Zhang, Qianqian Sahana, Goutam Su, Guosheng Guldbrandtsen, Bernt Lund, Mogens Sandø Calus, Mario P L
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Genetics, selection, evolution : GSE
Availability of whole-genome sequence data for a large number of cattle and efficient imputation methodologies open a new opportunity to include rare and low-frequency variants (RLFV) in genomic prediction in dairy cattle. The objective of this study was to examine the impact of including RLFV that are within genes and selected from whole-genome se...
Mastrangelo, Salvatore Ciani, Elena Ajmone Marsan, Paolo Bagnato, Alessandro Battaglini, Luca Bozzi, Riccardo Carta, Antonello Catillo, Gennaro Cassandro, Martino Casu, Sara
...
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Genetics, selection, evolution : GSE
In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic re...
Calus, Mario P L Vandenplas, Jérémie
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Genetics, selection, evolution : GSE
High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, this warrants pruning of genotyping data for high LD. We developed an algorithm, named SNPrune, which enables the rapid detection of any pair o...
Teissier, Marc Larroque, Hélène Robert-Granié, Christèle
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Genetics, selection, evolution : GSE
In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain the same fraction of genetic variance. However, ssGBLUP is not suitable for protein content, which is controlled by a major gene, i.e. α s 1 c...
Bush, Stephen J Muriuki, Charity McCulloch, Mary E B Farquhar, Iseabail L Clark, Emily L Hume, David A
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Genetics, selection, evolution : GSE
Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNAs in other species.
Padilla-Jacobo, Gabriela Cano-Camacho, Horacio López-Zavala, Rigoberto Cornejo-Pérez, María E Zavala-Páramo, María G
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Genetics, selection, evolution : GSE
The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mit...
Ruiz-Larrañaga, Otsanda Langa, Jorge Rendo, Fernando Manzano, Carmen Iriondo, Mikel Estonba, Andone
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Genetics, selection, evolution : GSE
The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under ...
Derks, Martijn F L Herrero-Medrano, Juan M Crooijmans, Richard P M A Vereijken, Addie Long, Julie A Megens, Hendrik-Jan Groenen, Martien A M
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Genetics, selection, evolution : GSE
Sex-linked slow (SF) and fast (FF) feathering rates at hatch have been widely used in poultry breeding for autosexing at hatch. In chicken, the sex-linked K (SF) and k+ (FF) alleles are responsible for the feathering rate phenotype. Allele K is dominant and a partial duplication of the prolactin receptor gene has been identified as the causal mutat...
Esfandyari, Hadi Berg, Peer Sørensen, Anders Christian
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Genetics, selection, evolution : GSE
Genomic selection can be applied to select purebreds for crossbred performance (CP). The average performance of crossbreds can be considered as the summation of two components, i.e. the breed average (BA) of the parental breeds and heterosis (H) present in crossbreds. Selection of pure breeds for CP based on genomic estimated breeding values for cr...
Ilska, Joanna J. Meuwissen, Theo H. E. Kranis, Andreas Woolliams, John A.
AbstractBackgroundMolecular data is now commonly used to predict breeding values (BV). Various methods to calculate genomic relationship matrices (GRM) have been developed, with some studies proposing regression of coefficients back to the reference matrix of pedigree-based relationship coefficients (A). The objective was to compare the utility of ...
