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PubMed2005

Where are we in genomics?

Genomic studies provide scientists with methods to quickly analyse genes and their products en masse. The first high-throughput techniques to be developed were sequencing methods. A great number of genomes from different organisms have thus been sequenced. Genomics is now shifting to the study of gene expression and function. In the past 5-10 years genomics, proteomics and high-throughput microarray technologies have fundamentally changed our ability to study the molecular basis of cells and tissues in health and diseases, giving a new comprehensive view. For example, in cancer research we have seen new diagnostic opportunities for tumour classification, and prognostication. A new exciting development is metabolomics and lab-on-a-chip techniques (which combine miniaturization and automation) for metabolic studies. However, to interpret the large amount of data, extensive computational development is required. In the coming years, we will see the study of biological networks dominating the scene in Physiology. The great accumulation of genomics information will be used in computer programs to simulate biologic processes. Originally developed for genome analysis, bioinformatics now encompasses a wide range of fields in biology from gene studies to integrated biology (i.e. combination of different data sets from genes to metabolites). This is systems biology which aims to study biological organisms as a whole. In medicine, scientific results and applied biotechnologies arising from genomics will be used for effective prediction of diseases and risk associated with drugs. Preventive medicine and medical therapy will be personalized. Widespread applications of genomics for personalized medicine will require associations of gene expression pattern with diagnoses, treatment and clinical data. This will help in the discovery and development of drugs. In agriculture and animal science, the outcomes of genomics will include improvement in food safety, in crop yield, in traceability and in quality of animal products (dairy products and meat) through increased efficiency in breeding and better knowledge of animal physiology. Genomics and integrated biology are huge tasks and no single lab can pursue this alone. We are probably at the end of the beginning rather than at the beginning of the end because Genomics will probably change Biology to a greater extent than previously forecasted. In addition, there is a great need for more information and better understanding of genomics before complete public acceptance.

Animals↗
PubMed1976

The embryology of the common marmoset (Callithrix jacchus).

Earlier studies have noted the unusual placental anatomy of marmosets and the high frequency of biovular, synchorial twinning. The maintenance of a captive colony of Callithrix jacchus has enabled further studies to be made of embryonic development in this species. Thirty-six embryos from seventeen pregnancies were examined in detail and assigned to horizons on the basis of Streeter's classification of external form and internal structure. The specimens represented tha major part of the embryonic period and, with few exceptions, the structural development of the marmoset closely resembled that of the other primates that have been described. Marmoset embryos of a given horizon were consistently shorter than those of man. The timing of morphogenesis in C. jacchus was different from that observed in man and other primates. There was a considerable delay in early embryogenesis in the marmoset, although subsequent to stage XI, development proceeded at approximately the same rate as other primates. The available evidence suggested that this anomaly was not due to delayed implantation or embryonic diapause but to a generally slower rate of early development. The evolution of synchorial twinning is considered as a possible reason for this mode of development.

Abortion, Induced↗
PubMed2005

Oblique decision trees for spatial pattern detection: optimal algorithm and application to malaria risk.

BACKGROUND: In order to detect potential disease clusters where a putative source cannot be specified, classical procedures scan the geographical area with circular windows through a specified grid imposed to the map. However, the choice of the windows' shapes, sizes and centers is critical and different choices may not provide exactly the same results. The aim of our work was to use an Oblique Decision Tree model (ODT) which provides potential clusters without pre-specifying shapes, sizes or centers. For this purpose, we have developed an ODT-algorithm to find an oblique partition of the space defined by the geographic coordinates. METHODS: ODT is based on the classification and regression tree (CART). As CART finds out rectangular partitions of the covariate space, ODT provides oblique partitions maximizing the interclass variance of the independent variable. Since it is a NP-Hard problem in RN, classical ODT-algorithms use evolutionary procedures or heuristics. We have developed an optimal ODT-algorithm in R2, based on the directions defined by each couple of point locations. This partition provided potential clusters which can be tested with Monte-Carlo inference. We applied the ODT-model to a dataset in order to identify potential high risk clusters of malaria in a village in Western Africa during the dry season. The ODT results were compared with those of the Kulldorff' s SaTScan. RESULTS: The ODT procedure provided four classes of risk of infection. In the first high risk class 60%, 95% confidence interval (CI95%) [52.22-67.55], of the children was infected. Monte-Carlo inference showed that the spatial pattern issued from the ODT-model was significant (p < 0.0001). Satscan results yielded one significant cluster where the risk of disease was high with an infectious rate of 54.21%, CI95% [47.51-60.75]. Obviously, his center was located within the first high risk ODT class. Both procedures provided similar results identifying a high risk cluster in the western part of the village where a mosquito breeding point was located. CONCLUSION: ODT-models improve the classical scanning procedures by detecting potential disease clusters independently of any specification of the shapes, sizes or centers of the clusters.

Africa, Western↗
PubMed1992

Dementia and the nursing home: association with care needs.

OBJECTIVE: To determine whether RUG reimbursement categories accurately predict requirements for care in nursing homes. DESIGN: Prospective descriptive study of residents in lower reimbursement categories according to RUG. SETTING: Three nursing homes in New York City. PARTICIPANTS: Convenience sample of 173 residents who agreed to participate, not significantly different from 201 who did not agree to participate. MAIN MEASURES: Chart review; assessment of residents' cognitive and functional abilities; nursing assistants' ratings of residents' functional abilities, behavioral problems, the amount of effort required in care; and time-motion studies of staff-resident interactions. RESULTS: Both the residents' RUG classification (P less than 0.01) and the level of ADL independence (P less than 0.001) had significant impacts on the staff effort required in their care, with more dependent residents requiring greater effort. The residents' level of cognitive impairment also had a significant impact on the staff effort, with the severely impaired requiring greater effort (P less than 0.05). The time-motion analysis indicated that residents within the same RUG category differed in the number of staff-resident interactions based on their level of cognitive impairment. CONCLUSIONS: Cognitive impairment is a significant morbidity (or co-morbidity) in determining the quantity of staff effort required by the resident, and behavioral interventions are an important care component. There is marked heterogeneity within lower (RUG) reimbursement categories which translates into strikingly different care requirements.

Activities of Daily Living↗
PubMed2002

Analysis of age-specific predicted transmitting abilities for final scores in Holsteins with a random regression model.

Conformation final scores obtained by the Holstein Association were used in this study. Five subsets were sampled from the original complete data, which contained about 7 million records, and (co)variance components for additive genetic, permanent environmental, and residual effects were estimated with a multiple-trait (MT) model at different ages of cows and with a random regression model. Transmitting abilities were predicted with the random-regression (RR) model and with the repeatability model for the national evaluation, using the entire data set. The RR model included fixed and random regressions on age at classification for additive genetic and permanent environmental effects. Additive genetic and residual variances estimated with the MT model increased with aging. Genetic correlations between age groups decreased with their distance. Heritability and repeatability estimates with the RR model were 0.27 and 0.88 on average, increasing with cow's age. Correlations between transmitting abilities predicted with the RR model at various ages and with the repeatability model were in the range of 0.89 to 0.99. In the 1980s, predicted transmitting abilities (PTA) of sires increased with their daughters' age, but in 1991 and 1995, the PTA decreased. In general, sires whose daughters were evaluated at mature ages tended to have higher PTA. For sires and cows, genetic trends estimated from the repeatability model and from the RR model were similar. The low genetic trend of cows at 60 mo for recent years was due to many grade cows that had only single records and little pedigree information.

Aging↗
PubMed1992

A survey of epithelial odontogenic tumors and cysts in dogs and cats.

A retrospective histologic study of 12 canine and eight feline epithelial odontogenic tumors and cysts was conducted from oral masses (n = 3,917) obtained between 1980 and 1990. No sex or breed predilection was identified. Ameloblastoma was observed in two dogs (case Nos. 1, 2) 6 and 8 months of age. Calcifying epithelial odontogenic tumors were seen in a dog (case No. 3) and in two cats (case Nos. 4, 5) between 8 and 16 years of age. Ameloblastic fibroma (or fibroameloblastoma) was observed in cats (case Nos. 6-10) only. Inductive fibroameloblastoma was observed in four cats (case Nos. 6-9) up to 1 year of age, whereas ameloblastic fibroma was seen in a 14-year-old cat (case No. 10). A single ameloblastic odontoma was identified in a 20-month-old dog (case No. 11). Two complex odontomas occurred in a 6-month-old (case No. 12) and a 4-year-old (case No. 13) dog. Odontogenic cysts were identified in five dogs (case Nos. 14-18) aged 4.5 months to 16 years and in a 1-year-old cat (case No. 19) and have not been previously reported in these species. These cysts were lined by a stratified epithelium reminiscent of the appearance of ameloblastic epithelium. An odontogenic keratocyst with prominent central parakeratotic keratinization was identified in one 9-year-old female dog (case No. 20). Almost all epithelial odontogenic tumors were circumscribed, benign tumors that warranted a good prognosis for survival, although local recurrence may have followed (or may follow) incomplete excision. Calcifying epithelial odontogenic tumors may be locally invasive. Of six odontogenic cysts (case Nos. 14-19), two (case Nos. 15, 18) gave rise to basi-squamous carcinomas. The classification and behavior of epithelial odontogenic tumors and cysts in human beings, dogs, and cats are discussed.

Animals↗
PubMed2003

Heritabilities and correlations among body condition score, dairy form and selected linear type traits.

The objectives of this study were to estimate the heritability of body condition score (BCS) with data that could be used to generate genetic evaluations for BCS in the US, and to estimate the relationship among BCS, dairy form and selected type traits. Body condition score and linear type trait records were obtained from Holstein Association USA Inc. Because BCS was a new trait for classifiers, scoring distribution and accuracy was not normal. Records from 11 of 29 classifiers were eliminated to generate a data set that should represent BCS data recorded in the future. Edited data included 128,478 records for analysis of first lactation cows and 207,149 records for analysis of all cows. Heritabilities and correlations were estimated with ASREML using sire models. Models included age at calving nested within lactation, 5th order polynomials of DIM, fixed herd-classification visit effects and random sire and error. Genetic correlation estimates were generated between first lactation data that had records from 11 classifiers removed and data with no classifiers removed. Genetic correlation estimates were 0.995 and above between data with and without classifiers removed for scoring distributions, but heritability estimates were higher with the classifiers edited from the data. Heritability estimates for type traits and final score were similar to previously reported estimates. The heritability estimate for BCS was 0.19 for first lactation cows and 0.22 for all cows. The genetic correlation estimate for first lactation cows between BCS and dairy form was -0.73, whereas the genetic correlation estimate between BCS and strength was 0.72. Genetic correlation estimates were nearly identical when cows from all lactations were included in the analyses. Body condition score had a genetic correlation with final score closer to zero (0.08) than correlations of final score with dairy form, stature or strength.

Animals↗
PubMed2000

T-maze behaviour in broiler chicks is not sensitive to right-left preferences, test order or time-of-day.

There is substantial individual variation in the time taken by broiler chicks to traverse a T-maze and thereby reinstate visual contact with their companions. Chicks completing this task quickly (high performance, HP) subsequently grew faster in the laboratory and on farm, exhibited greater sociality, and showed less pronounced adrenocortical responses to a partial water immersion stressor than did their slower (low performance, LP) counterparts [Marin, R.H., Jones, R.B., 1999. Latency to traverse a T-maze at 2 days of age and later adrenocortical responses to an acute stressor in domestic chicks. Physiol. Behav. 66, 809-813.; Marin, R.H., Arce, A., Martijena, I.D., 1997. T-maze performance and body weight relationship in broiler chicks. Appl. Anim. Behav. Sci. 54, 197-205.; Jones, R.B., Marín, R.H., García, D.A., Arce, A., 1999. T-maze behaviour in domestic chicks: a search for underlying variables. Anim. Behav. 58, 211-217.]. Given its simplicity, rapidity and non-invasiveness, the T-maze test might represent a commercially attractive selection criterion for future breeding programmes if this behavioural trait exhibits sufficient genetic variability. However, it is first necessary to ensure that performance in the T-maze is not sensitive to potentially confounding variables, such as existing preferences to turn right or left at the junction of the maze, the order of testing, or the time of day. In the present study, 240 newly hatched, mixed-sex broiler chicks (Cobb) were randomly allocated to 12 groups of 20 upon receipt. When they were 2 days of age a group of 20 chicks was placed in the brood area of each of two T-mazes at 0830 h; the brood areas were positioned on either the right or the left sides of the mazes. After acclimatisation, one chick from each group was placed in the isolation chamber of the T-maze and we recorded the time it took to traverse the maze. This procedure was repeated until all 20 chicks and all 12 groups had been tested. The locations of the brood areas were rotated after each block of 20 tests. Testing was completed in the same day and two groups were tested at each of the following times: 0900, 1030, 1200, 1330. 1500, and 1630 h. Analyses of variance (ANOVA) revealed no detectable effects of: positioning the brood area on the right or the left side of the T-maze (F(1,200)=0.06, P<0.80), test order (F(19,200)=0.48; P<0.96), or time-of-day (F(5,234)=0.44; P<0.81). These findings strongly suggest that the future classification and possible selection of broiler chicks according to their T-maze responses are unlikely to be confounded by right-left preferences, test order, or the time of day.

Journal Article↗
PubMed2006

Genetic and phenotypic relationships among locomotion type traits, profit, production, longevity, and fertility in Spanish dairy cows.

The phenotypic and genetic relationships of 3 locomotion traits with profit, production, longevity, and fertility traits were studied to determine the importance of locomotion traits for dairy producers. Two data sets including official milk records and type classification scores of 62,293 cows, and reproductive records of 24,561 cows from the Basque and Navarra Autonomous Regions were analyzed. Higher scores for feet and legs (FL), foot angle (FA), and rear legs set (RLS) were positively related to production and functional traits, whereas fertility was not significantly affected. The cows that scored the highest for FL were $213/yr more profitable, produced 575 kg more milk per year, and remained in the herd for 307 more functional days than the cows scoring the lowest. Feet and legs was the trait most genetically correlated to profit, although a low value (0.10) was obtained, whereas RLS was the trait most correlated to milk production (0.12). Genetic correlations among FL, FA, RLS, and longevity traits (from -0.10 to 0.05) were low. Quadratic curves were the best fit for both profit and functional herd life for EBV of each of the 3 locomotion traits. Further studies dealing with profitability and lameness, instead of using conformation traits, could be performed directly if a larger data pool of lameness was routinely recorded.

Animals↗
PubMed2000

Heritability of clinical mastitis incidence and relationships with sire transmitting abilities for somatic cell score, udder type traits, productive life, and protein yield.

The objective of this study was to determine the relationships among daughter clinical mastitis during first and second lactations and sire transmitting abilities for somatic cell score, udder type traits, productive life, and protein yield. Data on clinical mastitis during first lactation were available for 1795 daughters (in six Pennsylvania herds, one Minnesota herd, and one Nebraska herd) of 283 Holstein sires. Data on clinical mastitis during second lactation were available for 1055 of these daughters. A total of 479 cows had 864 clinical episodes during first lactation, and 230 cows had 384 clinical episodes during second lactation. Clinical mastitis incidence and the total number of clinical episodes during each lactation were regressed on herd-season of calving (a classification variable), age at first calving, lactation length, and sire transmitting abilities taken one at a time. Linear effects, nonlinear effects, and odds ratios were estimated for sire transmitting abilities. Separate analyses were conducted on dependent variables that considered clinical mastitis from: all organisms, coagulase-negative staphylococci, coliform species, streptococci other than Streptococcus agalactiae, and the most common environmental organisms (coliform species and streptococci other than Streptococcus agalactiae). Heritability of clinical mastitis ranged from 0.01 to 0.42. Daughters of sires that transmit the lowest somatic cell score had the lowest incidence of clinical mastitis and the fewest clinical episodes during first and second lactations. Daughters of sires that transmit longer productive life, shallower udders, deeper udder cleft, and strongly attached fore udders had either fewer clinical episodes or lower clinical mastitis incidence during first and second lactations. The incidence of clinical mastitis and the number of clinical episodes per lactation may be reduced by selection for lower somatic cell score, longer productive life, shallower udders, deeper udder cleft, or strongly attached fore udders.

Animals↗
PubMed2004

Body condition scores and dairy form evaluations as indicators of days open in US Holsteins.

The objectives of this study were to estimate genetic correlations among body condition score (BCS), dairy form, milk yield, and days open in US Holsteins and investigate the potential of using BCS or dairy form evaluations as early indicators of days open. Dairy form and BCS obtained from the Holstein Association USA, Inc., were merged with mature equivalents (ME) for milk yields and days open data from AIPL-USDA. Cows were required to be classified between 24 and 60 mo of age, before 335 d in milk (DIM) and have ME milk of at least 4537 kg. A minimum of 20 daughters per sire and 10 cows per herd-classification visit (HV) or herd-year-season of calving (HYS) were required. The final data set included 159,700 records. Heritabilities and correlations among dairy form, BCS, milk yield, and days open were estimated with multiple trait sire models. Fixed effects included age at classification for dairy form and BCS, age at calving for milk yield, HV for dairy form and BCS, HYS for milk yield and days open, DIM within lactation group for dairy form and BCS and lactation group for milk yield and days open. Correlations among dairy form, BCS, and days open were generated with and without a ME milk covariable. Correlations between ME milk and days open were generated with and without covariables for dairy form or BCS. Random effects included sire and error. The genetic correlation estimates of days open with dairy form, BCS, and ME milk were 0.48, -0.30, and 0.38, respectively. The genetic correlation estimate between days open and dairy form was 0.38 after adjustment for ME milk, whereas the genetic correlation between days open and BCS was -0.24 after adjustment for ME milk. Combining dairy form evaluations with days open evaluations for 19 recently proven bulls resulted in an average increase of 0.06 for reliability of days open evaluations. The addition of BCS evaluations did not increase reliability when dairy form observations were available.

Aging↗
PubMedDate not supplied

Exploratory celiotomy in 200 nontraumatized dogs and cats.

Two hundred dogs and cats undergoing exploratory celiotomy for reasons other than trauma were grouped by disease classification and by body system affected. There were 61 animals in which infection or inflammation predominated, 63 animals with neoplasia, and 76 animals with noninflammatory and non-neoplastic conditions. Body systems affected were digestive, lymphatic, urinary, reproductive, other, and undetermined. Seventy-three percent of the animals survived the hospitalization period; survival rates for animals with infection or inflammation, neoplasia, and other disorders were 69%, 60%, and 86%, respectively. Within the same groups, the exploratory celiotomy provided strictly diagnostic information in 72%, 79%, and 24% of the animals, and surgical treatment was provided to 28%, 21%, and 58% of the animals, respectively. Intraoperative cytologic and histologic diagnoses were consistent in 78% of the animals; the consistency rates for animals with infection or inflammation, neoplasia, and other disorders were 81%, 88%, and 59%, respectively. Complications after surgery were observed in 30% of the animals, with 60% of the complications disease related. Complications were observed in six animals with reproductive disorders (67%), six animals with urinary disease (46%), 35 animals with digestive disease (29%), and three animals with lymphatic disease (13%).

Abdomen↗
PubMed2005

Candidate gene database and transcript map for peach, a model species for fruit trees.

Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].

Breeding↗
PubMed2002

Assessment of strawberry aroma through SPME/GC and ANN methods. Classification and discrimination of varieties.

To provide an efficient and running analytical tool to strawberry plant breeders who have to characterize and compare the aromatic properties of new cultivars to those already known, a HS-SPME/GC-MS analysis method has been coupled with a statistical treatment method issued from the current development of artificial neuron networks (ANN), and more specifically, the unsupervised learning systems called Kohonen self-organizing maps (SOMs). So, 70 strawberry samples harvested at CIREF from 17 known varieties have been extracted by using a DVB/Carboxen/PDMS SPME fiber according to the headspace procedure, and then chromatographed. A panel of 23 characteristic aromatic constituents has been selected according to published results relative to strawberry aroma. The complex resulting matrix, collecting the relative abundance of the 23 selected constituents for each sample, has been input into the SOM software adapted and optimized from the Kohonen approach described by one of the authors. After a period of training, the self-organized system affords a map of virtual strawberries to which real samples are compared and plotted in the best matching unit (BMU) of the map. The efficiency for discriminating the real samples according to their variety is dependent on the number of units selected to define the map. In this case, a 24-unit map allowed the complete discrimination of the 17 selected varieties. Moreover, to test the validity of this approach, two additional samples were blind-analyzed and the results were computed according to the same procedure. At the end of this treatment, both samples were plotted into the same unit as those of the same variety used for training the map.

Breeding↗
PubMed2002

The effects of heat stress and sperm quality classification on broiler breeder male fertility and semen ion concentrations.

1. The present study was undertaken to determine the effects of heat exposure on fertility, semen quality, and semen ion concentrations of broiler breeders classified on sperm quality index (SQI) before heat stress. 2. Cobb males (108) were individually caged in 6 temperature-controlled rooms. Each room contained an equal number of males from each of the 4 SQI population quartiles as follows: best (B), good (G), fair (F), and poor (P). Three rooms were heated to 35 degrees C, and the other three rooms were maintained at a constant 23 degrees C as controls. For each SQI group in each room, 15 Leghorn hens were artificially inseminated (5 x 10(7) sperm/hen) once a week for 8 weeks for fertility observations. 3. Body weight, sperm concentration, SQI, and fertility of P males were lower than in the other three SQI groups. Body temperature of the top three SQI groups was increased by heat exposure, but body temperature was not altered by heat stress in the P group. Fertility, sperm viability, and SQI of the top three SQI groups, but not the P group, was decreased by heat stress. Seminal plasma K+ of P males was lower than that of B males. However, seminal plasma Ca2+ concentration of P males was higher than that of B males. 4. In conclusion, high ambient temperatures had more impact on semen quality and fertility of males in the top 75% of the SQI population than in males in the bottom 25% of the population. In addition, calcium ions (Ca2+) appear to play a major role in heat stress infertility.

Animals↗
PubMed2002

Microsatellite DNA fingerprinting, differentiation, and genetic relationships of clones, cultivars, and varieties of six poplar species from three sections of the genus Populus.

Accurate identification of Populus clones and cultivars is essential for effective selection, breeding, and genetic resource management programs. The unit of cultivation and breeding in poplars is a clone, and individual cultivars are normally represented by a single clone. Microsatellite DNA markers of 10 simple sequence repeat loci were used for genetic fingerprinting and differentiation of 96 clones/cultivars and varieties belonging to six Populus species (P. deltoides, P. nigra, P. balsamifera, P. trichocarpa, P. grandidentata, and P maximowiczii) from three sections of the genus. All 96 clones/cultivars could be uniquely fingerprinted based on their single- or multilocus microsatellite genotypes. The five P. grandidentata clones could be differentiated based on their single-locus genotypes, while six clones of P. trichocarpa and 11 clones of P. maximowiczii could be identified by their two-locus genotypes. Twenty clones of P. deltoides and 25 clones of P. nigra could be differentiated by their multilocus genotypes employing three loci, and 29 clones of P. balsamifera required the use of multilocus genotypes at five loci for their genetic fingerprinting and differentiation. The loci PTR3, PTR5, and PTR7 were found to be the most informative for genetic fingerprinting and differentiation of the clones. The mean number of alleles per locus ranged from 2.9 in P. trichocarpa or P. grandidentata to 6.0 in P. balsamifera and 11.2 in 96 clones of the six species. The mean number of observed genotypes per locus ranged from 2.4 in P. grandidentata to 7.4 in P. balsamifera and 19.6 in 96 clones of the six species. The mean number of unique genotypes per locus ranged from 1.3 in P. grandidentata to 3.9 in P. deltoides and 8.8 in 96 clones of the six species. The power of discrimination of the microsatellite DNA markers in the 96 clones ranged from 0.726 for PTR4 to 0.939 for PTR7, with a mean of 0.832 over the 10 simple sequence repeat loci. Clones/cultivars from the same species showed higher microsatellite DNA similarities than the clones from the different species. A UPGMA cluster plot constructed from the microsatellite genotypic similarities separated the 96 clones into six major groups corresponding to their species. Populus nigra var. italica clones were genetically differentiated from the P. nigra var. nigra clones. Microsatellite DNA markers could be useful in genetic fingerprinting, identification, classification, certification, and registration of clones, clultivars, and varieties as well as genetic resource management and protection of plant breeders' rights in Populus.

DNA Fingerprinting↗
PubMed2005

Study of codes of disposal at different parities of Large White sows using a linear censored model.

To study the genetic relationship between three grouped reasons for sow removal (SR) in consecutive parities, accounting for censoring, 13,838 records from Large White sows were analyzed. Data were from seven pure-line farms having, on average, 5.9% unknown SR. Three traits were subjectively defined, each corresponding to a classification of SR (reproductive [RR], nonreproductive [RN], and others [RO]). Records for each trait could take one of five categories, according to parity at removal (0 to 4 or later). A multivariate linear censored model was implemented. The model to estimate (co)variance components and parameters included the effects of year-season, region, contemporary group, and additive genetic effects. The most common SR was related to reproduction (48.5%). Diseases of different origin and cause, old age/parity, and sow death or loss accounted for about 18, 7, and 4% of total culls, respectively. Estimates of variance components showed heterogeneity of additive genetic and residual variances for the three traits. Estimates of heritability were 0.18, 0.13, and 0.15 for RR, RN, and RO, respectively. Genetic correlations between removal codes were high (> or =0.90). Results suggest sizeable additive genetic variances exist for parity at removal and different codes of removal. Different SR reasons seem to operate similarly or as a closely related genetic trait associated with fitness. In particular, RN and RO seem to be genetically indistinguishable. Data structure, definition, and volume are major limitations in studies of sow survival. A multiple-trait censored model is preferred to evaluate reasons of sow disposal. Grouped removal causes seem to be strongly genetically correlated but with heterogeneous variances, suggesting that combining all removal causes and treating the trait as parity at disposal is an alternative approach.

Animal Husbandry↗
PubMed2002

Ram mating behavior after long-term selection for reproductive rate in Rambouillet ewes.

Mating behavior is known to be heritable in several species, but it is not known if selection schemes for ewe reproductive traits affect mating behavior of rams. Therefore, our objectives were to determine if divergent (high vs low index) selection of a female reproductive trait (lambs born divided by age of ewe minus one) affects mating behavior patterns of male offspring during training to service an artificial vagina (AV) in a less than natural setting (Exp. 1) or during serving capacity tests (SCT) in simulated natural mating conditions (Exp. 2). The method for evaluating male mating behavior was a series of serving capacity tests to estimate sexual performance. For Exp. 1, five, 30-min observations were conducted to assess the mating behavior of 29 rams (22 mo old) being trained to service an AV. In Exp. 1, percentages of rams mounting (73 vs 36%) and ejaculating (67 vs 29%) differed (P < 0.05) between rams from high and low Rambouillet ewe selection lines, respectively. In Exp. 2, ram classification consisted of exposing each 22- to 24-mo-old ram (n = 48) to three unrestrained ewes in estrus for 18, 30-min tests. Any ram that had not mounted or ejaculated during SCT was evaluated for sexual orientation in a 30-min preference test in which each ram had access to both restrained estrual ewes and restrained rams. In Exp. 2, there was no difference (P > 0.2) in percentages of rams mounting (92 vs 78%) and ejaculating (88 vs 74%) between rams from high and low Rambouillet ewe selection lines, respectively. There was no difference (P > 0.33) between high and low ewe selection line rams for mounts or ejaculations for 18 SCT. Only one male-oriented ram was identified, which was from the high line. In Exp. 2, six SCT were necessary to obtain 95% reliability in sexual performance scores. Results of these studies indicate that long-term selection of ewes for litter size did not alter ram sexual performance after SCT under simulated natural mating conditions or affect incidence of male-oriented rams. Mating behavior observed during training to service an AV was lower for rams from ewes of the low selection line than for rams from ewes of the high selection line. We concluded that long-term selection for reproductive rate in ewes did not alter mating behavior patterns of male offspring; however, test conditions, such as restrained and unrestrained ewes and number of serving capacity tests, may affect conclusions in studies that evaluate sexual performance of rams.

Animals↗