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PubMed2002

A hierarchical statistical model for estimating population properties of quantitative genes.

BACKGROUND: Earlier methods for detecting major genes responsible for a quantitative trait rely critically upon a well-structured pedigree in which the segregation pattern of genes exactly follow Mendelian inheritance laws. However, for many outcrossing species, such pedigrees are not available and genes also display population properties. RESULTS: In this paper, a hierarchical statistical model is proposed to monitor the existence of a major gene based on its segregation and transmission across two successive generations. The model is implemented with an EM algorithm to provide maximum likelihood estimates for genetic parameters of the major locus. This new method is successfully applied to identify an additive gene having a large effect on stem height growth of aspen trees. The estimates of population genetic parameters for this major gene can be generalized to the original breeding population from which the parents were sampled. A simulation study is presented to evaluate finite sample properties of the model. CONCLUSIONS: A hierarchical model was derived for detecting major genes affecting a quantitative trait based on progeny tests of outcrossing species. The new model takes into account the population genetic properties of genes and is expected to enhance the accuracy, precision and power of gene detection.

Algorithms↗
PubMed2004

Endocrine and paracrine control of follicular development and ovulation rate in farm species.

Productivity in farm species is controlled by many factors, including ovulation rate. In cattle, single ovulations occur most frequently and in sheep (and goats) the number of ova released can range from one to many depending upon the breed, whilst the pig is polyovular. The processes of recruitment and selection determine the number of ovulatory follicles in all these species with FSH and subsequently LH playing major roles. GnRH-agonist models in which endogenous gonadotrophin secretion is suppressed and exogenous LH and/or FSH are administered at specific concentrations in defined patterns, are useful in all three species for elucidating the precise roles of specific hormones in stimulating follicular development. Differences in the hypothalamic-pituitary-ovarian feedback response lead to the differences in the number of ovulatory follicles, as does the pool of antral follicles from which the ovulatory ones are selected. Precocious development of follicles is also associated with more ovulations, as is the case with the Booroola due to the single gene acting through bone morphogenetic proteins (BMPs). It is well established that ovulation rate can also be influenced by exogenous hormone administration and by environmental factors such as nutrition. It has become apparent that these nuritional effects are mediated by a direct action at the level of the ovary, involving insulin, insulin-like growth factors (IGF) I and II and their binding proteins among other factors. These factors can also affect the quality of the oocyte and consequently embryo development and survival. Recently, the regulation of follicular angiogenesis has been shown to be important for the development of ovulatory follicles, particularly vascular endothelial growth factor (VEGF) which is produced primarily by the granulosa cells within the ovary and can be stimulated by gonadotrophins. Administration of VEGF has been shown to stimulate pre-antral follicular growth and increase the number of pre-ovulatory follicles. In summary both extra- and intra-ovarian factors are involved in the control of ovulation rate. Manipulation of the angiogenic process may also provide new opportunities for regulating the quality and number of follicles that ovulate.

Animal Nutritional Physiological Phenomena↗
PubMed1999

Estimating genetic correlations in natural populations.

Information on the genetic correlation between traits provides fundamental insight into the constraints on the evolutionary process. Estimates of such correlations are conventionally obtained by raising individuals of known relatedness in artificial environments. However, many species are not readily amenable to controlled breeding programmes, and considerable uncertainty exists over the extent to which estimates derived under benign laboratory conditions reflect the properties of populations in natural settings. Here, non-invasive methods that allow the estimation of genetic correlations from phenotypic measurements derived from individuals of unknown relatedness are introduced. Like the conventional approach, these methods demand large sample sizes in order to yield reasonably precise estimates, and special precautions need to be taken to eliminate bias from shared environmental effects. Provided the sample consists of at least 20% or so relatives, informative estimates of the genetic correlation are obtainable with sample sizes of several hundred individuals, particularly if supplemental information on relatedness is available from polymorphic molecular markers.

Animals↗
PubMed2006

Epigenetic silencing and tissue independent expression of a novel tetracycline inducible system in double-transgenic pigs.

The applicability of tightly regulated transgenesis in domesticated animals is severely hampered by the present lack of knowledge of regulatory mechanisms and the long generation intervals. To capitalize on the tightly controlled expression of mammalian genes made possible by using prokaryotic control elements, we have used a single-step transduction to introduce an autoregulative tetracycline-responsive bicistronic expression cassette (NTA) into transgenic pigs. Transgenic pigs carrying one NTA cassette showed a mosaic transgene expression restricted to single muscle fibers. In contrast, crossbred animals carrying two NTA cassettes with different transgenes, revealed a broad tissue-independent and tightly regulated expression of one cassette, but not of the other one. The expression pattern correlated inversely with the methylation status of the NTA transcription start sites indicating epigenetic silencing of one NTA cassette. This first approach on tetracycline regulated transgene expression in farm animals will be valuable for developing precisely controlled expression systems for transgenes in large animals relevant for biomedical and agricultural biotechnology.

Animals↗
PubMed2006

Parentage analysis detects cryptic precapture dispersal in a philopatric rodent.

Locating birthplaces using genetic parentage determination can increase the precision and accuracy with which animal dispersal patterns are established. We re-analyse patterns of movement away from the birthplace as a function of time, sex and population density for a sample of 303 banner-tailed kangaroo rats, Dipodomys spectabilis. We located birth sites using a combination of likelihood-based parentage analysis with live-trapping of mothers during the breeding season. The results demonstrate that natal-breeding site distances are density dependent in this species; in particular, both sexes emigrate earlier in the year, and females disperse farther than males, at low population densities. Banner-tailed kangaroo rats were chosen as a study system because live-trapping easily detects maternal and offspring locations; nevertheless, parentage analysis reveals that some offspring evade early detection and move substantial distances before their first capture. In a few cases, the approach even detects dispersal out of the natal 'deme' prior to first capture. Parentage analysis confirms the extreme philopatry of both sexes but indicates that prior estimates of median dispersal distance were too low. For D. spectabilis, more accurate location of individual birthplaces clarifies patterns of sex bias and density dependence in dispersal, and may resolve apparent discrepancies between direct and indirect estimates of dispersal distance. For species in which mothers can be more reliably trapped than juveniles, using offspring genotypes to locate parents is a novel way that genetic techniques can contribute to the analysis of animal dispersal.

Animal Migration↗
PubMed2006

Animal models for hypertension/blood pressure recording.

Hypertension is an important disease with polygenic inheritance. In order to identify the genes involved in blood pressure regulation, hypertensive rat and mouse models have been developed either by selective breeding or by transgenic technology. The most essential technological prerequisite in these studies is a reliable assessment of the blood pressure in rodents. Three methods are used most frequently for this purpose: tail cuff plethysmography, intra-arterial catheters, and radiotelemetry. Plethysmography is noninvasive, relatively simple, and suitable for a large number of animals, but also imprecise. Intra-arterial catheters are more precise, but require surgery. And both methods restrain and thereby stress the animals, which leads to alterations in blood pressure. Therefore, the telemetric blood pressure measurement, which allows the study of conscious, freely moving animals, has become the gold standard for measuring blood pressure in rodents. However, this method is extremely expensive. Thus, for each experiment the costs have to be put in relation to the quality of data required. This chapter will describe blood pressure measurement methods in technical detail.

Animals↗
PubMed1989

Correlation of sperm and endocrine measures with reproductive success in rodents.

This paper compares the statistical precision and biological sensitivity of multiple indices of reproductive function to infertility in the male rodent. The studies discussed include those that examined reproductive function in the male following perinatal exposure to reproductive toxicants and others in which the compounds were administered to young-adult males, often with very diverse results. For example, some chemicals that alter sex differentiation reduce fertility by affecting breeding performance alone (polychlorinated biphenyls (PCBs), fenarimol, or losulazine), without altering sperm and testicular measures. Others also markedly alter sex differentiation of the genitalia, the accessory glands and the testis in addition to their effects on central nervous system (CNS) sex differentiation and mating behavior (testosterone, flutamide, cyproterone acetate, tamoxifen, estradiol and diethylstilbestrol (DES)). In contrast, prenatal exposure to compounds that alter primary germ cell survival (busulphan, congo red) induce partial gonadal/germ cell agenesis without altering sex differentiation. These chemicals dramatically reduce testicular sperm production in the male offspring, and the most severely affected males are infertile. In a series of studies conducted in our laboratory, young male rats were exposed to known reproductive toxicants in a dose related manner from puberty, through young adulthood and breeding. We have found that the profile of effects varies considerably depending upon the chemical's mechanism of toxicity. When a compound produced infertility through direct effects of testicular function (Carbendazim (MBC) and dibutyl phthalate (DBP)), then testis weight, testicular histology, and testicular sperm head counts provided sensitive indicators of toxicity. In general, dramatic reductions in sperm production are required to induce infertility and these changes were accompanied by elevated serum luteinizing hormone (LH) and follicle-stimulating hormone (FSH) and changes in human chorionic gonadotropin (hCG)-stimulated testosterone synthesis. Chemicals that have hormonal activity, alter the internal endocrine environment, or directly effect CNS function induce a completely different profile of effects. For example, estrogen administration alters the function of the seminal vesicle and the endocrine system, and reduces epididymal sperm reserves; while testicular measures are relatively unaffected. Since very different spectrums of effects are produced by different compounds, no single endpoint will consistently be the most sensitive indicator of reproductive toxicity.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2025

Deep learning-based annotation of plant abiotic stress resistance genes for crops.

The declining costs of DNA sequencing have expanded genomic data, crucial for understanding plant abiotic stress responses and crop improvement. However, accurate gene annotation remains challenging. To address this limitation, we propose the PASRGA, a deep learning approach that leverages transfer learning and contrastive learning to annotate genes related to drought, salt, cold, and UV resistance. PASRGA achieves high F1-scores, area under the receiver operating characteristic (AUROC), area under the precision-recall curve (AUPRC), and Matthews correlation coefficient (MCC) in annotating stress resistance genes, significantly outperforming the general protein annotation model CLEAN, the plant phosphatase gene annotation model PF-NET, the top-ranked model in the CAFA5 challenge NetGO 4.0, and four traditional machine learning methods. Its effectiveness was further validated with a salt stress treatment experiment in Eutrema salsugineum. To facilitate crop breeding practices, we utilized PASRGA to annotate the genomes of 17 major crops. To improve accessibility and utility, we incorporated both manually curated and PASRGA-predicted gene data, together with the PASRGA tool, into the PlantASRG database (https://bioinfor.nefu.edu.cn/PlantASRG/). This comprehensive resource aims to support crop breeding initiatives and ensure food security.

Crops, Agricultural↗
PubMed2006

Within- and across-person uniformity of body condition scoring in Danish Holstein cattle.

Body condition scores (BCS) are very useful for dairy herd management and breeding programs, but the consistency and quality of recordings made by consultants in the field are unknown. The objectives of this study were 1) to estimate the agreement in BCS within and among practicing dairy veterinarians and 2) to provide an indication of the effects of training and the value of calibration, and of what efforts need to be made to obtain a validity and precision in BCS adequate for management purposes. A total of 2,230 scores were recorded by 51 practicing dairy veterinarians and 6 highly trained instructors. The 6 instructors were cross-trained to validate calibration consistency in assigning BCS. Each individual scored approximately 20 cows twice, with the second scoring occurring approximately 2.5 h after the first. Between the 2 recordings, the respective instructors conducted a training session for the practicing veterinarians using other cows. A weighted kappa coefficient was used to assess agreement among and within classifiers. Excellent agreement (kappa > or = 0.86) was documented between repeated BCS recorded for the same cows by the highly trained instructors. In addition, the BCS provided by multiple classifiers from the instructor team appeared to be comparable across herds and classifiers. This legitimizes the use of BCS for benchmarking at both the cow and the herd level. The within-classifier and between-classifier kappa values were in the ranges of 0.22 to 0.75 and 0.17 to 0.78, respectively, in the group of practicing dairy veterinarians. Many of the veterinarians provided estimates of average BCS that differed considerably from the BCS recorded by the instructors. Between-classifier comparisons of herd BCS are not warranted unless a validation has been performed. If scores are collected by multiple classifiers with varying experience, a valid but imprecise estimate of the true population mean of BCS may be obtained if classifiers are inexperienced. The limited training effort used in this study seemed to have brought about substantial improvement in the validity and precision of the BCS determined by practicing veterinarians, compared with the BCS recorded on the same cows by highly trained classifiers.

Animals↗
PubMed2003

Determinants of meat quality: tenderness.

Meat quality is a term used to describe a range of attributes of meat. Consumer research suggests that tenderness is a very important element of eating quality and that variations in tenderness affect the decision to repurchase. The present paper highlights recent information on the factors that affect tenderness. While the precise aetiology is not fully understood, a number of factors have been shown to affect tenderness. Of these factors, postmortem factors, particularly temperature, sarcomere length and proteolysis, which affect the conversion of muscle to meat, appear most important. However, it is now becoming clear that variation in other factors such as the muscle fibre type composition and the buffering capacity of the muscle together with the breed and nutritional status of the animals may also contribute to the observed variation in meat tenderness.

Animals↗
PubMed2004

Validating internal controls for quantitative plant gene expression studies.

BACKGROUND: Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. RESULTS: Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. CONCLUSION: Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments.

Analysis of Variance↗
PubMed2002

A statistical model for the genetic origin of allometric scaling laws in biology.

Many biological processes, from cellular metabolism to population dynamics, are characterized by particular allometric scaling (power-law) relationships between size and rate. Although such allometric relationships may be under genetic determination, their precise genetic mechanisms have not been clearly understood due to a lack of a statistical analytical method. In this paper, we present a basic statistical framework for mapping quantitative genes (or quantitative trait loci, QTL) responsible for universal quarter-power scaling laws of organic structure and function with the entire body size. Our model framework allows the testing of whether a single QTL affects the allometric relationship of two traits or whether more than one linked QTL is segregating. Like traditional multi-trait mapping, this new model can increase the power to detect the underlying QTL and the precision of its localization on the genome. Beyond the traditional method, this model is integrated with pervasive scaling laws to take advantage of the mechanistic relationships of biological structures and processes. Simulation studies indicate that the estimation precision of the QTL position and effect can be improved when the scaling relationship of the two traits is considered. The application of our model in a real example from forest trees leads to successful detection of a QTL governing the allometric relationship of third-year stem height with third-year stem biomass. The model proposed here has implications for genetic, evolutionary, biomedicinal and breeding research.

Animals↗
PubMed2004

Instability of the insertional mutation in CftrTgH(neoim)Hgu cystic fibrosis mouse model.

BACKGROUND: A major boost to the cystic fibrosis disease research was given by the generation of various mouse models using gene targeting in embryonal stem cells. Moreover, the introduction of the same mutation on different inbred strains generating congenic strains facilitated the search for modifier genes. From the original CftrTgH(neoim)Hgu CF mouse model we have generated using strict brother x sister mating two inbred CftrTgH(neoim)Hgu mouse lines (CF/1 and CF/3). Thereafter, the insertional mutation was introgressed from CF/3 into three inbred backgrounds (C57BL/6, BALB/c, DBA/2J) generating congenic animals. In every backcross cycle germline transmission of the insertional mutation was monitored by direct probing the insertion via Southern RFLP. In order to bypass this time consuming procedure we devised an alternative PCR based protocol whereby mouse strains are differentiated at the Cftr locus by Cftr intragenic microsatellite genotypes that are tightly linked to the disrupted locus. RESULTS: Using this method we were able to identify animals carrying the insertional mutation based upon the differential haplotypic backgrounds of the three inbred strains and the mutant CftrTgH(neoim)Hgu at the Cftr locus. Moreover, this method facilitated the identification of the precise vector excision from the disrupted Cftr locus in two out of 57 typed animals. This reversion to wild type status took place without any loss of sequence revealing the instability of insertional mutations during the production of congenic animals. CONCLUSIONS: We present intragenic microsatellite markers as a tool for fast and efficient identification of the introgressed locus of interest in the recipient strain during congenic animal breeding. Moreover, the same genotyping method allowed the identification of a vector excision event, posing questions on the stability of insertional mutations in mice.

Animals↗
PubMed1976

[Transmissible Gastroenteritis in Swine (author's transl)].

Transmissible gastroenteritis or TGE is a virus diarrhoea which occurs in pigs of all ages and is associated with high mortality rates in the young piglets. Growth of virus in the columnar epithelium of the small intestine causes atrophy of the intestinal villi, malabsorption, watery diarrhoea and dehydration. Faecal excretion of virus usually continues up to fourteen days after infection but chronic carriers have been found to occur. TGE is self-limiting on the majority of pig-breeding farms but the virus may persist in particular conditions and an enzootic form of the disease will appear in this case. In typical outbreaks, the diagnosis can usually be based on clinical symptoms. When the disease runs an enzootic course, a clinical diagnosis will be out of the question. TGE should be differentiated from colibacillosis and from another virus diarrhoea, the aetiology of which is not precisely known. A rapid and correct diagnosis may be established by direct fluorescent antibody studies of frozen sections of the small intestine in infected piglets. When sows have been spontaneously infected, their offspring will be protected by lactogenic immunity. The presence of TGE antibodies of IgA class in the milk is required to ensure complete immunity of the piglets lasting for weeks on end. Intramuscular inoculation of a commercially available vaccine in sows will only stimulate the production of antibodies of the IgG class in the milk. These antibodies will merely afford short-lived immunity. The vaccine cannot prevent symptoms of disease from appearing in piglets following infection with virulent TGE virus but it does reduce mortality

Animals↗
PubMed2006

Mapping of the apple scab-resistance gene Vb.

Apple scab, caused by the fungus Venturia inaequalis, is the major production constraint in temperate zones with humid springs. Normally, its control relies on frequent and regular fungicide applications. Because this control strategy has come under increasing criticism, major efforts are being directed toward the breeding of scab-resistant apple cultivars. Modern apple breeding programs include the use of molecular markers, making it possible to combine several different scab-resistance genes in 1 apple cultivar (pyramiding) and to speed up the breeding process. The apple scab-resistance gene Vb is derived from the Siberian crab apple 'Hansen's baccata #2', and is 1 of the 6 "historical" major apple scab-resistance genes (Vf, Va, Vr, Vbj, Vm, and Vb). Molecular markers have been published for all these genes, except Vr. In testcross experiments conducted in the 1960s, it was reported that Vb segregated independently from 3 other major resistance genes, including Vf. Recently, however, Vb and Vf have both been mapped on linkage group 1, a result that contrasts with the findings from former testcross experiments. In this study, simple sequence repeat (SSR) markers were used to identify the precise position of Vb in a cross of 'Golden Delicious' (vbvb) and 'Hansen's baccata #2' (Vbvb). A genome scanning approach, a fast method already used to map apple scab-resistance genes Vr2 and Vm, was used, and the Vb locus was identified on linkage group 12, between the SSR markers Hi02d05 and Hi07f01. This finding confirms the independent segregation of Vb from Vf. With the identification of SSR markers linked to Vb, another major apple scab-resistance gene has become available; breeders can use it to develop durable resistant cultivars with several different resistance genes.

Ascomycota↗
PubMed1985

Flow cytometric determination of the proportions of X- and Y-chromosome-bearing sperm in samples of purportedly separated bull sperm.

A rapid assay for determining the proportions of X- and Y-chromosome-bearing sperm in semen samples would benefit research aimed at sex ratio control through sperm separation. It also would be of value for quality control should a separation technique be developed. Flow cytometric methods capable of measuring sperm DNA content precisely enough to resolve and quantify the X and Y populations in many mammalian species have been developed. They are effective for fresh and cryopreserved sperm of most domestic animals. Results are reported of flow cytometric analyses of bull sperm samples from seven commercial and academic sources after processing with procedures purported to separate the X and Y populations. In no case was enrichment of either sperm population observed. Breeding trials carried out by the sources of two of the sets of samples showed these procedures were ineffective in altering the sex ratio.

Animals↗
PubMed1997

Developments in transgenic techniques in pigs.

Manipulation of the pig genome is currently restricted to the random insertion of new DNA using pronuclear microinjection. This method suffers from a number of inherent limitations, the majority of which result from the inability to control the site at which the transgene becomes integrated. These drawbacks, together with the need to be able to target existing genes, will result in the replacement of pronuclear injection by new methods that have the capability to direct insertion to a particular genomic site that does not influence expression. Currently, it is possible to control the site of insertion in mice using embryonic stem (ES) cell and homologous recombination technologies. However, pluripotent ES cells have yet to be isolated in pigs. The possibility of using nuclear transfer to reprogramme early differentiated embryonic cells as well as somatic cells from adult animals may provide an alternative method for generating precise genetic modifications. Methods that allow these changes to be carried out in situ are also likely to be developed in the future.

Animals↗
PubMed2006

Nuclear transfer in nonhuman primates.

The nonhuman primate is a highly relevant model for the study of human diseases, and currently there is a significant need for populations of animals with specific genotypes that can not be satisfied by the capture of animals from the wild or by conventional breeding. There is an even greater need for genetically identical animals in vaccine development or tissue transplantation research, where immune system function is under study. Efficient somatic cell nuclear transfer (SCNT) procedures could provide a source for genetically identical nonhuman primates for biomedical research. SCNT offers the possibility of cloning animals using cultured cells and potentially provides an alternative approach for the genetic modification of primates. The opportunity to introduce precise genetic modifications into cultured cells by gene targeting procedures, and then use these cells as nuclear donors in SCNT, has potential application in the production of loss-of-function monkey models of human diseases. We were initially successful in producing monkeys by NT using embryonic blastomeres as the source of donor nuclei and have repeated that success. However, when somatic cells are used as nuclear donor cells, the developmental potential of monkey SCNT embryos is limited, and somatic cell cloning has not yet been accomplished in primates. High rates of in vitro development to blastocysts, comparable with in vitro fertilization controls, and successful production of rhesus monkeys by NT from embryonic blastomeres suggests that basic cloning procedures, including enucleation, fusion, and activation, are consistent with the production of viable embryos. Although modifications or additional steps in SCNT are clearly warranted, the basic procedures will likely be similar to those extant for embryonic cell NT. In this chapter, we describe detailed protocols for rhesus macaque embryonic cell NT, including oocyte and embryo production, micromanipulation, and embryo transfer in nonhuman primates.

Animals↗