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PubMed2005

Trends in population parameters and best linear unbiased prediction of progeny performance in a European F(2) maize population under modified recurrent full-sib selection.

Recurrent selection is a cyclic breeding procedure designed to improve the mean of a population for the trait(s) under selection. Starting from an F(2) population of European flint maize (Zea mays L.) intermated for three generations, we conducted seven cycles of a modified recurrent full-sib (FS) selection scheme. The objectives of our study were to (1) monitor trends across selection cycles in the estimates of the population mean, additive and dominance variances, (2) compare predicted and realized selection responses, and (3) investigate the usefulness of best linear unbiased prediction (BLUP) of progeny performance under the recurrent FS selection scheme applied. Recurrent FS selection was conducted at three locations using a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme, where the selected FS families were divided into an upper-ranking group of parents mated to the lower-ranking group. Variance components were estimated with restricted maximum likelihood. Average grain yield increased 9.1% per cycle, average grain moisture decreased 1.1% per cycle, and the selection index increased 11.2% per cycle. For the three traits we observed, no significant changes in additive and dominance variances occurred, suggesting future selection response at or near current rates of progress. Predictions of FS family performance in Cn+1 based on mean performance of parental FS families in Cn were of equal or higher precision as those based on the mean additive genetic BLUP of their parents, and corresponding correlations were of moderate size only for grain moisture. The significant increase in grain yield combined with the decrease in grain moisture suggest that the F(2) source population with use of a pseudo-factorial mating scheme is an appealing alternative to other types of source materials and random mating schemes commonly used in recurrent selection.

Breeding↗

PubMed2005

Assessment of urine and fecal testosterone metabolite excretion in Chinchilla lanigera males.

Endemic chinchilla (Chinchilla spp.) populations are nearly extinct in the wild (South America). In captive animals (Chinchilla lanigera and C. brevicaudata), reproduction is characterized by poor fertility and limited by seasonal breeding patterns. Techniques applied for studying male reproductive physiology in these species are often invasive and stressful (i.e. repeated blood sampling for sexual steroids analysis). To evaluate endocrine testicular function, the present experiments were designed to (a) determine the main route of testosterone excretion (14C-testosterone infusion in four males); (b) validate urine and fecal testosterone metabolite measurements (HPLC was used to separate metabolites and immunoreactivity was assessed in all metabolites using a commercial testosterone radioimmunoassay, and parallelism, accuracy and precision tests were conducted to validate the immunoassay); and (c) investigate the biological relevance of the techniques applied (quantification of testosterone metabolite excretion into urine and feces from five males injected with hCG and comparison between 10 males and 10 females). Radiolabelled metabolites of 14C-testosterone were excreted, 84.7+/-4.2 % in urine and 15.2+/-3.9 % in feces. A total of 82.7+/-4.2% of urinary and 45.7+/-13.6% of fecal radioactivity was excreted over the first 24 h period post-infusion (metabolite concentration peaked at 8.2+/-2.5 h and 22.0+/-7.0 h, respectively). Several urinary and fecal androgen metabolites were separated by HPLC but only fecal metabolites were associated with native testosterone; however, there was immunoreactivity in more than one metabolite derived from 14C-testosterone. After hCG administration, an increase in androgen metabolite excretion was observed (p<0.05). Males excreted greater amounts daily of urinary androgen metabolites as compared with females (p<0.05); this difference was not evident in feces. Results of the present study indicate that the procedure used is a reliable and non-invasive method to repeatedly monitor variations in testicular endocrine activity in this species. It can be a useful tool that would help ensure the survival of the wild populations as well as to provide the basis for a more efficient use by the fur industry.

Androgens↗

PubMed1992

Detection of genetic variation between and within populations of Gliricidia sepium and G. maculata using RAPD markers.

Gliricidia sepium and G. maculata are multi-purpose leguminous trees native to Central America and Mexico. Research programmes have been initiated to define the native distribution of Gliricidia and sample the spectrum of genetic variation. To date, there has been little systematic assessment of genetic variability in multi-purpose tree species. Accurate estimates of diversity between- and within-populations are considered a prerequisite for the optimization of sampling and breeding strategies. We have used a PCR-based polymorphic assay procedure (RAPDs) to monitor genetic variability in Gliricidia. Extensive genetic variability was detected between species and the variability was partitioned into between- and within-population components. On average, most (60 per cent) of the variation occurs between G. sepium populations but oligonucleotide primers differed in their capacity to detect variability between and within populations. Population-specific genetic markers were identified. RAPDs provide a cost-effective method for the precise and routine evaluation of variability and may be used to identify areas of maximum diversity. The approaches outlined have general applicability to a range of organisms and are discussed in relation to the exploitation of multi-purpose tree species of the tropics.

Americas↗

PubMed1991

The disease characteristics of different strains of scrapie in Sinc congenic mouse lines: implications for the nature of the agent and host control of pathogenesis.

Mouse lines which are congenic for Sinc, the major gene controlling scrapie incubation period, have been produced by selective breeding from the inbred C57BL(Sincs7) and VM(Sincp7) strains; the s7 allele of Sinc has been introduced into a VM background by 18 serial backcrosses, at each generation selecting on the basis of the incubation period with the ME7 scrapie strain. The characteristics of the disease produced by seven scrapie strains have been compared in Sincs7 and Sincp7 congenic mice and in the F1 cross between them. As previously found in non-congenic mice, each scrapie strain has a characteristic, precisely reproducible incubation period pattern in the three Sinc genotypes. The Sinc gene controls the incubation period for all scrapie strains tested but the direction of allelic action and the apparent dominance pattern differs between scrapie strains. Comparison with non-congenic mice shows that other genes also have a minor effect on incubation period. The distribution of vacuolar degeneration in the brain depends mainly on the scrapie strain but is also influenced by Sinc and other unspecified mouse genes. Restriction fragment length polymorphism analysis has already shown that the close linkage between Sinc and the gene encoding PrP has been maintained in the Sinc congenic lines, strengthening the possibility that PrP is the Sinc gene product. The present study confirms that scrapie strains carry information which is independent of the host but nevertheless suggests that host PrP protein interacts with this information to regulate the progression of the disease.

Alleles↗

PubMed2006

Development of a fecal sample collection strategy for extraction and quantification of fecal immunoglobulin A in dogs.

OBJECTIVE: To develop a fecal sample collection strategy and quantification method for measurement of fecal IgA concentrations in dogs. SAMPLE POPULATION: Fecal samples from 23 healthy pet dogs of various breeds. PROCEDURES: Immunoglobulin A was extracted from fecal samples. An ELISA for the measurement of fecal IgA concentrations was established and analytically validated. Intraindividual variation of fecal IgA was determined by calculation of coefficients of variation. A sample collection strategy was developed on the basis of results of intraindividual variation of fecal IgA concentrations. A reference range for fecal IgA concentrations was determined. RESULTS: The method for extraction and quantification of fecal IgA was determined to be sufficiently sensitive, reproducible, accurate, and precise. On the basis of the intraindividual variability of our results, the determined fecal sample collection strategy required analysis of a total of 4 fecal samples/dog, with each fecal sample collected on 2 consecutive days with 28 days between sample collection periods (ie, days 1 and 2 followed by days 28 and 29). Reference range values for fecal IgA concentration were 0.22 to 3.24 mg/g of feces. CONCLUSIONS AND CLINICAL RELEVANCE: Methods of fecal IgA extraction and quantification used in our study allow for identification of dogs with consistently low fecal IgA concentrations. Use of these techniques will enable future investigations into possible associations between low fecal IgA concentrations and signs of gastrointestinal disease in dogs.

Animals↗

PubMed2026

Efficient homologous replacement and deletion of large genomic fragments through template-jumping prime editing in rice.

Homologous replacement of genomic sequences with large DNA fragments (> 100 bp) holds great potential for crop breeding, yet an efficient method to achieve such edits is lacking in plants. Here, in rice, we developed template-jumping prime editing (TJ-PE), a recently reported PE strategy for large targeted insertion, as an efficient tool for homologous replacement with DNA fragments ranging from dozens to hundreds of base pairs, and using TJ-PE, we replaced genomic fragments of up to 340 bp with homologous fragments of the same length. In addition, our TJ-PE tool also enabled precise deletion of 944- to 2024-bp fragments in rice, with efficiencies of up to 34.6% for c. 2000-bp precise deletions. Collectively, this study expands the editing scope of PE in rice and establishes TJ-PE as a generalist tool for precise deletion and replacement of large DNA fragments.

Oryza↗

PubMed1997

Physiological limits to further improvement in the efficiency of oestrous synchronization in goats.

The variability between animals in the timing of oestrus after administration of a synchronization treatment seems to explain the low rate of fertility in goats inseminated at a predetermined time after progesterone withdrawal. Two experiments were performed during the breeding season to test whether the variation was due to the exogenous hormone regime or to the endogenous physiology of the animals. Twenty-one goats were given a synchronization treatment consisting of a vaginal sponge impregnated with 45 mg of fluorogestone acetate (FGA) for 11 days associated with intramuscular injection of 400 I.U. of equine chorionic gonadotrophin (eCG) and 50 microg of cloprostenol 48 h before sponge removal. Progesterone concentrations were measured during the subsequent cycle and the patterns were modelled to allow precise determination of the onset of luteolysis. Oestrus and the luteinizing hormone (LH) surge began 33.0+/-6.8 h and 76.0+/-33.0 h after sponge withdrawal, v. 43.4+/-5.7 h and 90.0+/-36.0 h after natural luteolysis. For both observations, the between-goat variability was larger during the natural than during the synchronized oestrus (P < 0.05). The duration of the oestrous cycle was independent of the number of corpora lutea (CL), whereas the duration of luteal phase was shorter in goats with 2-3 CL (16.4+/-0.9 day than in those with 1 CL: 17.7+/-1.3 day; P < 0.05). In the second experiment, 20 goats were ovariectomized and given a vaginal sponge as described above. Sixteen h after sponge removal, they were injected with 50 microg of oestradiol benzoate (ODB). This treatment was repeated with the second sponge being inserted 1-2 days after observation of oestrus. Oestrus and LH surge were observed: 32.8+/-6 8 h v. 27.8+/-7.8 h after the first ODB injection, and 36.6+/-7.3 h v. 34.3+/-4.8 h after the second ODB injection. No relationship was observed between data of the two experiments. In both cases, the variability in the occurrence of oestrus and LH surge was of the same order as observed in the first experiment. This study shows that the timing of oestrus and LH surge is less variable after progestagen treatment than during a natural oestrous cycle. Moreover, a significant proportion of variability is inherent in the delays following the oestradiol peak, suggesting that further improvement in the synchronizing capacity of treatment based on progestagen administration is unlikely.

Animals↗

PubMed2006

Sampling variability and estimates of density dependence: a composite-likelihood approach.

It is well known that sampling variability, if not properly taken into account, affects various ecologically important analyses. Statistical inference for stochastic population dynamics models is difficult when, in addition to the process error, there is also sampling error. The standard maximum-likelihood approach suffers from large computational burden. In this paper, I discuss an application of the composite-likelihood method for estimation of the parameters of the Gompertz model in the presence of sampling variability. The main advantage of the method of composite likelihood is that it reduces the computational burden substantially with little loss of statistical efficiency. Missing observations are a common problem with many ecological time series. The method of composite likelihood can accommodate missing observations in a straightforward fashion. Environmental conditions also affect the parameters of stochastic population dynamics models. This method is shown to handle such nonstationary population dynamics processes as well. Many ecological time series are short, and statistical inferences based on such short time series tend to be less precise. However, spatial replications of short time series provide an opportunity to increase the effective sample size. Application of likelihood-based methods for spatial time-series data for population dynamics models is computationally prohibitive. The method of composite likelihood is shown to have significantly less computational burden, making it possible to analyze large spatial time-series data. After discussing the methodology in general terms, I illustrate its use by analyzing a time series of counts of American Redstart (Setophaga ruticilla) from the Breeding Bird Survey data, San Joaquin kit fox (Vulpes macrotis mutica) population abundance data, and spatial time series of Bull trout (Salvelinus confluentus) redds count data.

Algorithms↗

PubMed1998

New procedures to estimate water temperatures and water depths for application in climate-dengue modeling.

Two new approaches have been developed to estimate water temperatures and water depths in containers that commonly are used as breeding sites for mosquitoes, the primary vectors of dengue viruses. These estimates are incorporated in recently developed stochastic simulation models used to describe the daily dynamics of dengue virus transmission in the urban environment. Water temperature estimates are provided through a regression model that includes meteorological variables not previously used; results show that they are significantly better than those used in previous dengue transmission models. Water depth models use a climatic water budget approach which estimates moisture storage within containers. The water depth models are less precise than those developed for water temperature; however, results are superior to those used in previous models. These new approaches should improve estimates of the impact of water conditions on dengue vectors.

Aedes↗

PubMed1985

Evaluation of the arterial blood pressure of dogs by two noninvasive methods.

The determination of the arterial blood pressure was done on 12 healthy mixed breed dogs in both the anesthetized and the conscious state, to evaluate two instruments (Doppler flow detector and infrasonde D4000), in their ability to indirectly determine arterial blood pressure. The coefficients of variation were higher with indirect methods when compared with the results obtained by cannulation. These coefficients were lower with the Doppler flow detector. The correlation study showed that both apparatuses were reliable in most situations. The infrasonde D4000 was more accurate than the Doppler in the conscious animals. However the results showed a lack of precision in hypertensive conscious dogs. The diastolic arterial blood pressure was particularly precise in the case of the anesthetized hypotensive dogs. Its sensitivity allowed it to register muscle movement artifacts. The Doppler flow detector showed less variation and was particularly accurate in both anesthetized and conscious hypertensive dogs. Its sensitivity allowed artifact movement sounds to be detected. The Doppler should be used in quiet surroundings or earphones should be worn by the evaluator. Some form of restraint is needed with the use of both instruments. Even if the correlations with the direct arterial blood pressure values were better with the infrasonde D4000, greater variations were found in the individual readings. The Doppler instrument represents in the hands of the investigators a better instrument for routine monitoring of blood pressure in the dog.

Animals↗

PubMedDate not supplied

Morphometric assessment of the proximal portion of the tibia in dogs with and without cranial cruciate ligament rupture.

Based on the clinical observation that dogs with a steep tibial plateau slope had variable tibial morphology, we hypothesized that these dogs could be further characterized using measurements developed by examining computer generated models of specific proximal tibial malformations. A 3D tibial model was created from a normal canine tibia. The model was manipulated to reproduce two specific proximal tibial anomalies representing deformities originating from the tibial plateau or the proximal tibial shaft. Data from these models were used to create specific measurements that would characterize the shape of these anomalies. These measurements included the diaphyseal tibial axis (DTA)/proximal tibial axis (PTA) angle, which defined the orientation of the proximal portion of the shaft in relation to the tibial mid-shaft. These measurements were then made on radiographs of dogs with and without cranial cruciate ligament (CCL) rupture. Models with tibial plateau and proximal shaft deformities had a steep tibial plateau slope (TPS). Models with proximal shaft deformity had a markedly increased DTA/PTA angle. The model with a 10 degree proximal shaft deformity had a DTA/PTA angle of 11.23 degrees. Six dogs (9.0%) had a DTA/PTA angle larger than 11.23 degrees (range, 11.4-13.9 degrees). Dogs in this group had ruptured CCL and a steep TPS. Dogs with CCL rupture had higher TPS (mean, 31.8 +/- 4.1 degrees) and DTA/PTA angle (mean, 6.0 +/- 3.3 degrees) than dogs without CCL rupture (means, 23.6 +/- 3.4 degrees and 4.1 +/- 2.2 degrees, respectively). Dogs with proximal shaft deformity represented a distinct group, which could not be identified using the magnitude of the TPS alone. Characterizing more precisely the shape of the proximal portion of the tibia in dogs contributes to our understanding of the pathogenesis of steep TPS and may facilitate the optimization of the surgical management of dogs with CCL rupture.

Animals↗

PubMed1992

[Iterative estimation of variance components for a mixed model with a numerator relationship matrix: apply to compute K of variance ratio in BLUP and genetic parameters].

An iterative procedure is presented for the estimation of variance components in the mixed model with a numerator relationship matrix from non-balanced data. This method has been shown to be feasible if only designing matrix for fixed effects of the mixed model and Henderson method 3 hypothetic condition of the fixed effect to compute correctly the reduction in sum of squares, we would obtain more precise estimation of variance components, furthermore, the sizes of the initial value K could not affect to last result of the iterative solution. This is because in the iterative process may adjust automatically by designing matrix. Also, the variance components could apply not only to compute variance ratio in BLUP, but also to estimate genetic parameters.

Animals↗

PubMed2006

Regulation of intravenous cocaine self-administration in rats selectively bred for high (HiS) and low (LoS) saccharin intake.

RATIONALE: Rats selectively bred for high saccharin (HiS) intake consume more alcohol and acquire intravenous (i.v.) cocaine self-administration more rapidly than their low saccharin (LoS)-consuming counterparts. The present experiment was designed to determine whether HiS and LoS rats differed in other aspects of drug abuse. OBJECTIVE: The purpose of the present experiment was to use a two-lever dose self-selection procedure to investigate the regulation/dysregulation of i.v. cocaine self-administration in female HiS and LoS rats. MATERIALS AND METHODS: HiS and LoS rats were trained to self-administer eight different doses of cocaine during daily 5-h sessions, with the cocaine doses ranging from 0.2 to 1.6 mg/kg in steps of 0.2 mg/kg. The dose size increased after a response on one lever (infusion duration lengthened by 3 s) and decreased after a response on the other lever (infusion duration shortened by 3 s), with a lower limit of 0 s and with an upper limit of 24 s (a corresponding range of 0 to 1.6 mg/kg); the animals increased or decreased their self-administered dose in nine discrete steps. RESULTS: The HiS rats showed less precise regulation of their postinfusion interval (PII) than LoS rats based on the size of the previously self-administered cocaine dose. Correlations between these variables were lower for HiS than for LoS rats during the acquisition and maintenance phases, and HiS rats had lower PIIs than LoS rats after many of the cocaine doses. The HiS rats also self-administered significantly more cocaine infusions during the maintenance phase than the LoS rats, especially at the highest dose. CONCLUSIONS: These data indicate that HiS rats are more likely to self-administer more cocaine infusions, at higher doses, and with less precise dose-time regulation than LoS rats. Thus, rats selectively bred for HiS showed less inhibitory control over their cocaine intake than LoS rats, suggesting that a genetic predisposition for saccharin preference is related to the rewarding effects of i.v. cocaine.

Analysis of Variance↗

PubMed2025

Cis-regulatory elements: systematic identification and horticultural applications.

Cis-regulatory elements (CREs) are the genetic DNA fragments bound by transcription factors (TFs). CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression. The systematic identification of CREs not only facilitates the annotation of the functional non-coding genome but also provides essential insights into the architecture of gene regulatory networks and sheds light on an accurate selection of the target sites for genetic engineering of crops. In this review, we summarize the current high-throughput methodologies used for identifying CREs, illustrate the associations between CREs and agronomic traits in horticultural crops, and discuss how CREs can be exploited to facilitate crop breeding.

Breeding↗

PubMedDate not supplied

Experimental evaluation of central venous pressure monitoring in the dog.

The measurement of central venous pressure (CVP) will provide objective information about intravascular blood volume. Limitations exist with direct and indirect methods of measuring CVP; however, the purpose of this study was to determine if such factors as catheter size, patient position, or measurements taken with either a water manometer or a strain-gauge transducer would affect the accuracy of CVP measurements. The study population consisted of six adult, mixed-breed dogs. Catheter sizes evaluated were 16- and 19-gauge. Patient positions evaluated were right and left lateral recumbencies. Right atrial pressures (RAPs) were used as the reference standards for CVP measurements. Measurements of RAP and CVP were obtained with a water manometer and a strain-gauge transducer. No significant differences were observed in measured CVPs for the effects of catheter size and right versus left lateral recumbency. A 2.7-mmHg difference in water manometry was demonstrated when compared to strain-gauge transducer measurements. Also, strain-gauge transducer measurements had less precision compared to water manometer measurements.

Animals↗

PubMedDate not supplied

[From gene to behavior, a new way for elaborating new psychotropic agents].

Traditionally, the screening of new neuropsychotropic agents started from the observation of behavioural effects resulting from the administration of a new chemical. Then, one tried to precise its mechanism of action. Since about a decade the way for discovering psychotropic agents tends to be inverse. It starts from the characterization of genes and investigates on their expression products which are new biological targets. Ligands for these targets are developed and then the effects resulting from their administration are considered. In this new strategy, we will consider the cloning of genes and their expression in cultured cells; the knock out of these genes by homologous recombination; the extinction of gene expression by antisense oligodeoxynucleotides; the concentration of behavioural phenotypes by selective breeding.

Behavior↗

PubMed2004

Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley.

Advanced backcross (AB)-quantitative trait locus (QTL) analysis has been successfully applied for detecting and transferring QTLs from unadapted germplasm into elite breeding lines in various plant species. Here, we describe the application of a modified AB breeding scheme to spring barley. A BC3-doubled haploid (DH) population consisting of 181 lines derived from the German spring barley cultivar 'Brenda' (Hordeum vulgare subsp. vulgare) as the recurrent parent and the wild species line 'HS213' (H. vulgare subsp. spontaneum) as the donor line was evaluated for yield and its components as well as malting quality traits. A set of 60 microsatellite markers was used to genotype the population, and phenotypic data were collected at two locations in Germany in continuous years. Altogether, 25 significant QTLs were detected by single-marker regression analysis and interval mapping. Most positive QTLs originated from the recurrent parent 'Brenda'. A QTL, Qhd2.1, on chromosome 2HS from 'Brenda' explained 18.3% and 20.7% of the phenotypic variation for yield and heading date, respectively. Due to the small percentage of donor-parent genome of 6.25%, the BC3-DH lines could be directly used for the extraction of near-isogenic lines (NILs) for Qhd2.1. Consequently, it was possible to determine the precise location of the locus hd2.1 within a region of 6.5 cM, using an F2 population consisting of 234 individuals developed from a cross between an NIL containing a defined donor segment at this locus and 'Brenda'. The location of this QTL was consistent with the presence of a major photoperiod response gene, Ppd-H1, previously reported in this region, which is associated with pleiotropic effects on yield components. In summary, the analysis of a BC3-DH population in barley provides a compromise between the analysis of QTLs by means of an AB scheme and the generation of defined substitution lines. Several lines carrying defined different donor segments for only one single chromosome or trait in the genetic background of 'Brenda' could be selected for further genetic studies.

Breeding↗

PubMed2025

Breeding of yeast strains with intracellular amino acid accumulation for value-added alcoholic beverages.

The yeast Saccharomyces cerevisiae converts amino acids into volatile compounds with fruity and floral aromas during fermentation. These amino acid-derived aroma compounds play a critical role in defining the taste and flavor of alcoholic beverages such as sake, beer, and wine. The productivity of amino acid-derived aroma compounds depends on the intracellular availability of their precursor amino acids. Therefore, breeding yeast strains that accumulate amino acids provides a practical approach to developing alcoholic beverages with more unique and attractive sensory characteristics. In this minireview, we describe the isolation of yeast strains that overproduce branched-chain amino acids and phenylalanine, obtained through conventional mutagenesis of industrial brewing yeasts. We also discuss the mechanisms responsible for the increased production of these amino acids in the mutant strains, including altered feedback regulation and transcriptional control of key enzymes involved in their biosynthesis. In addition, we briefly introduce a plasmid-free genome editing system that enables precise modification of metabolic pathways without the integration of foreign DNA, allowing the construction of strains that are not classified as genetically modified organisms. This method represents a promising tool that allows flexible and fine-tuned engineering of yeast metabolic pathways, including the development of strains with tailored aroma profiles.

Saccharomyces cerevisiae↗