Genetics Selection Evolution

Abstract Background In genetic terms, the history of a population can be described by its effective population size over time. We know that domestic cattle have gone through dramatic changes in recent history, including intensifying selection in modern breeding programs and replacement of traditional breeds. In this work, we use linkage disequilibrium-based methods to estimate recent population h…

The goal of managing genetic diversity is to maintain both the genomic uniqueness and adaptability of a population. This entails both maintaining heterozygosity and avoiding deleterious alleles from drifting to higher frequencies. Thus, genomic management strategies should not systematically change frequencies at neutral loci, as has been observed in current genomic management. We simulated 50 re…

Our findings provide new insights into the genetic architecture of iris pigmentation in pigs and indicate that KITLG plays a key role. The identification of a putative causal missense variant offers a foundation for further functional studies aiming to better understand pigmentation traits in pigs.

This study demonstrates that the inbreeding load variance is low compared to the additive genetic variance across a range of growth, carcass, and reproductive traits. The results were also consistent with a previous study that theoretically demonstrated a negative correlation between additive effects and inbreeding load. The potential to purge deleterious alleles appears limited, largely due to t…

An approximate computationally efficient multipoint linkage analysis algorithm was developed to estimate unbiased IBD-based relationship and inbreeding coefficients. Its unbiasedness and precise definition of the base population makes it well suited for the genomic management of inbreeding and genomic optimal contribution selection. In addition, G_la based optimal contribution selection…

Genome-wide association studies (GWAS) in cattle populations have traditionally relied on progeny-derived phenotypes such as estimated breeding values as input phenotypes to identify additive quantitative trait loci (QTL) for complex traits. Increasing availability of cow genotype data now enables GWAS using own performance records to detect both additive and non-additive QTL. Sequence-variant ge…

Altogether, our results provide an atlas of parent-of-origin expressed genes in the pig, making it the most documented species for genomic imprinting after humans and rodents. Our findings indicate weak conservation of this mechanism across species and tissues, suggesting a small number of core imprinted genes shared across eutherians and another imprinted genes that seem specific to species or t…

The gains in accuracy from inclusion of SNP genotype data show that genomic prediction using single-step GBLUP can improve selection by identifying the cohort of young dogs that have the highest genetic merit for the desired traits. Gains in validation accuracy were limited by the small number of genotyped animals and are expected to increase as more animals are genotyped.

Coat color variation is a key phenotypic trait in domestic animals. Among the genetic factors involved, the KIT gene has frequently been associated with pigmentation diversity across species. In cattle, spotting or piebald phenotypes have been linked to variation in the genomic region encompassing KIT, but the identification of causal variants was not always possible. This is largely due to the r…

To extend the egg production period of laying hens, it is important to understand the energy trade-offs during the late laying period (after 80 weeks of age) to avoid decreasing egg production or compromising health through inadequate body reserves. Although egg production is routinely recorded, fatness is not. In this study, we were interested in backfat thickness as a new selection criterion fo…

The performance of existing methods for computing inbreeding coefficients-including tabular-based methods, Cholesky decomposition-based methods, and indirect methods-has been limited by either memory usage, pedigree depth, or average half-sib family size. In this note, we present a modified indirect method that efficiently identifies, computes, and stores the necessary elements for computing inbr…

Our results provide valuable insight into the genetic architecture of susceptibility to AGD and IGL, suggesting that both traits may be partly under the same genetic control. Future studies are warranted, especially on the genetic correlation between AGD and IGL.

This study demonstrated the challenge of achieving accurate genomic evaluation in smallholder settings. By leveraging spatial modelling we maximised the use of available data and improved the separation of genetic and environmental effects. Further work is required to improve smallholder genetic evaluations by understanding environmental and genetic processes that drive the large phenotypic varia…

Evaluating the longer-term impacts of OCS and other methods employed requires multi-generation simulations, ideally starting from the current real data as a base. However, the current approach of using a real implementation scenario is important in decision making for real-life applications. Similar benefits from the selection and mating strategies used here are expected in breeding programs for …

The current level of genetic diversity and population structure was quantified for the U.S. Suffolk breed. While the rate of inbreeding was at an acceptable level, the effective population size was modest, indicating that monitoring of genetic diversity and strategic mating of less related animals in the breed should continue. As the sheep industry moves forward, regular assessments of genetic di…

We introduced a novel deep learning method for genomic prediction, which integrates residual units, attention mechanisms and frequency-encoded genomic data. Comprehensive evaluation on pig, dairy cow, Huaxi cattle, wheat and rice datasets demonstrated that ReaGP was a promising tool for most traits. Thus, ReaGP could be considered as an efficient deep learning method for genomic prediction in far…