ASReml-SA | Rich Statistical Analysis Software Specially Designed for Linear Mixed Models

KWS

KWS is one of the world’s leading suppliers of seeds to the farming industry and it is therefore no surprise that research into plant breeding and seeds is a crucial part of their work. ## KWS value precision and security For centuries people have been breeding plants, trying to fine-tune individual plants to obtain or change a particular trait. Today plant breeders look at addressing concerns such as drought or environment tolerance, pesticide, herbicide, fungi or bacteria tolerance, improving nutritional value or increasing yields.  This, by definition, ranges from “classical” propagation techniques to the modern methods of molecular breeding and genetical modification. However, one thing is very apparent: the scientists engaged in any form of plant breeding need to be sure their data analysis is based on sound, solid and secure statistics. KWS is one of the world’s leading suppliers of seeds to the farming industry and it is therefore no surprise that research into plant breeding and seeds is a crucial part of their work. The research and development teams at KWS focus on yield, seed quality, resistance to disease and pests, enhancing the nutrient quality and improved processing capability of the plants. Recently the researchers at KWS decided to change their data analysis software portfolio by introducing Genstat. During the last 2 years main emphasis was put on establishing Genstat for statistical analysis of phenomic data from their field. Genstat was chosen, because it was possible to analyse data from trials with large Alpha Designs with the REML techniques. Plus, Genstat’s REML algorithm dealt with missing values in a more superior way than the previous software. REML itself can be used to analyse models with several types of error variation (multi-level models) and to fit models to correlated data like repeated measurements. Genstat’s powerful command language streamlined the data analyses, reducing the calculation time by at least 70%. Additionally Genstat’s efficient data handling meant that far less data pre-processing was needed. Genstat allows the full integration into automated analysis pipelines, thus decreasing calculation times by 30%. This allows the flexible addition of new statistical methods into the pipelines. KWS researchers use a wide variety of different factors in their trials, using Block Designs, Alpha Designs, Lattice, Split Plot, Multi factorial Experiments. Genstat allows the researchers to easily design and analyse these and other types of experiments. Genstat also effortlessly handles large and complex data sets, which will be essential for the analysis of genomic data and their association with phenomic informations. Combine these factors with Genstat’s ability to easily export and import data from other databases and the plant breeder has very powerful analysis tools. As well as the extensive technical capabilities of Genstat, KWS chose Genstat because of its history within agricultural science and research; it was originally designed by statisticians working on agricultural research at Rothamsted Research; where Fisher, Yates and Nelder (to mention but 3) developed statistical techniques that are central to modern statistics. Genstat’s connection with Rothamsted continues today. Developments in each new version of Genstat reflect the needs of the agricultural scientist, including ANOVA, design of experiments a host of multivariate analysis techniques and linear mixed model analysis. A huge variety and complexity of data analysis is possible in Genstat, and an understanding of the requirements of experiments in this area is reflected in the terminology and thinking behind Genstat. But Genstat’s history not only shows its suitability to any form of agricultural research but also shows the stability of its performance; it has been tried and tested for over 30 years. Coupled with the power and background of Genstat, VSNi were able to provide a bespoke consultancy service to KWS to assist with their specific needs; this is possible because our developers have been working with agricultural researchers and statistics for years. The VSNi statisticians were able to talk to the researchers at KWS, in their language to find more efficient ways to run their analyses. In a subject area that demands precision and security Genstat provides the data analysis solution that removes the unknowns surrounding the research. You can trust the statistics within Genstat, because it is developed by people who know and understand the issues in agricultural research today.

Nofima

Aquaculture is the name given to the farming of salt water and freshwater fish and marine animals. It is a rapidly growing division of farming across the world; reports from the UN’s FAO suggest that it has been growing more rapidly than any other area of animal food production.  A report published in September 2009 suggested that farm-reared fish accounted for 50% of world fish consumption. This rise in aquaculture production isn’t much of a surprise when you consider the emphasis on the health-giving properties of fish (particularly Omega-3 from oily fish) and the subsequent encouragement for people to eat more oily fish; and it’s certainly good news for the aquaculture producers across the world. However, growth of this level in any industry, whilst exciting and positive in many ways, also brings with it its own complications. The complexities of all types of farming mean that research and understanding is vital in helping the industry to grow safely as well as rapidly. This is particularly important if the current consumption levels of fish continue: the FAO predict that we will need an extra 27 million tonnes of fish by 2030 to meet the demand.  Any farmer will tell you of the importance of vaccination in controlling disease, and this is no different for fish farmers, or specifically Atlantic salmon farmers. Vaccinations against diseases such as furunculosis, vibriosis, cold-water vibriosis, winter ulcer and infectious pancreatic necrosis, which could otherwise decimate a farm, are vital in protecting the fish and farms and controlling these diseases in farmed Atlantic salmon. However, vaccinations can cause reactions at the injection site such as adhesions and discoloration, reduced appetite and growth, and in severe cases a downgrading of the carcass at market. Not only can this have an economic impact on the salmon farms, but also may create a negative perception of the farms with the general public. As with all aspects of farming the public is concerned not just with the food in question, but also of the welfare of the production animals, which means that breeding companies need to be sure of the actual physical health and safety of their fish. As with many aspects of farming and agriculture, all aspects of aquaculture are the subject of scientific research to enable better understanding and improved planning for the future, including prevention of disease and improved fish health. The results from challenge tests have indicated substantial genetic variation in disease resistance to a variety of bacterial and viral diseases (including some of those listed earlier), significant but relatively low genetic correlations among the different diseases and a high genetic correlation between the survival of non-vaccinated pre-smolts (smolts are young salmon as they migrate from freshwater to the sea) and the survival of older non-vaccinated full and half sibs under natural break-outs of the diseases. With this in mind Atlantic salmon breeding companies are looking at both the development of efficient vaccinations and the breeding of fish with higher disease resistance. The results from the challenge test research may suggest that genetic variation in immune systems might lead to genetic variation in innate disease resistance and variation in reactions to the vaccinations. One question researchers in this area need an answer to is whether there is significant genetic correlation between vaccine reactions and innate resistance, as this could mean a change of vaccine dose or a breeding programme to produce fish with the lowest reaction rate to vaccines and the highest natural resistance to diseases. And it is these issues that a recent project, undertaken by researchers from [Nofima Marin](http://www.nofima.no/marin/en), the [Norwegian School of Veterinary Scienc](http://www.veths.no/)e and [Aqua Gen AS](http://www.aquagen.no/En/Specialfolder/Latest_News/) and funded by the [Research Council of Norway](http://www.forskningsradet.no/servlet/Satellite?c=Page&cid=1177315753906&p=1177315753906&pagename=ForskningsradetEngelsk%2FHovedsidemal) (published in the Elsevier journal Aquaculture 287 (2009) 52-58) has looked at. Atlantic salmon were taken from farmed strains and from offspring of wild salmon, and reared at different farms. Data was collected on sex, size (at different stages), adhesion scores and melanin scores of fish at harvest size and survival data from challenge tests of their full- and halfsibs. The data collected was analysed using [ASReml](https://www.vsni.co.uk/software/asreml/) to fit a multivariate linear mixed animal model to obtain estimates for the variance and covariance components for the random effects of the studied traits. A single trait sire and dam model, which included the same fixed effects was used to obtain across year-class heritability estimates (using an alpha version of [ASReml 3](https://www.vsni.co.uk/software/asreml/)). Results from the project indicate that the severity of vaccine injuries in Atlantic salmon could be reduced through selective breeding. Additionally the relatively high correlation that was found between adhesion scores and melanin scores show that there is unlikely to be a need to select against both of these traits. The researchers warned that including an additional breeding trait objective would reduce the genetic gain for other traits, and therefore recommended that other solutions to the vaccine injuries be found, such as improved vaccines or vaccination procedures. The results also indicated a negative genetic correlation between body weight and adhesion or melanin score; however, these estimates are most likely biased towards the negative end of the scale, since vaccine injuries are expected to reduce growth rate for non-genetic reasons.  The study also indicated “no genetic association between resistance to furunuculosis and ISA (infectious salmon anaemia) and vaccine injuries”, which suggest that the vaccine injuries are caused by other aspects of the immune system, not associated with the genetic variation in innate resistance to these diseases.  Research of this kind is extremely important to the aquaculture industry to enable it to continue to develop, expand and improve, not just the industry, but the procedures, processes and systems associated with it. ASReml is widely respected and used in situations such as this. Our thanks to [Dr Bjarne Gjerde](http://www.nofima.no/marin/en/person/bjarne.gjerde) of [Nofima Marin](http://www.nofima.no/marin/en) for his help with this story. \<p>Testing\</p>