High-throughput phenotyping (Htp) technologies can produce data on thousands of phenotypes per unit being monitored. these data can be used to breed for economically and environmentally relevant traits (e.g., drought tolerance); however, incorporating high-dimensional phenotypes in genetic analyses and in breeding schemes poses important statistical and computational challenges. to address this problem, we developed regularized selection indices; the methodology integrates techniques commonly used in high-dimensional phenotypic regressions (including penalization and rank-reduction approaches) into the selection index (Si) framework. Using extensive data from ciMMYt's (international Maize and Wheat improvement center) wheat breeding program we show that regularized Sis derived from hyper-spectral data offer consistently higher accuracy for grain yield than those achieved by standard Sis, and by vegetation indices commonly used to predict agronomic traits. Regularized SIs offer an effective approach to leverage HTP data that is routinely generated in agriculture; the methodology can also be used to conduct genetic studies using high-dimensional phenotypes that are often collected in humans and model organisms including body images and whole-genome gene expression profiles.
Summary Breeding objectives were derived for pasture‐fed Uruguayan beef cattle production systems, based on multi‐purpose breeds. The traits in the breeding objective were weaning rate, calving ease (direct and maternal), sale weight (offspring and cows), and feed intake (offspring and cows). Economic values for sale weight and calving ease (direct) were similar across the systems, but varied considerably for other traits. The economic‐genetic variation for weaning rate was greater than that for sale weight in three out of the four systems studied, whereas for feed intake (offspring plus cows) it was greater in two out of the four. For calving ease (direct plus maternal) it was smaller but still important (25–50% that of sale weight). The consequences of changes in some of the assumptions made are examined. The approach adopted to handle feed intake traits (fixed or variable feed base) had important genetic and economic repercussions. Compared with the selection for liveweight alone, selection for a comprehensive breeding objective (which included reproduction and feed intake traits as well) was economically advantageous. The use of calving day and scrotal circumference as selection criteria in the index leads to increases in the genetic gain measured in economic units. The implementation of our findings in Uruguayan genetic evaluation services for beef cattle is recommended. Resumen Objetivos de selectión para vacunos de carne en pasturas en Uruguay Objetivos de selección fueron derivados para sistemas pastoriles de producción de carne vacuna en Uruguay basados en razas multipropósito. Los rasgos en el objetivo de selección fueron tasa reproductiva, facilidad de parto (directa y materna), peso a la faena (animales jóvenes y vacas) y consumo de alimento (animales jóvenes y vacas). Los valores económicos para peso a la faena y facilidad de parto (directa) fue similar en todos los sistemas, pero variaron considerablemente para otros rasgos. La variación económica‐genética para tasa de destete fue mayor que la de peso a la faena en tres de cuatro systemas, mientras que para consumo de alimento (animales jóvenes y vacas) fue mayor en dos de los cuatro. Para facilidad de parto (directa mas materna) fue menor pero aún importante (25 a 50% de la de peso a la faena). Las consecuencias de los cambios en algunos de los supuestos son examinados. El enfoque adoptado para tratar los rasgos de consumo de alimento (base alimenticia fija o variable) tuvo importantes repercusiones genéticas y económicas. Comparado con selección solo por peso vivo, selección por un objetivo completo (incluyendo además rasgos reproductivos y de consumo) fue económicamente ventajosa. El uso de día de parto y circunferencia escrotal como criterios de selefcción en un índice condujo a incrementos en la ganancia genética media en unidades económicas. La implementación de nuestros hallazgos en los servicios de evaluación genética de vacunos de carne de Uruguay es recomendada. Zusammenfassung Zuchtziele für Weidemast‐Fleischringer in Uruguay Die Zuchtzie...
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