Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola

Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola. This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 503 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07 and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of A. thaliana and B. napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola

Identifying the seeds of heterotic pools for Southern and Eastern Africa from global elite spring wheat germplasm

Hybrid breeding can increase the competitiveness of wheat (Triticum aestivum L.) in Sub-Saharan Africa by fostering more public-private partnerships and promoting investment by the private sector. The benefit of hybrid wheat cultivars in South Africa has previously been demonstrated but due to the high cost of hybrid seed production, hybrid breeding has not received significant attention in the past decade. Considering the renewed commitment of the private sector to establish wheat as a hybrid crop globally, coupled with significant research investment into enhancement of outcrossing of wheat, hybrid wheat breeding in Southern and Eastern Africa should be revisited. Our study aimed to identify genetically distinct germplasm groups in spring wheat that would be useful in the establishment of heterotic pools targeting this region. Multi-environment yield testing of a large panel of F1 test hybrids, generated using global elite germplasm, was carried out between 2019 and 2020 in Argentina, Africa, Europe, and Australia. We observed significant genotype by environment interactions within our testing network, confirming the distinctiveness of African trial sites. Relatively high additive genetic variance was observed highlighting the contribution of parental genotypes to the grain yield of test hybrids. We explored the genetic architecture of these parents and the genetic factors underlying the value of parents appear to be associated with their genetic subgroup, with positive marker effects distributed throughout the genome. In testcrosses, elite germplasm from the International Maize and Wheat Improvement Center (CIMMYT) appear to be complementary to the genetically distinct germplasm bred in South Africa. The feasibility of achieving genetic gain via heterotic pool establishment and divergence, and by extension the viability of hybrid cultivars in Sub-Saharan Africa, is supported by the results of our study

Circadian Rhythm and Sleep Disruption: Causes, Metabolic Consequences and Countermeasures.

Circadian (∼ 24 hour) timing systems pervade all kingdoms of life, and temporally optimize behaviour and physiology in humans. Relatively recent changes to our environments, such as the introduction of artificial lighting, can disorganize the circadian system, from the level of the molecular clocks that regulate the timing of cellular activities to the level of synchronization between our daily cycles of behaviour and the solar day. Sleep/wake cycles are intertwined with the circadian system, and global trends indicate that these too are increasingly subject to disruption. A large proportion of the world's population is at increased risk of environmentally-driven circadian rhythm and sleep disruption, and a minority of individuals are also genetically predisposed to circadian misalignment and sleep disorders. The consequences of disruption to the circadian system and sleep are profound and include myriad metabolic ramifications, some of which may be compounded by adverse effects on dietary choices. If not addressed, the deleterious effects of such disruption will continue to cause widespread health problems; therefore, implementation of the numerous behavioural and pharmaceutical interventions that can help restore circadian system alignment and enhance sleep will be important

Stable Quantitative Resistance Loci to Blackleg Disease in Canola (Brassica napus L.) Over Continents

The hemibiotrophic fungus, Leptosphaeria maculans is the most devastating pathogen, causing blackleg disease in canola (Brassica napus L). To study the genomic regions involved in quantitative resistance (QR), 259–276 DH lines from Darmor-bzh/Yudal (DYDH) population were assessed for resistance to blackleg under shade house and field conditions across 3 years. In different experiments, the broad sense heritability varied from 43 to 95%. A total of 27 significant quantitative trait loci (QTL) for QR were detected on 12 chromosomes and explained between 2.14 and 10.13% of the genotypic variance. Of the significant QTL, at least seven were repeatedly detected across different experiments on chromosomes A02, A07, A09, A10, C01, and C09. Resistance alleles were mainly contributed by ‘Darmor-bzh’ but ‘Yudal’ also contributed few of them. Our results suggest that plant maturity and plant height may have a pleiotropic effect on QR in our conditions. We confirmed that Rlm9 which is present in ‘Darmor-bzh’ is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several R genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors map in close proximity (within 200 Kb) of the significant trait-marker associations on the reference ‘Darmor-bzh’ genome assembly. More importantly, eight significant QTL regions were detected across diverse growing environments: Australia, France, and United Kingdom. These stable QTL identified herein can be utilized for enhancing QR in elite canola germplasm via marker- assisted or genomic selection strategies

Pacific food systems The role of fish and other aquatic foods for nutrition and health

This report is intended for actors, policymakers and funders concerned with improving food and nutrition security with fisheries as an entry point. It is equally valuable for food system, agricultural, health and nutrition actors who are seeking to protect and enhance the benefits that fish and other aquatic foods provide to a diversity of nutrition goals. This report has been developed from an extensive review of published scientific articles and technical reports, as well as interviews and consultations with 17 experts. It also draws upon insights from the Pacific Food System regional dialogues, which were held in the lead-up to the United Nations Food Systems Summit 2021

A new REML (PX)EM algorithm for linear mixed models and factor analytic mixed models

Linear mixed models and factor analytic mixed models are routinely applied to biological data arising from designed experiments. The preferred method for estimating the parameters associated with these models is residual maximum likelihood (REML). Most statistical software packages available for the REML estimation of parameters associated with linear mixed models and factor analytic mixed models implement a Newton-Raphson type algorithm such as the expected information algorithm or the average information algorithm. There are two problems with these algorithms. Firstly, successive iterations of these algorithms are not guaranteed to increase the residual log-likelihood function. Secondly, parameter updates may not remain in their parameter space. Either may result in the algorithm failing to converge to a solution. The REML expectation maximisation (REML EM) algorithm and the parameter expanded version of this algorithm (REML PX EM) are alternatives to Newton-Raphson type algorithms. Features of these two algorithms are that the residual log-likelihood may not decrease with successive iterations and parameter updates remain in their parameter space. Before the REML EM or REML PX EM algorithm can be considered practical alternatives to Newton-Raphson type algorithms two issues need to be addressed. Firstly, they can be notoriously slow to converge, particularly the REML EM algorithm. Secondly, compared to the average information algorithm, current implementations of these two algorithms are computationally more expensive at each iterate. This increased computational expense relates to calculating the trace of a matrix of the same order as the length of the observed data vector. This thesis addresses the issues of speed and computational efficiency of the REML EM and REML PX EM algorithms for linear mixed models and factor analytic mixed models. The REML EM and REML PX EM algorithms require specification of the incomplete and missing data. A new specification of the incomplete data for linear mixed models and factor analytic mixed models is introduced which is shown be computationally more efficient and we describe the conditions under which this new specification will have a faster rate of convergence. For factor analytic mixed models, model specification, a new parameter expansion, a new missing data specification, and the efficacy of using a less stringent stopping rule are considered. In an example plant breeding data set and in a simulation study it is shown that these innovations can drastically reduce the number of iterations to convergence. The improvements to the REML EM and REML PX EM algorithms presented in this thesis make these two algorithms, particularly the latter, more likely to be implemented alongside Newton-Raphson type algorithms in statistical software packages for linear mixed models and factor analytic mixed models. In such a situation this would provide users of these models a viable alternative in the event of a Newton-Raphson type algorithm failing

Perspective: Are animal scientists forgetting the scientific method and the essential role of statistics?

Animal scientists and their funding organisations need to ensure investment in research is maximised by strict adherence to the scientific method and the rigorous design and analysis of experiments. Statisticians should be considered as equals in the research process, engaged from the beginning of research projects and appropriately funded. The importance of experimental design that accounts for factors affecting the primary experiment measurement is illustrated in two examples. One shows how failure to involve a statistician at the beginning of a project resulted in considerable waste of resources. Subsequent engagement of professional statisticians with rigorous experimental design and analysis led to greatly increased precision in the standard error of an estimate for the digestible energy content of cereal grains for pigs from 0.35 MJ/kg to 0.16 MJ/kg. The other example shows the effect of the percentage of diets replicated during pelleting and of the total number of pigs required in the experiment on theP-values associated with detecting a pairwise difference between two grains differing in digestible energy content by 0.33 MJ/kg. Decisions based on these relationships have animal welfare and resource allocation implications