Assessment of genetic diversity and population structure of U.S. Polypay sheep from breed origins to future genomic selection

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed’s origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020–2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright’s inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed

Assessment of genetic diversity and population structure of U.S. Polypay sheep from breed origins to future genomic selection

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed’s origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020–2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright’s inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats’ predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor’s (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species

Compact groups in theory and practice - II. Comparing the observed and predicted nature of galaxies in compact groups

We examine the properties of galaxies in compact groups identified in a mock galaxy catalogue based upon the Millennium Run simulation. The overall properties of groups identified in projection are in general agreement with the best available observational constraints. However, only ~30% of these simulated groups are found to be truly compact in 3 dimensions, suggesting that interlopers strongly affect our observed understanding of the properties of galaxies in compact groups. These simulations predict that genuine compact group galaxies are an extremely homogeneous population, confined nearly exclusively to the red sequence: they are best described as `red and dead' ellipticals. When interlopers are included, the population becomes much more heterogeneous, due to bluer, star-forming, gas-rich, late-type galaxies incorrectly identified as compact group members. These models suggest that selection of members by redshift, such that the line-of-sight velocity dispersion of the group is less than 1000 km/s, significantly reduces contamination to the 30% level. Selection of members by galaxy colour, a technique used frequently for galaxy clusters, is also predicted to dramatically reduce contamination rates for compact group studies.Comment: 15 pages, 9 figures, accepted for publication in MNRA

Applications and efficiencies of the first cat 63K DNA array

Correction, Volume: 8 Article Number: 8746 DOI: 10.1038/s41598-018-26885-5 Published: JUN 4 2018The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array's genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50-1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.Peer reviewe

Sodium Reduction in Processed Foods in Brazil: Analysis of Food Categories and Voluntary Targets from 2011 to 2017

Non-communicable diseases, including cardiovascular diseases, are responsible for over 70% of deaths in Brazil. Currently, over 25% of Brazilian adults are diagnosed as hypertensive; overall, current dietary sodium intake in Brazil (4700 mg/person) is over twice the international recommendations, and 70–90% of adolescents and adults consume excessive sodium. National sodium reduction strategies consider the main dietary sources of sodium to be added salt to foods, foods consumed outside of the household, and sodium in processed foods. The national voluntary strategy for sodium reduction in priority food categories has been continuously monitored over a 6-year period (2011–2017) and there was a significant 8–34% reduction in the average sodium content of over half food categories. Different food categories have undergone differing reductions in sodium over time, aiding gradual biannual targets to allow industries to develop new technologies and consumers to adapt to foods with less salt. By 2017, most products of all food categories had met the regional targets proposed by the Pan American Health Organization, showing that voluntary sodium reduction strategies can potentially contribute to food reformulation. Nevertheless, regulatory approaches may still be necessary in the future in order to reach all food producers and to allow stronger enforcement to meet more stringent regional targets

Flipping The Practice Based Pathology Laboratory—Can It Support Development Of Practitioner Capability For Trainee Pathologists in Gynaecological Cytopathology?

This study investigated the role of 'flipping', the practice-based pathology laboratory and classroom to support the development of trainee pathologist practitioners' in the field of gynaecological cytopathology, addressing development of their knowledge and practical application in the clinical setting. Content-rich courses traditionally involve lecture led delivery which restricts tutors from adopting approaches that support greater student engagement in the topic area and application of knowledge to practice. We investigated the role of 'flipping', the practice-based pathology laboratory and classroom where 'virtual lectures' were accessed outside of 'class time' allowing more time for students to engage in active learning under the supervision of a consultant histopathologist. 'Flipping' was used to support two gynaecological cytopathology training courses with cohorts of eight trainee pathologists on the first course and six on the second. Lectures were made available to the trainees to watch before attending the workshops. The workshops consisted of group activities and individual practical exercises allowing trainees to review and report on patient practice cases with the support of their peers and tutors. Focus group sessions were held after each course, allowing trainee pathologists to reflect on their experiences. Discussions were transcribed and thematic analysis was used to capture key themes discussed by the trainees. Trainees' identified that 'flipping' provided them with more time during face-to-face sessions, enabling a greater depth of questioning and engagement with the consultant histopathologists. Having already watched the lectures, trainees were able to attend the sessions having identified areas in which they needed additional support and development. Trainee pathologists reported they had more time to concentrate on developing their skills and practise under the guidance of the consultant histopathologists so developing their capability in gynaecological cytopathology. The role of alternative methods of delivery such as 'flipping' is suggested for short courses designed to support practitioner capability and continued professional development