A Comprehensive Genotype and Environment Assessment of Wheat Grain Ash Content in Oregon and Washington: Analysis of Variation

A comprehensive analysis of the variation in wheat grain ash content has not been previously conducted. This study assessed the relative contribution of genotype and environment to variation in ash content, with a particular aim of ascertaining the potential for manipulating the trait using contemporary adapted germplasm. A total of 2,240 samples were drawn from four years of multilocation field plots grown in the wheat production areas of Oregon and Washington states. Genotypes included commercial cultivars and advanced breeding lines of soft and hard winter, and soft and hard spring wheats with red and white kernel color, several soft white club wheats, and one soft white spring waxy wheat cultivar. In addition to ash, protein content, test weight, and Single Kernel Characterization System kernel hardness, weight and size were also measured. In total, 20 separate fully balanced ANOVA results were conducted. Whole model R² values were highly significant, 0.62–0.91. Nineteen of the 20 ANOVA results indicated significant genotype effects, but the effects were not large. In contrast, environment effects were always highly significant with F values often one to two orders of magnitude larger than the genotype F values. The grand mean for all samples was 1.368% ash. For individual data sets, genotype means across environments varied ≈0.1–0.3% ash. The genotypes judged noteworthy because they had the highest least squares mean ash content were OR9900553 and ClearFirst soft white winter, NuHills hard red winter, Waxy‐Pen and Cataldo soft white spring, and WA8010 and Lochsa hard spring wheats. Genotypes with lowest least squares mean ash were Edwin (club) soft white winter, OR2040073H hard red winter, WA7952 soft white spring, and WA8038 hard spring wheats. In conclusion, wheat grain ash is more greatly influenced by crop year and location than by genotype. However, sufficient genotype variation is present to plausibly manipulate this grain trait through traditional plant breeding.     

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

Background

Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation.

Results

In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP).

Conclusion

We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1].

     

Male reproductive traits and their relationship to reproductive traits in their female progeny: a systematic review

The overall objective of one of the major research programs in the Co-operative Research Centre (CRC) for Beef Genetic Technologies is to 'Improve female reproductive performance' in tropical, northern Australian beef cattle herds. To address this overall objective, a quantitative genetics project focused on investigation of male reproductive traits was designed and linked to three female reproduction-focussed projects, (i) discovery of genes associated with post-partum re-conception and age at puberty; (ii) expression of genes associated with post-partum re-conception; and (iii) early predictors of lifetime female reproductive performance. During the initial planning of this male reproductive traits project, the CRC Scientific Review Committee recommended that the research team investigate and evaluate potentially new, early-life (i.e able to be measured before 2 years of age) predictors of both male and female reproductive performance. To address this recommendation, the following was carried out: (i) criteria for selection of traditional and candidate traits were established; (ii) methodology for tabulation of potential traits/phenotypes that define male and female reproductive function was developed; and (iii) a systematic scientific review of early-life predictors of male and female fertility was prepared. This review concluded that although factors that might be useful in predicting male reproductive performance have been studied for many years, there was relatively little useful information available to meet the objectives of this review. It was also concluded that the direction of future research should be guided not only by previous research which was scarce, but also by speculative hypotheses arising from an understanding of the physiological, endocrinological and genetic processes active in reproduction. A small number of new traits were recommended in addition to traditional sperm morphology, sexual behaviour, anatomical structure and growth traits. Potential additional traits include measurement of gonadotrophin-releasing hormone-stimulated luteinizing hormone (GnRH-stimulated LH); inhibin; several seminal plasma proteins (osteopontin, spermadhesin and seminal plasma proteins BSP30 and phospholipase A(2) could be used in an index); 11β-hydroxysteriod dehydrogenase; and leptin. In addition, the potential also exists to screen animals for a number of genetic markers associated with age of puberty, follicular recruitment and ovulation rate and genes associated with bovine seminal plasma protein and testosterone production. Insulin-like growth factor-1 (IGF-1) measurements are included because of their association with growth parameters, and an additional analysis demonstrated associations with male and female reproductive traits. Some of these factors have been previously evaluated in small numbers of animals of various species under intensive management conditions. Therefore, there is a need to evaluate these factors in much larger numbers of beef cattle grazing semi-extensive tropical production systems in northern Australia to determine their value in improving beef cattle enterprise profitability through improved herd fertility.     

Technical note: Use of near-infrared reflectance spectroscopy to predict intake and digestibility in bulls and steers

Multiple fecal samples were collected from growing Angus bulls (264 to 419 kg of BW, 3.0 to 11.4 kg/d of DMI) to predict DMI of a corn-silage-based diet. Contemporaneous digestion trials were conducted with the same diet in 12 steers in yr 1 to 3 and bulls in yr 4. Near-infrared spectra from fecal samples (n = 730 from 282 growing bulls, n = 240 from 36 steers and 12 bulls for digestion trials) were obtained from dried and ground fecal samples, and modified partial least squares regression was used to develop equations to predict DMI and DM digestibility (DMD). Although mean predicted DMI of the growing bulls (7.52 ± 0.04 kg/d or 22.4 ± 0.1 g/kg of BW) was within 2% of mean measured DMI (7.63 ± 0.06 kg/d or 22.7 ± 0.1 g/kg of BW), the mean of paired differences within samples (0.11 ± 0.04 kg/d or 0.3 ± 0.1 g/kg of BW) was greater (P < 0.01) than zero. Measured DMD (72.3 ± 0.5%) was identical (P < 0.97) to predicted DMD (72.3 ± 0.5%), and DMD for bulls in the digestion trial did not differ (P < 0.27) from DMD for steers. Prediction of intake requires incorporation of some measured values from the set of fecal samples to be predicted. Lack of similarity between spectra of fecal grab samples from the growing bulls and daily fecal collection of steers and bulls in the digestion trials in this study indicates the need for further verification before prediction of DMD with fecal grab samples.     

Concurrent nephrosplenic entrapment and acquired inguinal herniation of the jejunum in a Standardbred stallion

A stallion presenting for surgical correction of an acquired inguinal hernia was also diagnosed with a nephrosplenic entrapment (NSE) intraoperatively. Surgical intervention resulted in a successful outcome. To date, these conditions have not been reported to occur simultaneously.