Accuracy and responses of genomic selection on key traits in apple breeding

open13siThe application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.openMuranty, H.; Troggio, M.; Sadok, I.B.; Mehdi A.R.; Auwerkerken, A.; Banchi, E.; Velasco, R.; Stevanato, P.; Eric van de Weg, W.; Di Guardo, M.; Kumar, S.; Laurens, F.; Bink, M.C.A.M.Muranty, H.; Troggio, M.; Sadok, I. B.; Mehdi, A. R.; Auwerkerken, A.; Banchi, E.; Velasco, R.; Stevanato, Piergiorgio; Eric van de Weg, W.; Di Guardo, M.; Kumar, S.; Laurens, F.; Bink, M. C. A. M

Mining large-scale human mobility data for long-term crime prediction

Traditional crime prediction models based on census data are limited, as they fail to capture the complexity and dynamics of human activity. With the rise of ubiquitous computing, there is the opportunity to improve such models with data that make for better proxies of human presence in cities. In this paper, we leverage large human mobility data to craft an extensive set of features for crime prediction, as informed by theories in criminology and urban studies. We employ averaging and boosting ensemble techniques from machine learning, to investigate their power in predicting yearly counts for different types of crimes occurring in New York City at census tract level. Our study shows that spatial and spatio-temporal features derived from Foursquare venues and checkins, subway rides, and taxi rides, improve the baseline models relying on census and POI data. The proposed models achieve absolute R^2 metrics of up to 65% (on a geographical out-of-sample test set) and up to 89% (on a temporal out-of-sample test set). This proves that, next to the residential population of an area, the ambient population there is strongly predictive of the area's crime levels. We deep-dive into the main crime categories, and find that the predictive gain of the human dynamics features varies across crime types: such features bring the biggest boost in case of grand larcenies, whereas assaults are already well predicted by the census features. Furthermore, we identify and discuss top predictive features for the main crime categories. These results offer valuable insights for those responsible for urban policy or law enforcement

The Economics of Agricultural Land Use Dynamics in Coconut Plantations of Sri Lanka

In this study a spatially explicit economic analysis was employed to determine the land use change in a traditional coconut growing district of Sri Lanka. From a theoretical model of land use, an econometric framework was developed to incorporate spatial and individual effects that would affect the land use decision. Markovian transition probabilities derived from the econometric analysis and spatial analysis was used to predict the land use change over the next 30 years. The results revealed that the fragmentation and conversion of coconut lands to urban continue in the areas close to the urban centre and also with less productive lands. Spatial analysis provides further evidence of the positive trend of conversion of coconut lands to urban uses close to the urban areas.Resource /Energy Economics and Policy,