Emre Karaman
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View article: Accuracy of local ancestry inference and its impact on genomic prediction in admixed dairy cattle populations
Accuracy of local ancestry inference and its impact on genomic prediction in admixed dairy cattle populations Open
Accurate local ancestry (LA) inference is important for genomic evaluations in admixed dairy cattle. This study had 2 main objectives: to compare the performance of 3 LA inference software: AllOr, BreedOrigin, and ChromoPainter, and to eva…
View article: Marker weighting improves single-step genomic prediction reliabilities of udder health traits in Nordic Red and Jersey dairy cattle populations
Marker weighting improves single-step genomic prediction reliabilities of udder health traits in Nordic Red and Jersey dairy cattle populations Open
The standard single-step genomic prediction model assumes that all SNP markers explain an equal amount of genetic variance, which, however, may not be true. This is because SNPs are located in or near different genes with different functio…
View article: Multibreed genomic prediction using summary statistics and a breed-origin-of-alleles approach
Multibreed genomic prediction using summary statistics and a breed-origin-of-alleles approach Open
Because of an increasing interest in crossbreeding between dairy breeds in dairy cattle herds, farmers are requesting breeding values for crossbred animals. However, genomically enhanced breeding values are difficult to predict in crossbre…
View article: A breed-of-origin of alleles model that includes crossbred data improves predictive ability for crossbred animals in a multi-breed population
A breed-of-origin of alleles model that includes crossbred data improves predictive ability for crossbred animals in a multi-breed population Open
Background Recently, crossbred animals have begun to be used as parents in the next generations of dairy and beef cattle systems, which has increased the interest in predicting the genetic merit of those animals. The primary objective of t…
View article: Study of fertility traits in Italian Jersey Cattle
Study of fertility traits in Italian Jersey Cattle Open
Selection Index of Italian Jersey cattle is composed by breeding values (BVs) of production traits, type traits and somatic cell score. Knowing selection for milk yield has been proved to deteriorate fertility performances, aim of the Ital…
View article: 272. Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde × Holstein × Red Danish)
272. Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde × Holstein × Red Danish) Open
In recent years, crossbreeding strategy has grown in dairy cattle farms at an international level. Breeders are interested in keeping crossbred cows in their herd both to combine the strengths of the pure breeds, compensate for their weakn…
View article: XSim version 2: simulation of modern breeding programs
XSim version 2: simulation of modern breeding programs Open
Simulation can be an efficient approach to design, evaluate, and optimize breeding programs. In the era of modern agriculture, breeding programs can benefit from a simulator that integrates various sources of big data and accommodates stat…
View article: Genomic prediction in Nordic Red dairy cattle considering breed origin of alleles
Genomic prediction in Nordic Red dairy cattle considering breed origin of alleles Open
This study investigated the reliability of genomic prediction (GP) using breed origin of alleles (BOA) approach in the Nordic Red (RDC) population, which has an admixed population structure. The RDC population consists of animals with vary…
View article: Genomic prediction using a reference population of multiple pure breeds and admixed individuals
Genomic prediction using a reference population of multiple pure breeds and admixed individuals Open
Background In dairy cattle populations in which crossbreeding has been used, animals show some level of diversity in their origins. In rotational crossbreeding, for instance, crossbred dams are mated with purebred sires from different pure…
View article: MeSCoT: the tool for quantitative trait simulation through the mechanistic modeling of genes’ regulatory interactions
MeSCoT: the tool for quantitative trait simulation through the mechanistic modeling of genes’ regulatory interactions Open
This work represents a novel mechanistic approach to simulate and study genomic networks with accompanying regulatory interactions and complex mechanisms of quantitative trait formation. The approach implemented in MeSCoT software is conce…
View article: Pooled genotyping strategies for the rapid construction of genomic reference populations1
Pooled genotyping strategies for the rapid construction of genomic reference populations1 Open
The growing concern with the environment is making important for livestock producers to focus on selection for efficiency-related traits, which is a challenge for commercial cattle herds due to the lack of pedigree information. To explore …
View article: Genomic Prediction Using Multi-trait Weighted GBLUP Accounting for Heterogeneous Variances and Covariances Across the Genome
Genomic Prediction Using Multi-trait Weighted GBLUP Accounting for Heterogeneous Variances and Covariances Across the Genome Open
Implicit assumption of common (co)variance for all loci in multi-trait Genomic Best Linear Unbiased Prediction (GBLUP) results in a genomic relationship matrix (G) that is common to all traits. When this assumption is violated, Bayesian wh…
View article: Supplemental Material for Karaman et al., 2018
Supplemental Material for Karaman et al., 2018 Open
File S1 includes Table S1 and Table S2, for accuracies of 200 and 500 QTL scenarios, respectively.Files named as "genoData5chr._X.gz" are:- Genotype data (10 replicates) for 6 generations (G0-G5 as indicated in the article) each with 2200 …
View article: Using additional single nucleotide polymorphisms selected from whole genome sequence data for genomic prediction in Danish Jersey
Using additional single nucleotide polymorphisms selected from whole genome sequence data for genomic prediction in Danish Jersey Open
International audience
View article: Bayesian Analysis for the Comparison of Nonlinear Regression Model Parameters: an Application to the Growth of Japanese Quail
Bayesian Analysis for the Comparison of Nonlinear Regression Model Parameters: an Application to the Growth of Japanese Quail Open
This paper discusses the Bayesian approach as an alternative to the classical analysis of nonlinear models for growth curve data in Japanese quail. A Bayesian nonlinear modeling method is introduced and compared with the classical nonlinea…
View article: An Upper Bound for Accuracy of Prediction Using GBLUP
An Upper Bound for Accuracy of Prediction Using GBLUP Open
This study aims at characterizing the asymptotic behavior of genomic prediction R2 as the size of the reference population increases for common or rare QTL alleles through simulations. Haplotypes derived from whole-genome sequence of 85 Ca…
View article: Bayesian inference of genetic parameters for ultrasound scanning traits of Kivircik lambs
Bayesian inference of genetic parameters for ultrasound scanning traits of Kivircik lambs Open
Ultrasound scanning traits have been adapted in selection programs in many countries to improve carcass traits for lean meat production. As the genetic parameters of the traits interested are important for breeding programs, the estimation…