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Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and intellectual disability (ID), are pervasive, often lifelong disorders, lacking evidence-based interventions for core symptoms. With no established biological markers, diagnoses are defined by behavioral criteria. Thus, preclinical in vivo animal models of NDDs must be optimally utilized. For this reason, experts in the field of behavioral neuroscience convened a workshop with the goals of reviewing current behavioral studies, reports, and assessments in rodent models. Goals included: (a) identifying the maximal utility and limitations of behavior in animal models with construct validity; (b) providing recommendations for phenotyping animal models; and (c) guidelines on how in vivo models should be used and reported reliably and rigorously while acknowledging their limitations. We concluded by recommending minimal criteria for reporting in manuscripts going forward. The workshop elucidated a consensus of potential solutions to several problems, including revisiting claims made about animal model links to ASD (and related conditions). Specific conclusions included: mice (or other rodent or preclinical models) are models of the neurodevelopmental insult, not specifically any disorder (e.g., ASD); a model that perfectly recapitulates a disorder such as ASD is untenable; and greater attention needs be given to validation of behavioral testing methods, data analysis, and critical interpretation. ispartof: GENES BRAIN AND BEHAVIOR vol:21 issue:5 ispartof: location:England status: published

Noninvasive genetic sampling (NGS) is commonly used to study elusive or rare species where direct observation or capture is difficult. Little attention has been paid to the potential effects of observer bias while collecting noninvasive genetic samples in the field, however. Over a period of 7 years, we examined whether different observers (n = 58) and observer experience influenced detection, amplification rates, and correct species identification of 4,836 gray wolf (Canis lupus) fecal samples collected in Idaho and Yellowstone National Park, USA and southwestern Alberta, Canada (2008-2014). We compared new observers (n = 33) to experienced observers (n = 25) and hypothesized experience level would increase the overall success of using NGS techniques in the wild. In contrast to our hypothesis, we found that new individuals were better than experienced observers at detecting and collecting wolf scats and correctly identifying wolf scats from other sympatric carnivores present in the study areas. While adequate training of new observers is crucial for the successful use of NGS techniques, attention should also be directed to experienced observers. Observer experience could be a curse because of their potential effects on NGS data quality arising from fatigue, boredom or other factors. The ultimate benefit of an observer to a project is a combination of factors (i.e., field savvy, local knowledge), but project investigators should be aware of the potential negative effects of experience on NGS sampling.

The development of Darwin's thought is traced from the uncritical acceptance of the theories of Independent Creation and Fixity of Species by his peers, through progressive dissatisfaction with the ability of these theories to account for the actual distribution of species in the natural world; and the formulation of his theory of Evolution through Natural Selection based on an analogy of the workings of nature, with the workings of the great English animal and plant breeders of the late 18th and early 19th centuries.

Aggressive (i.e. over-) feeding of broiler breeder females in the period preceding onset of lay results in higher mortality and subsequent deleterious effects on egg and chick production (the ‘over...

Summary. The genes encoding bovine prolactin and rhodopsin were assigned to syntenic groups on the basis of hybridization of DNA from a panel of bovine-hamster hybrid somatic cell lines with cloned prolactin and rhodopsin gene probes. Prolactin was found to be syntenic with previously mapped glyoxalase, BoLA and 21-hydroxylase genes, establishing a syntenic conservation with human chromosome 6. The presence of bovine rhodopsin sequences among the various hybrid cell lines was not concordant with any gene previously assigned to one of the 23 defined autosomal syntenic groups. Thus, rhodopsin marks a new bovine syntenic group, U24, leaving only five cattle autosomes unmarked by at least one biochemical or molecular marker.

The present status of the bovine gene map as well as some of the methods and strategies important for future efforts in completing the gene map of cattle are reviewed.

Two bovine populations, a Holstein-Friesian dairy stock and a synthetic (Baladi X Hereford X Simmental X Charolais) beef stock, were screened for restriction fragment length polymorphisms (RFLPs) at the growth hormone and prolactin genes. Most RFLPs at the growth hormone gene are apparently the consequence of an insertion/deletion event which was localized to a region downstream of the structural gene. The restriction map for the genomic region including the growth hormone gene was extended. Two HindIII RFLPs at the growth hormone locus, as well as several RFLPs at the prolactin gene, seemed to be the consequence of a series of point mutations. The results are discussed in terms of the possibility that minor genomic variability underlies quantitative genetic variation.

To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r 2 values of 0.10 and 0.46, respectively; outside the blocks, r 2 values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.

Protein yield (PY) is currently the major economic product of the dairy herd. Genome-wide scans for quantitative trait loci (QTL) affecting milk yield (MY) and milk protein percentage (PP) suggest that of the loci affecting the 2 traits, about 1/4 exclusively affect MY, 1/4 exclusively affect PP, and half affect both traits. Because PY is the product of MY and PP, it is of interest to evaluate the expected effects on PY of marker-assisted selection (MAS) applied to these 3 classes of QTL. It is clear that selection for the appropriate allele at QTL exclusively affecting MY or PP will have a positive effect on PY. The question arises as to the effect of MAS directed at QTL affecting both MY and PP. Because the observed genetic correlation of about -0.5 between MY and PP must be generated by these loci, and because they comprise about half the total number of loci affecting the 2 traits, it can be inferred that the genetic correlation between MY and PP at loci affecting both traits is close to -1.0. This seems to imply that generally such loci would be neutral in their effects on PY. In the present study, biometrical expressions originally developed to describe the relationships of MY, fat percentage, and fat yield were adapted to describe the relationships of MY, PP, and PY. The resultant expressions were validated by showing that they correctly predicted the observed phenotypic standard deviation and heritability of PY, and the vastly different genetic correlations of PY with MY (very high positive) and of PY with PP (very low positive). Contrary to initial impressions, further biometrical analysis of the projected effects on PY of MAS at the loci affecting both traits, showed that even under the assumption that the genetic correlation between MY and PP at these loci is -1.0, selection for the allele favoring MY will have a strong positive effect on PY, whereas selection for the allele favoring PP will have an equal but opposite negative effect on PY. These diametrically opposed effects are due to the lower genetic coefficient variation of PP compared with MY. It is speculated that the reduced coefficient of variation of PP may be because of more stringent homeostatic buffering of milk composition compared with milk yield.

Although numerous quantitative trait loci (QTL) mapping studies involving milk protein percent (PP), milk yield (MY), and protein yield (PY) have been carried out, there has not been any systematic evaluation of the effects of individual QTL on these 3 interrelated traits. Consequently, the aim of the present study was to investigate the effects on MY and PY of QTL for PP previously mapped in various laboratories. The study, based on selective DNA pooling of milk samples, included 10 Israeli Holstein artificial insemination bulls, each the sire of 1,800 or more milk-recorded daughters. For each sire-trait combination across the 10 sires, milk samples of the highest and lowest daughters with respect to estimated breeding values for PP, PY, and MY were collected for pooling. A total of 134 dinucleotide microsatellites distributed over 25 bovine autosomes were used. An empirical standard error for marker-QTL linkage testing was calculated based on the variation among split samples within the same tail. Threshold comparison-wise error rate P-values were set to control proportion of false positives at P = 0.10 level for declaring significant effects at the marker-trait level. Estimates of the number of true null hypotheses for each trait were obtained from the histogram of marker comparison-wise error rate P-values. Based on these estimates, effective power of the experiment at the marker-trait level was estimated as 0.75, 0.41, and 0.73 for PP, PY, and MY. The proportion of heterozygosity at the QTL was estimated as 0.46, 0.39, and 0.40, respectively. After correcting for incomplete power and proportion of false positives, it was estimated that 38.7 and 37.5% of the markers affecting PP and MY, respectively, also affected PY. Of the markers affecting PY, 68.9 and 76.5%, respectively, also affected PP and MY. Apparently, none of the significant markers affected PY exclusively, and only 6.5 and 16.0%, respectively, affected PP or MY exclusively. Thus, almost all significant markers, and by inference almost all QTL, had effects on at least 2 of the 3 traits.

Quantitative trait loci (QTL) mapping projects have been implemented mainly in the Holstein dairy cattle breed for several traits. The aim of this study is to map QTL for milk yield (MY) and milk protein percent (PP) in the Brown Swiss cattle populations of Austria, Germany, and Italy, considered in this study as a single population. A selective DNA pooling approach using milk samples was applied to map QTL in 10 paternal half-sib daughter families with offspring spanning from 1,000 to 3,600 individuals per family. Three families were sampled in Germany, 3 in Italy, 1 in Austria and 3 jointly in Austria and Italy. The pools comprised the 200 highest and 200 lowest performing daughters, ranked by dam-corrected estimated breeding value for each sire-trait combination. For each tail, 2 independent pools, each of 100 randomly chosen daughters, were constructed. Sire marker allele frequencies were obtained by densitometry and shadow correction analyses of 172 genome-wide allocated autosomal markers. Particular emphasis was placed on Bos taurus chromosomes 3, 6, 14, and 20. Marker association for MY and PP with a 10% false discovery rate resulted in nominal P-values of 0.071 and 0.073 for MY and PP, respectively. Sire marker association tested at a 20% false discovery rate (within significant markers) yielded nominal P-values of 0.031 and 0.036 for MY and PP, respectively. There were a total of 36 significant markers for MY, 33 for PP, and 24 for both traits; 75 markers were not significant for any of the traits. Of the 43 QTL regions found in the present study, 10 affected PP only, 8 affected MY only, and 25 affected MY and PP. Remarkably, all 8 QTL regions that affected only MY in the Brown Swiss, also affected MY in research reported in 3 Web-based QTL maps used for comparison with the findings of this study (http://www.vetsci.usyd.edu.au/reprogen/QTL_Map/; http://www.animalgenome.org/QTLdb/cattle.html; http://bovineqtl.tamu.edu/). Similarly, all 10 QTL regions in the Brown Swiss that affected PP only, affected only PP in the databases. Thus, many QTL appear to be common to Brown Swiss and other breeds in the databases (mainly Holstein), and an appreciable fraction of QTL appears to affect MY or PP primarily or exclusively, with little or no effect on the other trait. Although QTL information available today in the Brown Swiss population can be utilized only in a within family marker-assisted selection approach, knowledge of QTL segregating in the whole population should boost gene identification and ultimately the implementation and efficiency of an individual genomic program.

Controlling the false discovery rate (FDR) has been proposed as an alternative to controlling the genomewise error rate (GWER) for detecting quantitative trait loci (QTL) in genome scans. The objective here was to implement FDR in the context of regression interval mapping for multiple traits. Data on five traits from an F2 swine breed cross were used. FDR was implemented using tests at every 1 cM (FDR1) and using tests with the highest test statistic for each marker interval (FDRm). For the latter, a method was developed to predict comparison-wise error rates. At low error rates, FDR1 behaved erratically; FDRm was more stable but gave similar significance thresholds and number of QTL detected. At the same error rate, methods to control FDR gave less stringent significance thresholds and more QTL detected than methods to control GWER. Although testing across traits had limited impact on FDR, single-trait testing was recommended because there is no theoretical reason to pool tests across traits for FDR. FDR based on FDRm was recommended for QTL detection in interval mapping because it provides significance tests that are meaningful, yet not overly stringent, such that a more complete picture of QTL is revealed.

Many large, half-sib sire families are an integral component of chicken genetic improvement programs. These family structures include a sufficient number of individuals for mapping quantitative trait loci (QTL) at high statistical power. However, realizing this statistical power through individual or selective genotyping is yet too costly to be feasible under current genotyping methodologies. Genotyping costs can be greatly reduced through selective DNA pooling, involving densitometric estimates of marker allele frequencies in pooled DNA samples. When using dinucleotide microsatellite markers, however, such estimates are often confounded by overlapping "shadow" bands and can be confounded further by differential amplification of alleles. In the present study a shadow correction procedure provided accurate densitometric estimates of allele frequency for dinucleotide microsatellite markers in pools made from chicken purified DNA samples, fresh blood samples, and frozen-thawed blood samples. In a retrospective study, selective DNA pooling with thawed blood samples successfully identified two QTL previously shown by selective genotyping to affect resistance in chickens to Marek's disease. It is proposed that use of selective DNA pooling can provide relatively low-cost mapping and use in marker-assisted selection of QTL that affect production traits in chickens.

During the 1990s, various disturbances arose affecting broiler breeder females at entry into lay. These disturbances were associated with even slight overfeeding during release of feed restriction in this critical maturation period. The present experiment was carried out to gain some insight into the causes of these disturbances by comparing the effect of fast (FF) and slow (SF) release from feed restriction at entry into lay in 2 broiler breeder populations: B1980, representing the genetic level of 1980, and B2000, the genetic level of 2000. Under the FF treatment, B1980 entered lay 19.2 d earlier than B2000; this increased to 37.4 d earlier under SF. The B1980 population entered lay at virtually the same mean age for SF and FF, whereas B2000 entered lay 15.7 d earlier under the FF. Body weight at first egg were 2,621 g for the B1980 and 3,591 g for B2000. Differences in BW at first egg between feeding treatments within lines were minor. As a percentage of BW, ovary, oviduct, and follicle weights were the same for B1980 and B2000; breast weight was 14.9% for B1980 and 21.2% for B2000; abdominal fat pad weight was 5.37% for B1980 and 2.67% for B2000. Follicle weight and absolute difference in weight between successive follicles was greater in B2000 than in B1980. It is concluded that body fat content does not limit entry into lay, and that threshold BW for onset of sexual maturity of broiler breeder hens increased by about 1,000 g between 1980 and 2000, indicating a tight association between juvenile growth rate and threshold BW for onset of sexual maturity. It is also concluded that disturbances at entry into lay due to overfeeding are not due to smaller differences between successive follicles in B2000 compared with B1980. There are hints, however, that overfeeding may contribute to these disturbances by decreasing differences between successive follicles.

A selective DNA pooling approach was applied to identify QTL for conjugated linoleic acid (CLA), vaccenic acid (VA) and Δ(9) -desaturase (D9D) milk content in Italian Brown Swiss dairy cattle. Milk samples from 60 animals with higher values (after correction for environmental factors) and 60 animals with lower values for each of these traits from each of five half-sib families were pooled separately. The pools were genotyped using the Illumina BovineSNP50 BeadChip. Sire allele frequencies were compared between high and low tails at the sire and marker level for SNPs for which the sires were heterozygous. An r procedure was implemented to perform data analysis in a selective DNA pooling design. A correction for multiple tests was applied using the proportion of false positives among all test results. BTA 19 showed the largest number of markers in association with CLA. Associations between SNPs and the VA and Δ(9) -desaturase traits were found on several chromosomes. A bioinformatics survey identified genes with an important role in pathways for milk fat and fatty acids metabolism within 1 Mb of SNP markers associated with fatty acids contents.

Previous studies indicate that responsiveness to photoperiod (PR) has deteriorated in White Rock heavy breed females and males, and that selection for increased PR in females has a positive effect on egg production. In order to determine whether PR can be affected by selection in males, a two-way selection experiment for high and low PR, as expressed through early and late onset of mature semen production under suboptimal photoperiod, was implemented in White Rock heavy breed males. In each selection line, the selected males in each generation were mated to unselected females of the same line. After four generations of selection, males and females of the two selection lines did not differ significantly in 6-wk body weight. Males of the high-PR line, however, achieved mature semen production 18.9 d earlier (P < 0.01) and at a body weight 587 g lighter (P < 0.01) than the males of the low-PR line. Females of the high-PR line came into lay 25.9 d earlier (P < 0.01) and at a body weight 375 g lighter (P < 0.01) than females of the low-PR line; they also produced 13.9 more eggs over a 14-wk test period (P < 0.01). These results show that it is possible to affect PR by selection in males, with parallel effects on female PR and reproductive performance. This result carries the potential of improving reproductive performance of male and female broiler chickens through mass selection for early sexual maturity among males.

SSCP analysis of the bovine growth hormone (bGH) gene in Israel Holstein dairy cattle uncovered five intragenic haplotypes, denoted A to E. Of these, Haplotype E differed from the others at six fragments; one of which corresponded to the polymorphic MspI site in intron III, at which haplotype E carried the disabled MspI (-) allele. Haplotype E was observed in a single sire only, carrying haplotype A as the second bGH allele. In 523 daughters of this sire genotyped for the MspI polymorphism, heterozygous (+/-) as compared to homozygous (+/+) daughters, showed a significant increasing effect on protein percentage and kg protein per year; and a decreasing effect (P < 0.10) on milk somatic cell counts (MSSC). None of the daughters were homozygous (-/-), indicating that the frequency of this allele in the general population was essentially zero. Calculated skewness (g1) values for the two daughter groups differed significantly with (+/-) daughters showing negative skewness (in the direction of lower protein percentage), and (+/+) daughters positive skewness (in the direction of higher protein percentage). The direction of skewness in each group is indicative of the presence of a QTL having an increasing effect on milk protein percentage in coupling linkage with the MspI (-) allele in this sire, but at some distance from it. Maximum likelihood estimates of the proportion of recombination (r) between the putative QTL and bGH, and the allele substitution effect at the QTL (d), were r = 0.33, a = 0.07% protein, with standard errors 0.058 and 0.009% protein, respectively.

Selection for high and low threshold weight for onset of lay (ThrWtLay), carried out in a broiler line over six generations, was previously found to increase reproductive performance in the low line (LL). Because of the potential importance of this effect, a two-generation replication of the original experiment was carried out using a modern broiler line. Selection was on the basis of ThrWtLay, measured as body weight at first egg, following gradual release from feed restriction. The total response to selection over two generations was 382 g, giving a realized heritability of .42. The difference in 6-wk body weight of the two lines was +19 g in favor (P > .05) of the high line (HL). Reproductive performance was measured in the S2 generation and in the first (R1) generation of relaxed selection. On the average, age at first egg of LL was 17.6 d earlier, and prepeak, postpeak, and total egg production of LL to a fixed age was 9.9, 1.1, and 11.1 eggs greater, respectively, than that of HL. The differences in age at first egg, prepeak, and total egg production were significant; those in postpeak production were not. There was a difference of 1.1 g in favor (P > .05) of HL for egg weight. Thus, the results of this short-term selection experiment are broadly consistent with those of the original, long-term selection. Namely, ThrWtLay responded strongly to selection, with a powerful accompanied response in age at onset of lay and in prepeak egg production, and only a small effect on 6-wk body weight. However, in contrast to the results obtained previously, LL in the present experiment showed only a small increase (P > .05) in postpeak production relative to HL. Nevertheless, although an effect on postpeak production was not obtained in the present experiment, the results do provide general support for the previously expressed view that selection for early onset of lay, on release from feed restriction, may provide a means of increasing photoperiodic drive and consequent reproductive performance of broiler breeders.

Avian eggshell quality is an important trait for commercial egg production, as the eggshell is the primary packaging material and antimicrobial barrier for the internal food resource. Strong eggshells are essential to ensure that eggs can reach their final destination without damage. Ovocalyxin-32 (OCX32) is a matrix protein found within the outer layers of the eggshell and in the cuticle. Numerous reports in the literature have identified association between variants in the gene encoding this protein, OCX32, and various eggshell quality traits. Thus, OCX32 is a candidate gene for selection for eggshell traits in commercial poultry populations. Sequencing of exons 2-6 of the OCX32 gene in eight elite brown and white eggshell commercial egg-laying lines revealed 28 SNPs and one SNP/indel. Eighteen of these SNPs were predicted to alter the amino acid sequence of the protein. Clusters of SNPs in complete linkage disequilibrium were found in both exons 2 and 6. A total of 19 different versions or protein-sequence haplotypes of the OCX32 protein were inferred, revealing considerable variation within commercial lines. Genotypes for 13 of the SNPs were determined for 330-1819 individuals per line. Trait association studies revealed a significant effect of OCX32 on shell color in white egg lines and line-specific significant effects on albumen height, early egg weight, puncture score, and yolk weight. Three of the lines showed a significant change in OCX32 frequency over time, indicating selection pressure for certain variants of this gene during the breeding program.

Summary We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein-Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein-Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP.

The main force driving gene mapping in domestic animals, is the potential for using gene maps as a means of identifying and mapping the genetic loci responsible for genetic variation in traits of economic importance. The ultimate objective is utilizing this information for marker‐assisted selection (MAS) using DNA level polymorphisms. This overview considers: (1) The need for MAS, (2) The relationship of gene mapping to MAS, (3) Implementing MAS. Examples illustrating the potential contribution of MAS to animal genetic improvement are presented, including (I) Preselection of candidate bulls for progeny testing in dairy cattle improvement, (2) Introgression of trypanotolerance from N'Dama to other cattle breeds, and (3) Improvement of a successful layer cross.

Minisatellites, microsatellites, and short random oligonucleotides all uncover highly polymorphic DNA fingerprint patterns in Southern analysis of genomic DNA that has been digested with a restriction enzyme having a 4-bp specificity. The polymorphic nature of the fragments is attributed to tandem repeat number variation of embedded minisatellite sequences. This explains why DNA fingerprint fragments are uncovered by minisatellite probes, but does not explain how it is that they are also uncovered by microsatellite and random oligonucleotide probes. To clarify this phenomenon, we sequenced a large bovine genomic BamHI restriction fragment hybridizing to the Jeffreys 33.6 minisatellite probe and consisting of small and large Sau3A-resistant subfragments. The large Sau3A subfragment was found to have a complex architecture, consisting of two different minisatellites, flanked and separated by stretches of unique DNA. The three unique sequences were characterized by sequence simplicity, that is, a higher than chance occurrence of tandem or dispersed repetition of simple sequence motifs. This complex repetitive structure explains the absence of Sau3A restriction sites in the large Sau3A subfragment, yet provides this subfragment with the ability to hybridize to a variety of probe sequences. It is proposed that a large class of interspered tracts sharing this complex yet simplified sequence structure is found in the genome. Each such tract would have a broad ability to hybridize to a variety of probes, yet would exhibit a dearth of restriction sites. For each restriction enzyme having 4-bp specificity, a subclass of such tracts, completely lacking the corresponding restriction sites, will be present. On digestion with the given restriction enzyme, each such tract would form a large fragment. The largest fragments would be those that contained one or more long minisatellite tracts. Some of these large fragments would be highly polymorphic by virtue of the included minisatellite sequences; by virtue of their complex structure, all would be capable of hybridizing to a wide variety of probes, uncovering a DNA fingerprint pattern.

The association of cell chimerism with the freemartin condition, and of the absence of cell chimerism with normal female development, was confirmed by PCR amplification of a Y‐chromosome fragment in blood leukocytes and hair roots of cattle females co‐twin to males.

Results of a human observer performance study using a new ultrasound contrast‐detail (CD) phantom are reported. The new phantom allows estimates of the fundamental statistical uncertainties involved in CD analysis. Results of these experiments show that observers generally considered to be ‘‘trained’’ require experience at the specific task of low‐contrast target detection under signal known exactly (SKE) conditions, and that observers require an orientation period at the beginning of each observation session to obtain stable responses. The results obtained in this study can be used to estimate the number of independent images, observers, and repeat observation sessions required for a desired uncertainty in CD curves, and show that 10% fractional standard deviations are obtainable with modest observer effort.

Mastitis is an important and common dairy cattle disease affecting milk yield, quality, and consumer safety as well as cheese yields and quality. Animal welfare and residues of the antibiotics used to treat mastitis cause public concern. Considerable genetic variation may allow selection for increased resistance to mastitis. Because of high genetic correlation to milk somatic cell score (SCS), SCS can serve as a surrogate trait for mastitis resistance. The present study intended to identify quantitative trait loci (QTL) affecting SCS in Israeli and Italian Holstein dairy cattle (IsH and ItH, respectively), using selective DNA pooling with single and multiple marker mapping. Milk samples of 4,788 daughters of 6 IsH and 7 ItH sires were used to construct sire-family high- and low-tail pools, which were genotyped at 123 (IsH) and 133 (ItH) microsatellite markers. Shadow correction was used to obtain pool allele frequency estimates. Frequency difference between the tails and empirical standard error of D, SE(D), were used to obtain P-values. All markers significant by single marker mapping were also significant by multiple marker mapping, but not vice versa. Combining both populations, 22 QTL on 21 chromosomes were identified; all corresponded to previous reports in the literature. Confidence intervals were set by chi-squared drop method. Heterozygosity of QTL was estimated at 44.2%. Allele substitution effects ranged from 1,782 to 4,930 cells/mL in estimated breeding value somatic cell count units. Most (80%) of the observed variation in estimated breeding value somatic cell score could be explained by the QTL identified under the stringent criteria. The results found here can be used as a basis for further genome-wide association studies for the same trait.

Great interest was aroused by reports, based on microsatellite markers, of high levels of statistically significant long-range and nonsyntenic linkage disequilibrium (LD) in livestock. Simulation studies showed that this could result from population family structure. In contrast, recent SNP-based studies of livestock populations report much lower levels of LD. In this study we show, on the basis of microsatellite data from four cattle populations, that high levels of long-range LD are indeed obtained when using the multi-allelic D′ measure of LD. Long-range and nonsyntenic LD are exceedingly low, however, when evaluated by the standardized chi-square measure of LD, which stands in relation to the predictive ability of LD. Furthermore, specially constructed study populations provided no evidence for appreciable LD resulting from family structure at the grandparent level. We propose that the high statistical significance and family structure effects observed in the earlier studies are due to the use of large sample sizes, which accord high statistical significance to even slight deviations from asymptotic expectations under the null hypothesis. Nevertheless, even after taking sample size into account, our results indicate that microsatellites testify to the presence of usable LD at considerably wider separation distances than SNPs, suggesting that use of SNP haplotypes may considerably increase the usefulness of a given fixed SNP array.

While rearing birds in confinement and at high density are very successful practices for producing poultry meat and eggs, these conditions may promote the spread of infectious diseases. Consequently, the poultry industry places greatemphasis on disease control measures, primarily at the animal husbandry level. The field of genomics offers great promise to complement these current control measures by providing information on the molecular basis for disease, disease resistance, and vaccinal immunity. This briefly summarizes some of our efforts to apply several genomic and functional genomics approaches to identify genes and pathways that confer genetic resistance to Marek's disease (MD), a herpesvirus-induced T cell lymphoma of chickens. By utilizing the "top-down" approach of QTL to identify genomics regions, and integrating it with "bottom-up" approaches of transcript profiling and Marek's disease virus (MDV)-chicken protein-protein interactions, three genes that confer resistance to MD are revealed, plus a number of other positional candidate genes of high confidence. These genes can be further evaluated in poultry breeding programmes to determine if they confer genetic resistance to MD. This integrative genomics strategy can be applied to other infectious diseases. The impact of the genome sequence and other technological advancements are also discussed.

Parentage determination in cattle by means of DNA fingerprints is examined at a theoretical level and its implementation illustrated by way of a practical example.

There is considerable interest in bovine DNA-level polymorphic marker loci as a means of mapping quantitative trait loci (QTL) of economic importance in cattle. Progeny of a sire heterozygous for both a marker locus and a linked QTL, which inherit different alleles for the marker, will have different trait means. Based on this, power to detect QTL, as a function of QTL effect, heritability of the trait, and number of animals tested was determined for 1) daughter design, marker genotype and quantitative trait values assessed on daughters of sires heterozygous for the markers; and 2) granddaughter design, a newly devised alternative design in which marker genotype is determined on sons of heterozygous sires and quantitative trait value measured on daughters of the sons. For equal numbers of assays, power increased with the number of daughters per sire (design 1) and sons per grandsire (design 2). For equal power and heritability less than or equal to .2, design 2 required half as many marker assays as design 1, e.g., with heritability of .2, QTL effect of .2 SD units, and type 1 error of .01, power was .70 if 400 daughters of each of 10 sires were assayed for the markers and .95 if markers were assayed on 100 sons of each of 20 sires with 50 granddaughters per son.

A theoretical analysis of the potential benefits of marker-assisted selection (MAS) of candidate bulls prior to entry into a young sire progeny testing programme was carried out. It is assumed that quantitative trait loci (QTL) affecting milk production have been mapped with respect to known genetic markers, and MAS is based on evaluation of elite sires in order to identify marker alleles in coupling to favourable or unfavourable QTL alleles. Candidate bulls, descendants of the elite sire will then be selected, prior to conventional progeny testing, on the basis of the marker alleles derived from the elite-sire ancestor.The analysis considers recombination between marker and QTL, the difficulty of tracing specific marker alleles from sire to progeny, and the expectation that MAS, in practice, will be implemented in the grandsons, rather than in the sons of elite sires. It is shown that MAS of candidate bulls, based on the use of a single diallelic marker in linkage to a QTL will have only a negligible effect on the rate of genetic progress. Increases of 15 to 20% in the rate of genetic gain, however, can be obtained by the use of single polyallelic markers, and increases of 20 to 30% can be obtained by utilizing haplotypes of diallelic or polyallelic markers.

When heritability of the trait under investigation is low, replicated progenies can bring about a major reduction in the number of individuals that need to be scored for marker genotype in determining linkage between marker loci and quantitative trait loci (QTL). Savings are greatest when heritability of the trait is low, but are much reduced when heritability of the quantitative trait is moderate to high. Required numbers for recombinant inbred lines will be greater than those required for a simple F2 population when heritabilities are moderate to high and the proportion of recombination between marker locus and quantitative trait locus is substantial.

Length variation at the BTGL1 variable number of tandem repeat (VNTR) locus, which includes both minisatellite and microsatellite motifs, was examined in a wide sample of cattle. A total of 22 alleles were uncovered. The distribution of allele size variation implicated mechanisms involving both minisatellite and microsatellite sequences. This was confirmed by direct sequencing of two alleles. Differences between the two alleles involved repeat number variation of microsatellite motifs and a complex event involving the minisatellite motif, but point mutations were not observed.

We have developed a new contrast detail hantom for evaluating the low contrast Zetection ca abilities of medical ultrasound scanners. geliminary tests. show that this design results in significant1 improved human different phantom design. observer performance over t 1 at reported for a

Partial discharge measurements are used to validate the integrity of the insulation system when commissioning gas-insulated switchgear and lines (GIS, GIL). On the other hand, an increasing population of service aged GIS equipment has reached its originally projected lifetime. On-line partial discharge measurements utilizing acoustic as well as UHF sensors help keeping such equipment in service. External ring antennas, window sensors, or embedded sensors allow survey type measurements and monitoring of the partial discharge activity in the UHF range. Acoustic measurements offer excellent sensitivity with so-called bouncing particles. Field experience applying a compact instrument that combines the application of UHF and ultrasonic measurements is presented.

Phase resolved partial discharge measurements offer excellent possibilities to characterize the properties of defects in insulation materials. The appearance of the partial discharge pattern reflects the defect's geometry, the availability of the initial electron, and the properties of the contributing materials. With partial discharge measurements on large power transformers the complexity of the winding has a strong impact on the high frequency properties of the transformer and, thus, on the applicability and range of a charge impulse calibration in different frequency bands. Especially, when performing field measurements, using elevated frequencies offers sensitive partial discharge measurements even in electromagnetically polluted environments. However, the influence of effects such as attenuation, reflection, and cross coupling must be considered and evaluated both in the frequency and the time domain.

Numerous studies have found a large number of QTL associated with productive and functional traits in the cattle genome. Several Countries have already established research programs aiming at identification and exploitation of QTLs in dairy cattle (Bovenhuis and Schrooten 2002). However, the published results are not directly exploitable for MAS, as commercial interests limit the information in the literature, and because marker-QTL phase is specific to each family.

The effects of phase aberration in extracorporeal shock-wave lithotripsy (ESWL) were investigated. Some patients undergoing these treatments experience focal damage to normal soft tissue in areas away from the intended treatment site. The authors hypothesized that some of the reported soft tissue damage may be caused by mislocation of the focus due to phase aberration of the shock wave in fat layers. This hypothesis was tested by measuring acoustic pressure distributions under four propagational conditions involving the type of medium and type of aberrating layer. Shock-wave pressure distributions were measured in water and in an attenuating medium. A very durable hydrophone was used and shown to survive more than 6000 shocks. The properties of the attenuating medium, a description of the hydrophone, and the observed effects of phase aberration in shock-wave propagation are reported. >

The effects of feed restriction and photoperiod on body weight (WTSXM) and age (ASXM) at onset of mature semen production in males and onset of lay in females of a broiler female line were examined. Feeding treatments were as follows: ad libitum (AL) and quantitative feed restriction (QR). Photoperiod treatments were as follows: open shed (OS), in which the chicks were reared under naturally increasing daylight with supplemental light; dark room (DR), in which chicks were reared under short days, gradually increasing from 6 h of light (L) to 11.5L; and dark room to open shed (DR-OS), in which chicks reared under short days in the dark room were transferred to the open shed at 149 d. Treatment effects were similar in direction in males and females, suggesting similar control of entry into reproduction of the two sexes, although within a given treatment, males matured earlier than females. Effects of feeding and photoperiod treatments were additive. Relative to QR, the AL feeding treatment increased WTSXM by 832 g for males and 1,089 g for females; ASXM was decreased by 15.8 d for males and 9.3 d for females. Relative to OS, the DR photoperiod increased WTSXM by 591 g for males and 513 g for females; ASXM was increased by 17.5 d for males and 26.8 d for females. The DR-OS photoperiod increased WTSXM by 86 and 169 g for males and females, respectively; ASXM was increased by 6.1 d and 4.9 d, respectively. Under DR, the delay in onset of sexual maturity caused by QR was not due to failure to reach threshold body weight or age and, hence, appears to have resulted from the feed restriction itself. A similar delay for QR was found under OS but might have been due to failure to reach threshold body weight. It is speculated that the delay in onset of sexual maturity caused by feed restriction may be an ecological adaptation or, alternatively, a result of nutritional imbalance.

Drosophila melanogaster sex peptide (SP) and Ductus ejaculatorius peptide (DUP99B) are male pheromones transferred in the seminal fluid to the female during copulation. Both reduce sexual receptivity and stimulate oviposition in females. The presence of high-affinity SP and DUP99B binding sites in the female were investigated by incubation of cryostat tissue sections with (125)I-iodinated peptides and subsequent autoradiography. We found that in adult females radiolabeled SP and DUP99B bind to peripheral nerves, the subesophageal ganglion, the cervical connective, to discrete parts of the thoracic ganglion, and to the genital tract. Weak and uniform labeling was detected in the neuropil of the brain and the thoracic ganglion. The labeling pattern in the nervous system suggests binding of the peptides to sensory afferents or glial cells. Scatchard analysis of the binding of (125)I-DUP99B to antennal nerves yielded a dissociation constant K(d) of 6.4 nM. Competition experiments with peptide fragments show that the peptides bind with their homologous C-terminal regions. Binding sites in the nervous system of females are established throughout sexual maturation. Prominent binding of the peptides to afferent nerves suggests modification of sensory input.

A consensus linkage map has been developed in the chicken that combines all of the genotyping data from the three available chicken mapping populations. Genotyping data were contributed by the laboratories that have been using the East Lansing and Compton reference populations and from the Animal Breeding and Genetics Group of the Wageningen University using the Wageningen/Euribrid population. The resulting linkage map of the chicken genome contains 1889 loci. A framework map is presented that contains 480 loci ordered on 50 linkage groups. Framework loci are defined as loci whose order relative to one another is supported by odds greater then 3. The possible positions of the remaining 1409 loci are indicated relative to these framework loci. The total map spans 3800 cM, which is considerably larger than previous estimates for the chicken genome. Furthermore, although the physical size of the chicken genome is threefold smaller then that of mammals, its genetic map is comparable in size to that of most mammals. The map contains 350 markers within expressed sequences, 235 of which represent identified genes or sequences that have significant sequence identity to known genes. This improves the contribution of the chicken linkage map to comparative gene mapping considerably and clearly shows the conservation of large syntenic regions between the human and chicken genomes. The compact physical size of the chicken genome, combined with the large size of its genetic map and the observed degree of conserved synteny, makes the chicken a valuable model organism in the genomics as well as the postgenomics era. The linkage maps, the two-point lod scores, and additional information about the loci are available at web sites in Wageningen (http://www.zod.wau.nl/vf/ research/chicken/frame_chicken.html) and East Lansing (http://poultry.mph.msu.edu/).

Previous studies using SSCP and PCR-RFLP methodologies uncovered nine polymorphic sites within the bGH gene, defining eight intragenic haplotypes falling into two main groups. In the present study we report the DNA sequence of these eight haplotypes. A total of 1494 bp were sequenced uncovering a total of 12 sequence variants. Haplotypes within groups differed among themselves at one or two sites, compared across groups, haplotypes of the two groups differed consistently at six sites, each of which was monomorphic within the respective groups. This comes to 4 differentiating sites per kb, suggesting that the two haplotype groups began to diverge about 400,000 years ago. This corresponds approximately to the estimated time of divergence of the Bos taurus and Bos indicus lineages, raising the possibility, supported by other evidence, that the two haplotype classes represent taurine and indicine haplotypes, respectively. Nucleotide sequence divergence of taurine and indicine genomes of this magnitude has far reaching implications with respect to QTL mapping and marker assisted selection in breeds derived from taurine x indicine crosses.

SSCP analysis of the bovine growth hormone (bGH) gene in Israel Holstein dairy cattle uncovered five intragenic haplotypes, denoted A to E. Of these, Haplotype E differed from the others at six fragments; one of which corresponded to the polymorphic MspI site in intron III, at which haplotype E carried the disabled MspI (-) allele. Haplotype E was observed in a single sire only, carrying haplotype A as the second bGH allele. In 523 daughters of this sire genotyped for the MspI polymorphism, heterozygous (+/-) as compared to homozygous (+/+) daughters, showed a significant increasing effect on protein percentage and kg protein per year; and a decreasing effect (P0.10) on milk somatic cell counts (MSSC). None of the daughters were homozygous (-/-), indicating that the frequency of this allele in the general population was essentially zero. Calculated skewness (g1) values for the two daughter groups differed significantly with (+/-) daughters showing negative skewness (in the direction of lower protein percentage), and (+/+) daughters positive skewness (in the direction of higher protein percentage). The direction of skewness in each group is indicative of the presence of a QTL having an increasing effect on milk protein percentage in coupling linkage with the MspI (-) allele in this sire, but at some distance from it. Maximum likelihood estimates of the proportion of recombination (r) between the putative QTL and bGH, and the allele substitution effect at the QTL (d), were r = 0.33, a = 0.07% protein, with standard errors 0.058 and 0.009% protein, respectively.