Publications by authors named "Alison B Smith"

5 Publications

  • Page 1 of 1

A Multi-Environment Trial Analysis of Frost Susceptibility in Wheat and Barley Under Australian Frost-Prone Field Conditions.

Front Plant Sci 2021 19;12:722637. Epub 2021 Aug 19.

School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA, Australia.

Low temperatures during the flowering period of cereals can lead to floret sterility, yield reduction, and economic losses in Australian crops. In order to breed for improved frost susceptibility, selection methods are urgently required to identify novel sources of frost tolerant germplasm. However, the presence of genotype by environment interactions (i.e. variety responses to a change in environment) is a major constraint to select the most appropriate varieties in any given target environment. An advanced method of analysis for multi-environment trials that includes factor analytic selection tools to summarize overall performance and stability to a specific trait across the environments could deliver useful information to guide growers and plant breeding programs in providing the most appropriate decision making-strategy. In this study, the updated selection tools approached in this multi-environment trials (MET) analysis have allowed variety comparisons with similar frost susceptibility but which have a different response to changes in the environment or vice versa. This MET analysis included a wide range of sowing dates grown at multiple locations from 2010 to 2019, respectively. These results, as far as we are aware, show for the first-time genotypic differences to frost damage through a MET analysis by phenotyping a vast number of accurate empirical measurements that reached in excess of 557,000 spikes. This has resulted in a substantial number of experimental units (10,317 and 5,563 in wheat and barley, respectively) across a wide range of sowing times grown at multiple locations from 2010 to 2019. Varieties with low frost overall performance (OP) and low frost stability (root mean square deviation -RMSD) were less frost susceptible, with performance more consistent across all environments, while varieties with low OP and high RMSD were adapted to specific environmental conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2021.722637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8417324PMC
August 2021

Genomic selection in multi-environment plant breeding trials using a factor analytic linear mixed model.

J Anim Breed Genet 2019 Jul;136(4):279-300

National Institute for Applied Statistics Research Australia, Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, New South Wales, Australia.

Genomic selection (GS) is a statistical and breeding methodology designed to improve genetic gain. It has proven to be successful in animal breeding; however, key points of difference have not been fully considered in the transfer of GS from animal to plant breeding. In plant breeding, individuals (varieties) are typically evaluated across a number of locations in multiple years (environments) in formally designed comparative experiments, called multi-environment trials (METs). The design structure of individual trials can be complex and needs to be modelled appropriately. Another key feature of MET data sets is the presence of variety by environment interaction (VEI), that is the differential response of varieties to a change in environment. In this paper, a single-step factor analytic linear mixed model is developed for plant breeding MET data sets that incorporates molecular marker data, appropriately accommodates non-genetic sources of variation within trials and models VEI. A recently developed set of selection tools, which are natural derivatives of factor analytic models, are used to facilitate GS for a motivating data set from an Australian plant breeding company. The power and versatility of these tools is demonstrated for the variety by environment and marker by environment effects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jbg.12404DOI Listing
July 2019

Factor analytic mixed models for the provision of grower information from national crop variety testing programs.

Theor Appl Genet 2015 Jan 19;128(1):55-72. Epub 2014 Oct 19.

National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, Australia,

Key Message: Factor analytic mixed models for national crop variety testing programs have the potential to improve industry productivity through appropriate modelling and reporting to growers of variety by environment interaction. Crop variety testing programs are conducted in many countries world-wide. Within each program, data are combined across locations and seasons, and analysed in order to provide information to assist growers in choosing the best varieties for their conditions. Despite major advances in the statistical analysis of multi-environment trial data, such methodology has not been adopted within national variety testing programs. The most commonly used approach involves a variance component model that includes variety and environment main effects, and variety by environment (V × E) interaction effects. The variety predictions obtained from such an analysis, and subsequently reported to growers, are typically on a long-term regional basis. In Australia, the variance component model has been found to be inadequate in terms of modelling V × E interaction, and the reporting of information at a regional level often masks important local V × E interaction. In contrast, the factor analytic mixed model approach that is widely used in Australian plant breeding programs, has regularly been found to provide a parsimonious and informative model for V × E effects, and accurate predictions. In this paper we develop an approach for the analysis of crop variety evaluation data that is based on a factor analytic mixed model. The information obtained from such an analysis may well be superior, but will only enhance industry productivity if mechanisms exist for successful technology transfer. With this in mind, we offer a suggested reporting format that is user-friendly and contains far greater local information for individual growers than is currently the case.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-014-2412-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282718PMC
January 2015

Factor analytic and reduced animal models for the investigation of additive genotype-by-environment interaction in outcrossing plant species with application to a Pinus radiata breeding programme.

Theor Appl Genet 2014 Oct 22;127(10):2193-210. Epub 2014 Aug 22.

National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, Australia.

Key Message: Modelling additive genotype-by-environment interaction is best achieved with the use of factor analytic models. With numerous environments and for outcrossing plant species, computation is facilitated using reduced animal models. The development of efficient plant breeding strategies requires a knowledge of the magnitude and structure of genotype-by-environment interaction. This information can be obtained from appropriate linear mixed model analyses of phenotypic data from multi-environment trials. The use of factor analytic models for genotype-by-environment effects is known to provide a reliable, parsimonious and holistic approach for obtaining estimates of genetic correlations between all pairs of trials. When breeding for outcrossing species the focus is on estimating additive genetic correlations and effects which is achieved by including pedigree information in the analysis. The use of factor analytic models in this setting may be computationally prohibitive when the number of environments is moderate to large. In this paper, we present an approach that uses an approximate reduced animal model to overcome the computational issues associated with factor analytic models for additive genotype-by-environment effects. The approach is illustrated using a Pinus radiata breeding dataset involving 77 trials, located in environments across New Zealand and south eastern Australia, and with pedigree information on 315,581 trees. Using this approach we demonstrate the existence of substantial additive genotype-by-environment interaction for the trait of stem diameter measured at breast height. This finding has potentially significant implications for both breeding and deployment strategies. Although our approach has been developed for forest tree breeding programmes, it is directly applicable for other outcrossing plant species, including sugarcane, maize and numerous horticultural crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-014-2373-0DOI Listing
October 2014

GrainScan: a low cost, fast method for grain size and colour measurements.

Plant Methods 2014 8;10:23. Epub 2014 Jul 8.

CSIRO Computational Informatics, North Ryde NSW 2113, Australia.

Background: Measuring grain characteristics is an integral component of cereal breeding and research into genetic control of seed development. Measures such as thousand grain weight are fast, but do not give an indication of variation within a sample. Other methods exist for detailed analysis of grain size, but are generally costly and very low throughput. Grain colour analysis is generally difficult to perform with accuracy, and existing methods are expensive and involved.

Results: We have developed a software method to measure grain size and colour from images captured with consumer level flatbed scanners, in a robust, standardised way. The accuracy and precision of the method have been demonstrated through screening wheat and Brachypodium distachyon populations for variation in size and colour.

Conclusion: By using GrainScan, cheap and fast measurement of grain colour and size will enable plant research programs to gain deeper understanding of material, where limited or no information is currently available.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1746-4811-10-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105244PMC
July 2014
-->