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Improvement of the accuracy of breeding value prediction for egg production traits in Muscovy duck using low-coverage whole-genome sequence data.
Poult Sci
January 2025
Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China. Electronic address:
Low-coverage whole genome sequencing (lcWGS) is an effective low-cost genotyping technology when combined with genotype imputation approaches. It facilitates cost-effective genomic selection (GS) programs in agricultural animal populations. GS based on lcWGS data has been successfully applied to livestock such as pigs and donkeys.
View Article and Find Full Text PDFNanopore sequencing as a novel method of characterising anorexia nervosa risk loci.
BMC Genomics
December 2024
Pathology and Biomedical Science Department, University of Otago Christchurch, Christchurch, New Zealand.
Background: Anorexia nervosa (AN) is a polygenic, severe metabopsychiatric disorder with poorly understood aetiology. Eight significant loci have been identified by genome-wide association studies (GWAS) and single nucleotide polymorphism (SNP)-based heritability was estimated to be ~ 11-17, yet causal variants remain elusive. It is therefore important to define the full spectrum of genetic variants in the wider regions surrounding these significantly associated loci.
View Article and Find Full Text PDFOptimizing drought tolerance in cassava through genomic selection.
Front Plant Sci
December 2024
Nugene, Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia, Brazil.
The complexity of selecting for drought tolerance in cassava, influenced by multiple factors, demands innovative approaches to plant selection. This study aimed to identify cassava clones with tolerance to water stress by employing truncated selection and selection based on genomic values for population improvement and genotype evaluation . The Best Linear Unbiased Predictions (BLUPs), Genomic Estimated Breeding Values (GEBVs), and Genomic Estimated Genotypic Values (GETGVs) were obtained based on different prediction models via genomic selection.
View Article and Find Full Text PDFDiscarded sequencing reads uncover natural variation in pest resistance in .
Elife
December 2024
Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany.
Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labor-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress () that were grown in a common environment and spontaneously colonized by aphids, mildew, and other microbes.
View Article and Find Full Text PDFMapping genes for human face shape: Exploration of univariate phenotyping strategies.
PLoS Comput Biol
December 2024
Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
Human facial shape, while strongly heritable, involves both genetic and structural complexity, necessitating precise phenotyping for accurate assessment. Common phenotyping strategies include simplifying 3D facial features into univariate traits such as anthropometric measurements (e.g.
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