Screening of new lines of cereal grains for inclusion in Near Infra Red Scan calibrations

The project will provide enough data for a reliable and robust NIRs. It will more fully develop the in vitro method to enable less costly assessment of grains in the future. It will also provide a reliable assessment for DE which is the most expensive component of pig feed.

Assessment of internal quality attributes of mandarin fruit. 1. NIR calibration model development

The utility of near infrared spectroscopy as a non-invasive technique for the assessment of internal eating quality parameters of mandarin fruit (Citrus reticulata cv. Imperial) was assessed. The calibration procedure for the attributes of TSS (total soluble solids) and DM (dry matter) was optimised with respect to a reference sampling technique, scan averaging, spectral window, data pre-treatment (in terms of derivative treatment and scatter correction routine) and regression procedure. The recommended procedure involved sampling of an equatorial position on the fruit with 1 scan per spectrum, and modified partial least squares model development on a 720–950-nm window, pre-treated as first derivative absorbance data (gap size of 4 data points) with standard normal variance and detrend scatter correction. Calibration model performance for the attributes of TSS and DM content was encouraging (typical Rc2 of >0.75 and 0.90, respectively; typical root mean squared standard error of calibration of <0.4 and 0.6%, respectively), whereas that for juiciness and total acidity was unacceptable. The robustness of the TSS and DM calibrations across new populations of fruit is documented in a companion study.

Pitfalls and benefits of involving industry in fisheries research: A case study of the live reef fish industry in Queensland, Australia

Including collaboration with industry members as an integral part of research activities is a relatively new approach to fisheries research. Earlier approaches to involving fishers in research usually involved compulsory accommodations of research, such as through compulsory observer programs, in which fishers were seen as subjects of rather than participants in research. This new approach brings with it significant potential benefits but also some unique issues both for the researchers and the participating industry members. In this paper we describe a research project involving the Queensland Coral Reef Finfish Fishery that originated from industry and community concerns about changes in marketing practices in an established commercial line fishery. A key aspect of this project was industry collaboration in all stages of the research, from formulation of objectives to assistance with interpretation of results. We discuss this research as a case study of some of the issues raised by collaboration between industry and research groups in fisheries research and the potential pitfalls and benefits of such collaborations for all parties. A dedicated liaison and extension strategy was a key element in the project to develop and maintain the relationships between fishers and researchers that were fundamental to the success of the collaboration. A major research benefit of the approach was the provision of information not available from other sources: 300 days of direct and unimpeded observation of commercial fishing by researchers; detailed catch and effort records from a further 126 fishing trips; and 53 interviews completed with fishers. Fishers also provided extensive operational information about the fishery as well as ongoing support for subsequent research projects. The time and resources required to complete the research in this consultative framework were greater than for more traditional, researcher-centric fisheries research, but the benefits gained far outweighed the costs.

Resin defect impacts on the value of graded recovery and evaluation of technologies for internal defect detection in slash pine logs.

The key outcome will be to identify a technology that is practical to use to scan logs identified by the modelling as suspect or marginal for sawing and to confirm their unsuitability for value adding sawing by internal scanning.

Simultaneous prediction of acidity parameters (pH and titratable acidity) in Kefir using near infrared reflectance spectroscopy.

Acidity in terms of pH and titratable acids influences the texture and flavour of fermented dairy products, such as Kefir. However, the methods for determining pH and titratable acidity (TA) are time consuming. Near infrared (NIR) spectroscopy is a non-destructive method, which simultaneously predicts multiple traits from a single scan and can be used to predict pH and TA. The best pH NIR calibration model was obtained with no spectral pre-treatment applied, whereas smoothing was found to be the best pre-treatment to develop the TA calibration model. Using cross-validation, the prediction results were found acceptable for both pH and TA. With external validation, similar results were found for pH and TA, and both models were found to be acceptable for screening purposes.

Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum

Background Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘noise’ of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically. Results Progeny from defined genetic crosses of Tribolium castaneum (F4 and F19) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations. Conclusion We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.

A novel use of near infrared spectroscopy: ageing deepwater sharks

To age sharks, the growth bands in the shark vertebrae (like the rings in a tree) or on the spines in front of each dorsal fin (which only some sharks have) are manually counted using a microscope. This is time-consuming and is only possible on dead animals. NIR spectroscopy is shown to be able to detect age in dorsal fin spines of sharks and hand-held NIR spectroscopy units could potentially be used for ageing of sharks in the field, at sea, using a hand-held unit to scan the fin spine on a live animal.