed1997

Heart and neural tube defects in transgenic mice overexpressing the Cx43 gap junction gene.

Transgenic mice were generated containing a cytomegaloviral promoter driven construct (CMV43) expressing the gap junction polylpeptide connexin 43. RNA and protein analysis confirmed that the transgene was being expressed. In situ hybridization analysis of embryo sections revealed that transgene expression was targeted to the dorsal neural tube and in subpopulations of neural crest cells. This expression pattern was identical to that seen in transgenic mice harboring other constructs driven by the cytomegaloviral promoter (Kothary, R., Barton, S. C., Franz, T., Norris, M. L., Hettle, S. and Surani, M. A. H. (1991) Mech. Develop. 35, 25-31; Koedood, M., Fitchel, A., Meier, P. and Mitchell, P. (1995) J. Virol. 69, 2194-2207), and corresponded to a subset of the endogenous Cx43 expression domains. Significantly, dye injection studies showed that transgene expression resulted in an increase in gap junctional communication. Though viable and fertile, these transgenic mice exhibited reduced postnatal viability. Examination of embryos at various stages of development revealed developmental perturbations consisting of cranial neural tube defects (NTD) and heart malformations. Interestingly, breeding of the CMV43 transgene into the Cx43 knockout mice extended postnatal viability of mice homozygote for the Cx43 knockout allele, indicating that the CMV43 trangsene may partially complement the Cx43 deletion. Both the Cx43 knockout and the CMV43 transgenic mice exhibit heart defects associated with malformations in the conotruncus, a region of the heart in which neural crest derivatives are known to have important roles during development. Together with our results indicating neural-crest-specific expression of the transgene in our CMV-based constructs, these observations strongly suggest a role for Cx43-mediated gap junctional communication in neural crest development. Furthermore, these observations indicate that the precise level of Cx43 function may be of critical importance in downstream events involving these migratory cell populations. As such, the CMV43 mouse may represent a powerful new model system for examining the role of extracardiac cell populations in cardiac morphogenesis and other developmental processes.

Animals↗
PubMed2004

Idiopathic muscular hypertrophy of the oesophagus in the horse: a retrospective study of 31 cases.

REASONS FOR PERFORMING STUDY: To present the first report of a case series concerning equine idiopathic muscular hypertrophy of the oesophagus (IMHO). OBJECTIVES: To investigate the clinical and pathological features of the disorder. METHODS: The medical records of 31 horses suffering from the disorder were reviewed retrospectively. In all these animals the diagnosis was confirmed at post mortem examination. RESULTS: The median age of the affected horses was 12.5 +/- 5.6 years (range 1-26) without sex or breed predilection. Only 2 out of 31 horses showed clinical signs associated with oesophageal dysfunction, indicating that the muscular hypertrophy was rather a coincidental post mortem finding. Histology revealed thickening of the distal portion of the oesophagus mainly involving the circular layer of the tunica muscularis without fibrosis or inflammation. In 8 cases, the disorder was seen in concurrence with idiopathic hypertrophy of the tunica muscularis of various other parts of the gastrointestinal tract. CONCLUSIONS: In the majority of patients, IMHO was a coincidental finding at post mortem examination usually confined to the smooth, circular muscle layer of the tunica muscularis externa. POTENTIAL RELEVANCE: Further research is necessary to study the precise effect of IMHO on oesophageal function.

Animals↗
PubMed1994

[Age-related changes in bone mineral density, mean width and area of the lumbar vertebrae in male African green monkeys (Cercopithecus aethiops)].

We were able to measure bone mineral density (BMD), mean bone width and the area of the lumbar vertebrae in male African green monkeys with a dual-energy X-ray absorptiometry (DPX-alpha, Lunar, USA). For analysis of spinal bone mass, mean width and area of the bone, we scanned lumbar vertebrae L3-L5 using a pediatric analysis program. We used restraining bed made of formed polystyrol to support the animal in a supine position. The precision of the measuring technique was calculated by averaging the coefficients of variance of the 5 scans obtained in 5 animals aged from 5 to 7 years. The precision values for BMD, bone width and area were 1.9%, 0.9% and 2.6%, respectively. Furthermore, age-related changes in bone measurements were demonstrated using laboratory-bred males (n = 45) and, additionally, wild-originated males (n = 7, estimated ages over 15 years old). The values of B M D, bone width and area at 6 months old were about 0.3 g/cm2, 1.2cm and 4.5 cm2 respectively. These values increased with aging to about 0.7 g/cm2, 1.5 cm and 11cm2 at 5 years old, respectively, and were judged to reach plateau. However, animals over 10 years old and wild-originated animals which had been kept over 10 years in our breeding colony showed rather smaller BMD and area values than the animals aged 5 to 10 years. The animals aged between 5 and 10 years seemed to have retained a peak bone mass in this primate species.

Absorptiometry, Photon↗
PubMed1984

Adaptation of plants to mineral stress in problem soils.

Crop production depends on interactions among genetic potentials of plants and various stress factors in the environment. Mineral stresses in the form of toxicity or deficiency are not always economically correctable with current technology. But plant species, and genotypes within species, differ widely in tolerance to different mineral stresses, and some of these differences are known to be genetically controlled. Hence, a viable alternative or supplemental approach is to adapt plants more precisely to soils. Soil fertility programmes of the past have emphasized 'changing the soil to fit the plant'. As a result, many crop cultivars have been developed under nearly ideal conditions of pH and soil fertility and hence cannot tolerate the stresses encountered in marginal soils. There is, therefore, a great need for stress-tolerant plant genotypes for use in a 'minimum input' system of agriculture for problem soils. The merits of tailoring the plant to fit the soil have only recently been recognized, even by the scientific community. However, within the last decade multidisciplinary teams of scientists have been formed in several countries, and considerable progress is being made in selecting and breeding plants for greater nutrient efficiency and for tolerance to such factors as aluminium toxicity and salinity. In view of problems in world food and energy production and distribution, this approach should receive the highest priority.

Adaptation, Biological↗
PubMed1983

Inheritance of post-vaccinal resistance against Plasmodium berghei infection in mice.

The protective effect of specific vaccination against Plasmodium berghei (P. berghei) was compared in terms of survival percentage in DBA/2, C3H, outbred albino mice and in two lines of mice produced by selective breeding for either high or low antibody responsiveness to sheep erythrocyte (H and L lines respectively). The efficacy of induced protection varies according to genetic constitution. It is very strong in H line and albino mice, intermediate in DBA/2 and very weak in L line and C3H. The inheritance of post-vaccinal resistance to infection was studied in F1 hybrids and backcrosses between C3H and the other lines. The control was polygenic in all cases. The dominance of the characteristic depends on the strain combination. On the whole the results suggest the non-identity of the genes controlling protection in the various lines. The lack of a quantitative parameter for a more precise genetic analysis of protective immunity in inbred lines is stressed, since both anti-P. berghei antibody production and parasitaemia proved to be unreliable.

Animals↗
PubMed1994

Induction of parturition in cattle: effect of triamcinolone pretreatment on the incidence of retained placenta.

Two experiments were designed to determine whether pretreatment with triamcinolone acetonide (TRI)prior to induction of parturition with dexamethasone(DEX) and cloprostenol (CLO) would reduce the incidence of retained placenta. Experiment 1 was conducted to determine the optimum dosage of TRI and to approximate the optimum interval from TRI to induction with DEX+CLO. All cows received TRI on day 270 of gestation. Cows in group I received 1 mg/30 kg of body weight (BW) of TRI and were induced to calve with DEX+CLO on day 276. Cows in groups II and III received 1 mg/45 kg BW and were induced on days 276 or 277, respectively. Cows in groups IV and V received 1 mg/60 kg BW and were induced on days 277 or 278, respectively. Group VI cows served as untreated controls. There was no difference in the incidence of retained placenta among the treated and control groups. Experiment 2 was conducted to more precisely determine the optimum interval from pretreatment to induction treatment with the chosen dose of TRI. All cows in groups I, II, and III were pretreated with 1 mg/60 kg BW of TRI on day 270 of gestation and received DEX+CLO on days 275, 276 or 277,respectively. Group IV cows served as untreated controls. The incidence of retained placenta was higher (p < 0.05) in groups I and II than in the control group, with group III intermediate and not different from the others. Cows that retained their placentas had higher (p < 0.05) body temperatures from day 2 to day 7 after calving and tended to have a lower pregnancy rate in the subsequent breeding season than cows that did not retain their placentas.Results indicate that pretreatment with TRI seven days prior to induction of parturition with DEX+CLO resulted in a reduced incidence of retained placenta,apparently by advancing placental maturation.

Animals↗
PubMed2005

Canine awake head-out plethysmography (HOP): characterization of external resistive loading and spontaneous laryngeal paralysis.

We applied a novel head-out plethysmographic (HOP) method to study awake canine responses to external resistive loading and natural laryngeal paralysis. Measurements of inspiratory and expiratory specific airway resistance (sRaw(insp), sRaw(exp)) were obtained before and after uni- and bidirectional loading (R(add) = 5 cmH(2)O/L/s) in large-breed dogs (n = 9). Mean sRaw(insp) after inspiratory, and sRaw(exp) after expiratory loading were 31.4 and 33.3 cmH(2)Os, respectively. Bidirectional loads induced a significantly greater rise in both sRaw(insp) and sRaw(exp) (55.1 and 61.3 cmH(2)Os) compared to unidirectional loading (P < 0.001). Yet, type of loading did not affect flow-volume indices. The mean R(aw) of dogs was 4.81 cmH(2)O/L/s. Expiratory loading resulted in a significant 8.8% increase in functional-residual-capacity (FRC), compared to FRC(baseline) (76.7 ml/kg). Dogs (n = 5) with laryngeal paralysis demonstrated a significant increase in sR(aw) and R(aw) compared to controls without changes in FRC. In conclusion, HOP precisely characterized sR(aw) in response to external resistive loading. Hence, we could accurately quantify airway obstruction in awake dogs with laryngeal paralysis.

Airway Resistance↗
PubMed2001

From chicken coops to genome maps: generating phenotype from the molecular blueprint.

The tools of molecular and cellular biology can be used to precisely describe traits in terms of a sequence of nucleic acids when their molecular and cellular bases are well understood. The entire genome of elite production birds, however, cannot be written as a series of A's, T's, C's, and G's because the interaction between alleles at the same and different loci is too large and there is likely to be many genotypes that encode the same production trait phenotype. A first draft of the genetic map of the chicken is anticipated within the next few years, but a complete molecular description of the genome of birds with elite production characteristics is not anticipated in the near future. Quantitative genetics will remain the cornerstone of breeding programs for production traits. Novel sequences encoding traits such as enhanced nutritional capability (e.g., expression of phytase) and resistance to specific diseases could be introduced into lines of chickens using the tools of molecular and cellular biology. Cloning could be used by the poultry industry to disperse highly desirable genotypes without the need for grandparent and parent flocks for multiplication.

Animals↗
PubMed1984

The Amazon molly, Poecilia formosa, as a test animal in carcinogenicity studies: chronic exposures to physical agents.

The Amazon molly, Poecilia formosa, a small, live-bearing fish native to Texas, has an unusual mode of reproduction that makes it highly suitable for carcinogenicity studies. The species is easy to rear and breed, and withstands handling well. Large broods of young are born, numbering up to 90 when the parent fish are fully grown. The Amazon molly reproduces gynogenetically; eggs are activated after mating with males of closely related species. The male makes no genetic contribution; sperm provides only the stimulus for egg development. The offspring of a female comprise a clone with genotypes identical to that of the mother's so that cell and tissue transplants made between members of the clone are not rejected. We used the Amazon molly as an animal model to show that damage to DNA caused by UV and ionizing radiation and by certain chemicals results in tumor development. Thyroid cells were taken from donor mollies, treated precisely in vitro with the agents, and then injected into homologous recipients. Eight months later, recipient fish had developed large thyroid tumors. The genetic homogeneity of the clone also makes the Amazon molly invaluable in acute or chronic bioassays because variability in the responses of the individual fishes is minimal. Therefore, a limited number will suffice to give statistically significant results. The findings from a study of chronic exposure to asbestos are also described.

Animal Husbandry↗