Cryptorchidism is a condition whereby one or both testes fail to descend into the scrotal sac. Here, we performed a genome-wide association study (GWAS) with both a case-control analysis using the GEMMA software accounting for population structure and a BayesB approach in the GenSel software applied to every 1 Mb window of SNPs or haplotypes. The haplotypes were constructed from a genealogical ...

Although common datasets are an important resource for the scientific community and can be used to address important questions, genomic datasets of a meaningful size have not generally been available in livestock species. We describe a pig dataset that PIC (a Genus company) has made available for comparing genomic prediction methods. We also describe genomic evaluation of the data using methods...

Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. Previously, we reported high genomic prediction accuracy of 0.72 for BCWD resistance rainbow trout using the 57 K Axiom SNP array. Due to cost phenotyping genotyping breeding programs, it is paramount know if acceptable can be obtained subsequent generation without retraining model. In ...

Hierarchical mixed effects models have been demonstrated to be powerful for predicting genomic merit of livestock and plants, on the basis of high-density single-nucleotide polymorphism (SNP) marker panels, and their use is being increasingly advocated for genomic predictions in human health. Two particularly popular approaches, labeled BayesA and BayesB, are based on specifying all SNP-associa...

Machine learning (ML) is perhaps the most useful tool for interpretation of large genomic datasets. However, performance a single machine method in selection (GS) currently unsatisfactory. To improve predictions, we constructed stacking ensemble framework (SELF), integrating three methods, to predict estimated breeding values (GEBVs). The present study evaluated prediction ability SELF by analy...

Genomic selection methodologies and genome-wide association studies use powerful statistical procedures that correlate large amounts of high-density SNP genotypes phenotypic data. Actual 305-d milk (MY), fat (FY), protein (PY) yield data on 695 cows 76,355 genotyping-by-sequencing-generated marker from Canadian Holstein dairy were used to characterize linkage disequilibrium (LD) structure cows....

The research was undertaken during June-October 2020 at Seethanagaram and Draksharam villages of East Godavari district, Andhra Pradesh, India with an objective to evaluate efficiency genomic selection models involving 1545 recombinant inbred lines (RILs) derived from eleven bi-parental populations in Rice. During 2020, the F7 RILs were screened two hot spot locations. genotyping done Infinium ...

Abstract Markers are an important tool in plant breeding, which can improve conventional phenotypic generating more accurate information outcoming better decision making. This study aimed to apply and compare the fit of different Bayesian models BRR, BayesA, BayesB, BayesB (setting value from very low $$\pi$$ π </mml:mat...

The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F2, F3 and half-siblings to embryo transfer F2 calves with records for overall temperament at weaning (TEMP; n = 769) and Warne...

Fatty acid composition in milk is not only reflective of nutritional quality but also potentially predictive other attributes (e. g. including the cow's energy balance and its relative output methane emissions). Furthermore, a higher ratio long-chain to short-chain fatty acids or mean carbon number has been associated with negative dairy cows, whereas enhanced properties have generally levels u...