Review: Assessment of completeness of reporting in intervention studies using livestock: an example from pain mitigation interventions in neonatal piglets

Accurate and complete reporting of study methods, results and interpretation are essential components for any scientific process, allowing end-users to evaluate the internal and external validity of a study. When animals are used in research, excellence in reporting is expected as a matter of continued ethical acceptability of animal use in the sciences. Our primary objective was to assess completeness of reporting for a series of studies relevant to mitigation of pain in neonatal piglets undergoing routine management procedures. Our second objective was to illustrate how authors can report the items in the Reporting guidElines For randomized controLled trials for livEstoCk and food safety (REFLECT) statement using examples from the animal welfare science literature. A total of 52 studies from 40 articles were evaluated using a modified REFLECT statement. No single study reported all REFLECT checklist items. Seven studies reported specific objectives with testable hypotheses. Six studies identified primary or secondary outcomes. Randomization and blinding were considered to be partially reported in 21 and 18 studies, respectively. No studies reported the rationale for sample sizes. Several studies failed to report key design features such as units for measurement, means, standard deviations, standard errors for continuous outcomes or comparative characteristics for categorical outcomes expressed as either rates or proportions. In the discipline of animal welfare science, authors, reviewers and editors are encouraged to use available reporting guidelines to ensure that scientific methods and results are adequately described and free of misrepresentations and inaccuracies. Complete and accurate reporting increases the ability to apply the results of studies to the decision-making process and prevent wastage of financial and animal resources.     

Genetic diversity and molecular fingerprinting of Prunus cerasus var. austera from central Italy

In central Italy, Prunus cerasus var. austera is cultivated as small stands or scattered trees in marginal areas for the production of jam and wine. Thanks to the healthy attributes of its products and its ability to grow in different environmental conditions, this variety has gained new interest in the development of marginal areas. We assessed the level of the genetic variability of P. cerasus var. austera germplasm from central Italy and identified a ‘core collection’ representative of the present genetic diversity. A total of 161 trees, morphologically identified as var. austera, and one tree, identified as var. caproniana were collected and genotyped by 14 SSRs. Two individuals provided by a commercial plant nursery, one of P. cerasus var. caproniana and one of P. cerasus var. austera, were used as control. Thirteen SSRs presented private alleles in austera. Seven individuals morphologically identified as austera revealed private alleles specific to caproniana. The PCoA and Bayesian clustering analysis showed a main genetic group including var. austera, while a second group included all the caproniana-like genotypes. A core collection of 31 trees (46% of austera genotypes) was selected. This study can be considered as a starting point for future investigations on this variety.     

Endoparasitic flies,pollen-collection by bumblebees and a potential host-parasite conflict

Summary Conopid flies (Conopidae, Diptera) are common larval parasites of bumblebees. The larva develops inside the abdomen of workers, queens and males. Development is completed within 10–12 days after oviposition when the host is killed and the parasite pupates in situ. Development results in parasitised bees becoming unable to carry large loads of nectar, as the conopid larvae reside where the honey crop is normally located. Furthermore, an addition to the bee's unloaden body mass is likely (average larval weight reached at pupation by the common parasite species Sicus ferrugineus: ±SD 36.3±12.3 mg, n=59; by Physocephala rufipes: 55.8±16.9 mg, n=108). We here asked whether the propensity of workers of the bumblebee Bombus pascuorum to collect nectar rather than pollen is related to the presence of conopid larvae. For samples of bees (n=2254 workers) collected over 3 years of field studies in northwestern Switzerland, there was no difference in the frequency of bees caught as pollen collectors among parasitised (38.1% of cases, n=210) as compared to non-parastised bees (43.9%, n=360) ( ²=1.83, n.s.). However, compared to the non-parasitised bees (n=360), those hosts containing a third (last) instar larva (n=9) were less likely to collect pollen than expected by chance ²=6.91, P=0.003. Similarly, hosts with short survival time between capture and being killed by the developing larva (which hence must have harboured a late instar parasite at time of capture) were less likely to collect pollen (8%, n=25) than those found not parasitised (37.6%, n=891 ²=9.16, P<0.001). Late instar larvae grow so big that they fill the entire abdomen. Although there was also a tendency for presumably older bees to collect less pollen, this is unlikely to explain the observations. We also discuss whether these changes in foraging behaviour of bumblebees may reflect a host-parasite conflict over the type of resource to be collected.     

Allozyme and morphological variability,outcrossing rate and core collection formation in lentil germplasm

Summary A survey of qualitative genetic variation at 3 morphological trait loci, 17 isozyme loci and a putative isozyme locus (amylase) was made for 105 lentil (Lens culinaris Medikus) germplasm accessions from Chile, Greece and Turkey. New alleles were found for Lap-1, Me-2, Pgm-c, Pgm-p and 6-Pgd-c. The average proportion of polymorphic loci per population was 0.19, with a range of 0 to 0.42 over populations. Germplasm from Chile was equally variable to that from Greece and Turkey on the basis of individual loci and in a multilocus sense, despite its post-Columbus introduction to the New World. Evidence was found from associations between allelic states at different loci of a complex multilocus structure of lentil populations. A single multilocus genotype represented 10.2% of all plants sampled. The rate of outcrossing varied from 2.2% and 2.9% in Turkish and Greek landraces to 6.6% among Chilean populations. Using the survey data, a random sampling strategy for core collection formation was compared with two stratified sampling methods. The advantage of stratified sampling over random sampling was only significant at P=0.28.     

Genetic structure of Glycine canescens,a perennial relative of soybean

Summary Allozyme variation as detected by starch gel electrophoresis was used to assess the extent and spatial organization of genetic variation across the entire range of Glycine canescens sensu lato. Eleven enzyme systems were assayed in 116 accessions of this taxon and 102 alleles were detected at a total of 31 loci. Eighty-one percent of loci were polymorphic. Most of this variation occurred between and very little within accessions. Three major groupings were detected. These groupings (groups 1, 2, and 3) also differed with respect to mean seed size and their geographic distribution. A further ten accessions stood out from these distinct groups. These accessions were most closely related to group 3 but were variable among themselves. In general, they were collected from highly dissected terrain, often in the remote interior of the continent. A final group of 18 problematic accessions (group X), originally tentatively identified as G. canescens on morphological grounds, was shown to be isozymically distinct from this species and was reclassified as one form of the polytypic species G. clandestina.     

Prediction of total fecal output in sheep fed silage using the Captec chrome controlled-release capsule

Six Finnish wethers (average weight, 52.3 kg) were used to determine the effectiveness of a controlled-release Cr₂O₃ bolus and the internal marker acid insoluble ash (AIA) for predicting fecal output. Wethers were fed grass silage for ad libitum intake. Each wether was dosed orally with one continuous-release Cr₂O₃ bolus (CRC) on the first day of the experiment. Chronology of the trial was as follows: Day 0 to 14, marker adaptation period; Day 15 to 21, total fecal collection; Day 22 to 23, fecal grab sampling every 4 h; Day 25 to 35, once-daily fecal grab sampling. Accuracy of marker-estimated fecal output derived from each method was compared within a marker with total fecal collection values using a paired t-test. Concentrations of AIA and Cr varied (P < 0.10) between sampling times. Accuracy of fecal output estimates was better with the controlled-release Cr₂O₃ bolus (r = 0.97; P = 0.03) than with AIA (r = −0.08; P = 0.89). Grab samples taken once produced reliable (r = 0.96; P = 0.02) estimates of fecal output of silage-fed wethers using the controlled-release Cr₂O₃ bolus. The controlled-release Cr₂O₃ bolus is a better marker than acid-insoluble ash for predicting fecal output of silage-fed wethers.     

Linkages among RFLP,RAPD, isozyme,disease-resistance,and morphological markers in narrow and wide crosses of cucumber

An algorithm of automatic classification is proposed and applied to a large collection of perennial ryegrass wild populations from France. This method is based on an ascendant hierarchical clustering using the Euclidian distance from the principal components extracted from the variance-covariance matrix between 28 agronomic traits. A contiguity constraint is imposed: only those pairs of populations which are defined as contiguous are grouped together into a cluster. The definition of contiguity is based on a geostatistical parameter: the range of the variogramme, i.e. the largest distance above which the variance between pairs of population no longer increases. This method yields clusters that are generally more compact than those obtained without constraint. In most cases the contours of these clusters fit well with known ecogeographic regions, namely, for macroclimatic homogeneous conditions. This suggests that selective factors exert a major influence in the genetic differentiation of ryegrass populations for quantitatively inherited adaptive traits. It is proposed that such a method could provide useful genetic and ecogeographic bases for sampling a core collection in widespread wild species such as forage grasses.Institut National de la Recherche Agrononique     

热带林茎流收集及计算方法探索

热带林茎流收集及计算方法探索周光益,吴仲民,李意德,陈步峰（中国林科院热带林业研究所,广州５１０５２０）ＣｏｌｌｅｃｔｉｏｎａｎｄＣａｌｃｕｌａｔｉｏｎＭｅｔｈｏｄｓｆｏｒＳｔｅｍｆｌｏｗｉｎＴｒｏｐｉｃａｌＦｏｒｅｓｔ．￥ＺｈｏｕＧｕａｎｇｙｉ;Ｗ...     

Isozyme variation in germplasm accessions of the wild oat Avena sterilis L.

Summary Optimal exploitation of crop genetic resources requires a knowledge of the range and structure of the variation present in the gene pool of interest. Avena sterilis L., the cultivated oat progenitor, contains a store of genetic diversity that is readily accessible to the oat breeder. The objectives of the present paper were: (1) to evaluate isozyme polymorphisms in a sample of A. sterilis accessions from the U.S. National Small Grains Collection, (2) to analyze the distribution of isozyme diversity across the geographic range of the accessions, (3) to classify the accessions into groups based on isozyme variation, and (4) to suggest strategies for efficient sampling of this germplasm collection. One thousand and five accessions from 23 countries and 679 collection sites were screened for variation using 23 enzyme systems. Due to limited information about the genetic relationship among individual members of families of isozymes in hexaploid oat species, data were recorded solely for band presence. The frequencies of bands in accessions from the various countries were used to calculate the probability of genotypic identity (I_x.y), the probability of a unique genotype (U_x.y), and an adjusted polymorphic index (H_x). Accessions from Turkey and Lebanon had the largest polymorphic index values, Turkish and Moroccan accessions displayed the greatest numbers of bands. Accessions from Iran, Turkey, Iraq, and Lebanon had the largest mean probabilities of containing unique genotypes. Based on isozyme data, Turkey appeared to represent the center of diversity in this germplasm collection. Band frequencies calculated among countries were used in a principal component analysis. Accessions from Israel and Morocco clustered together; accessions from Iran, Iraq, Turkey, and Ethiopia formed another group; and Algerian accessions formed an outlying group. Several isozyme bands had a regional distribution. These results suggested that choosing accessions from countries based on their groupings in the principal component analysis should secure a greater range of diversity than sampling from the collection at random. Cluster analyses based on Jaccard's distances calculated for all pairwise combinations of the 1005 accessions revealed six broad genetic groups of accessions. Groups 1 and 6 contained accessions from many countries and encompassed half of all accessions. Groups 2 and 4 were heavily populated by accessions from Israel and Morocco. Groups 3 and 5 were composed almost exclusively of accessions from Iran, Iraq, and Turkey. By selecting representative accessions from these six groups, oat breeders could most effectively sample the range of genetic variation in this A. sterilis collection.     

Evaluation of five strategies for obtaining a core subset from a large genetic resource collection of durum wheat

The use of plant genetic resources contained in a large collection may be enhanced by specifying subsamples, called core samples. Five strategies for selecting a core sample from a collection of 3000 durum wheat accessions were applied and evaluated using four qualitative and eight quantitative spike characters. Each of the following strategies generated about 500 accessions for the core sample: random, random-systematic according to chronology of entry of the accessions into the collection, stratified by countryof-origin, stratified by log frequency by country-of-origin, and stratified by canonical variables. The first three strategies produced samples representative of the whole collection, but the remaining two produced the desired effect of increasing frequencies from less-represented countries-of-origin for several characters. The stratified canonical sample increased phenotypic variances. The quality of core samples is dependent upon good passport and evaluation data to partition the collection. The multivariate approach is extremely useful, but requires considerable data from the whole collection. Ecogeographic origin may be used in the absence of evaluation data on several characters to select useful core samples.