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The difficulty in finding causative mutations has hampered their use in genomic prediction. Here, we present a methodology to fine-map potentially causal variants genome-wide by integrating the functional, evolutionary and pleiotropic information of variants using GWAS, variant clustering and Bayesian mixture models. Our analysis of 17 million sequence variants in 44,000+ Australian dairy cattle for 34 traits suggests, on average, one pleiotropic QTL existing in each 50 kb chromosome-segment. We selected a set of 80k variants representing potentially causal variants within each chromosome segment to develop a bovine XT-50K genotyping array. The custom array contains many pleiotropic variants with biological functions, including splicing QTLs and variants at conserved sites across 100 vertebrate species. This biology-informed custom array outperformed the standard array in predicting genetic value of multiple traits across populations in independent datasets of 90,000+ dairy cattle from the USA, Australia and New Zealand. Genomic prediction of phenotype may be improved by using DNA mutations with functional, evolutionary, and pleiotropic consequences. Here the authors describe a method for genome-wide fine-mapping of QTLs and develop a genotyping array for improved prediction of genetic values for cattle traits. [ABSTRACT FROM AUTHOR]

Funds to combat biodiversity loss are insufficient, requiring conservation managers to make trade-offs between costs for actions to avoid further loss and costs for research and monitoring to guide effective actions. Using species' management plans for 2328 listed species from three countries we show that 50% of species' proposed recovery plan budgets are allocated to research and monitoring. The proportion of budgets allocated to research and monitoring vary among jurisdictions and taxa, but overall, species with higher proportions of budgets allocated to research and monitoring have poorer recovery outcomes. The proportion allocated to research and monitoring is lower for more recent recovery plans, but for some species, plans have allocated the majority of funds to information gathering for decades. We provide recommendations for careful examination of the value of collecting new information in recovery planning to ensure that conservation programs emphasize action or research and monitoring that directly informs action. How to best allocate limited resources for conserving imperilled species is a difficult challenge. Here the authors analyse data on over 2000 threatened species from USA, Australia, and New Zealand, finding that on average half of the budget is allocated to research and monitoring. Species with higher budget allocation to research and monitoring tend to have poorer recovery outcomes. [ABSTRACT FROM AUTHOR]