Functional and evolutionary analysis of host Synaptogyrin-2 in porcine circovirus type 2 susceptibility DOI Creative Commons

Lianna R. Walker,

Hiep L. X. Vu, Kristi L. Montooth

et al.

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(11), P. e1011029 - e1011029

Published: Nov. 27, 2023

Mammalian evolution has been influenced by viruses for millions of years, leaving signatures adaptive within genes encoding viral interacting proteins. Synaptogyrin-2 ( SYNGR2 ) is a transmembrane protein implicated in promoting bacterial and infections. A genome-wide association study pigs experimentally infected with porcine circovirus type 2b (PCV2b) uncovered missense mutation p . Arg63Cys associated load. In this study, CRISPR/Cas9-mediated gene editing the kidney 15 (PK15, wtSYNGR2 +p 63Arg cell line generated clones homozygous favorable 63Cys allele emSYNGR2 ). Infection edited resulted decreased PCV2 replication compared to wildtype PK15 (P<0.05), consistent effects across genetically distinct PCV2b PCV2d isolates. Sequence analyses wild domestic (n>700) revealed unique more predominant European than Asian breeds. haplotype defined was likely derived from an ancestral nearly fixed (0.977) but absent boar. We hypothesize that arose post-domestication swine. Decreased genetic diversity homozygotes , corroborates rapid increase frequency SYGNR2 via positive selection. Signatures mammalian species were also identified intraluminal loop domains, coinciding location Therefore, may reflect novel component host-virus evolutionary arms race mammals representing species-specific example putative evolution.

Language: Английский

Advanced median-based genetic similarity analysis in Kazakh Tazy dogs: A novel approach for breed conformity assessment DOI Creative Commons
Anastassiya Perfilyeva, Rustam Mussabayev, Kira Bespalova

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 20, 2024

Abstract The breed conformity evaluation is crucial for the preservation of traits that characterise each dog breed. use genetic markers this purpose provides a precision and objectivity can surpass reliability phenotypic evaluations. In study, we present new simple algorithm assessing conformity. creates similarity matrix based on genotypic data then uses median to calculate percentage an individual has in relation diversity To validate proposed algorithm, applied it 18 microsatellites 43,691 single nucleotide polymorphisms (SNPs) Kazakh Tazy dog, great cultural historical importance Kazakhstan now threatened with extinction due crossbreeding. showed moderate correlation between microsatellite SNP genotyping methods, reflecting different aspects similarity. particular, SNP-based evaluations agreed better expert judgements, highlighting their potential accurate analysis easily interpretable results, flexible, adapts may provide mechanism situations where there no reference population, incomplete pedigrees, unidentified meta-founders high population. Author summary Our research was initiated by urgent concern possible deep roots significance Kazakhstan. Information at DNA level lead faster improvement than relying only pedigrees. Genotypic be processed valuable insights into diversity, relatedness ancestry. However, existing methods do not measure used assess how closely particular matches typical composition These challenges have led us propose approach overcomes limitations allows assessed genotypes. It median-based analyze been but also adapted other markers. This method results even absence defined complete pedigrees or identified meta-pedigrees during within breeders researchers tool maintain purity unique breeds.

Language: Английский

Citations

1
Base Characteristics, Preservation Methods, and Assessment of the Genetic Diversity of Autochthonous Breeds of Cattle, Sheep and Pigs in Serbia: A Review DOI Creative Commons
Radica Djedović, D. Radojković, Dragan Stanojević

et al.

Animals, Journal Year: 2024, Volume and Issue: 14(13), P. 1894 - 1894

Published: June 27, 2024

Preserving local autochthonous domestic animal populations and the products derived from them is a crucial aspect of managing human utilization biosphere. This management approach aims to ensure sustainable benefits for both present future generations. The diversity plays vital role in functionality sustainability food production system. It encompasses productive non-productive aspects, contributing significantly overall health, nutrition, security landscape by providing wide range animal-derived resources. Based on data contained Draft Program Rural Development, significant presence more than 44 breeds animals has been noted Serbia. In order enable preservation animals, competent Ministry Agriculture Republic Serbia has, through number projects, implemented models farms (in situ), as well provided technical assistance small that keep collections. also helps population procure conducts product quality research, provides opportunities integrate conservation programs tourism. Given molecular characterization key factor breeds, Serbia, DNA markers are used identification investigate belonging specific or strain. All mentioned activities led an immediate increase which especially true cattle (Busha), sheep (Sjenicka, Svrljiska, Vlach-vitohorn) pigs (Mangalitsa, Moravka, Resavka) discussed this paper. addition measures undertaken preserve genetic resources (AnGR), it necessary continue work primarily ex situ prevent loss their gene pools. However, regardless evident effort made we believe there still lot room further improvement. refers advanced technologies have not applied so far, mostly related genomic regions associated with economic traits, resistance diseases, adaptability emerging climate changes. way, capacity functional characteristics species will be improved.

Language: Английский

Citations

1
Genetic characterisation of the Nero d’Aspromonte pig population in Southern Italy DOI Creative Commons

Ervin Shishmani,

Valentino Palombo, Giuseppina Schiavo

et al.

Italian Journal of Animal Science, Journal Year: 2024, Volume and Issue: 23(1), P. 1358 - 1372

Published: Sept. 6, 2024

Language: Английский

Citations

1
Genetic Diversity and Population Structure of the Native Pulawska and Three Commercial Pig Breeds Based on Microsatellite Markers DOI Open Access
Anna Radko, Anna Koseniuk, Grzegorz Smołucha

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(2), P. 276 - 276

Published: Jan. 20, 2023

Swine DNA profiling is highly important for animal identification and parentage verification also increasingly meat traceability. This work aimed to analyze the genetic structure diversity in selected Polish pig breeds. The study used a set of 14 microsatellite (STR) markers recommended by ISAG native Puławska (PUL, n = 85) three commercial breeds: Large White (PLW, 74), Landrace (PL, foreign breed Duroc (DUR, 84). Genetic differentiation among breeds accounted 18% total variability (AMOVA). Bayesian analysis (STRUCTURE) indicated that four distinct clusters obtained corresponded studied. Reynolds distances (Ɵw) showed close relationship between PL PLW most distant DUR PUL pigs. values (FST) were lower higher DUR. principal coordinate (PCoA) supported classification populations into clusters.

Language: Английский

Citations

3
Ascertaining the genetic background of the Celtic‐Iberian pig strain: A signatures of selection approach DOI Creative Commons
Katherine D. Arias,

Hanboreum Lee,

Riccardo Bozzi

et al.

Journal of Animal Breeding and Genetics, Journal Year: 2023, Volume and Issue: 141(1), P. 96 - 112

Published: Oct. 9, 2023

Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of 20th century. In 1990s, they nearly extinct as a result introduction foreign improved breeds. Despite its historical importance, genetic background strain is poorly documented. this study, we have identified genomic regions that might contain signatures selection peculiar lineage. A total 153 DNA samples pigs (Spanish Gochu Asturcelta Portuguese Bísara breeds), Iberian Alentejano Cinta Senese pig, Korean local Cosmopolitan (Hampshire, Landrace Large White individuals) analysed. pairwise-comparison approach was applied: test populations five other reference populations. Three different statistics (XP-EHH, FST ΔDAF) computed on each comparison. Strict criteria used to identify sweeps order reduce noise brought by breeds' severe population bottlenecks. Within population, SNPs construct potential candidate areas under only considered if four ten two-by-two pairwise comparisons at least two three statistics. Genomic constructed within subsequently overlapped putatively unique strain. These finally for enrichment analyses. 39 regions, mainly located SSC5 SSC9 covering 3130.5 kb, could be representative ancient Enrichment analysis allowed seven genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, LYPD6). Other studies reported WIF1 gene associated with ear size, one characteristic traits The function related reproduction, adaptation immunity traits, indirectly fitting rusticity non-improved traditionally exploited semi-extensive conditions.

Language: Английский

Citations

3
Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds DOI

A. Vani,

Amit Kumar, Sudarshan Mahala

et al.

Gene, Journal Year: 2023, Volume and Issue: 893, P. 147950 - 147950

Published: Nov. 1, 2023

Language: Английский

Citations

3
Genetic diversity and breed-informative SNPs identification in domestic pig populations using coding SNPs DOI Creative Commons
Ichrak Hayah, Chouhra Talbi, Narjice Chafai

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: Nov. 16, 2023

Background: The use of breed-informative genetic markers, specifically coding Single Nucleotide Polymorphisms (SNPs), is crucial for breed traceability, authentication meat and dairy products, the preservation improvement pig breeds. By identifying informative we aimed to gain insights into mechanisms that influence production traits, enabling informed decisions in animal management promoting sustainable meet growing demand products. Methods: Our dataset consists 300 SNPs genotyped from three Italian commercial populations: Landrace, Yorkshire, Duroc. Firstly, analyzed diversity among populations. Then, applied a discriminant analysis principal components identify most discriminating between these Lastly, conducted functional enrichment enriched pathways related variation observed Results: alpha indexes revealed high within higher proportion heterozygosity than expected an excess heterozygotes populations was supported by negative values fixation index (FIS) deviations Hardy-Weinberg equilibrium. Euclidean distance, pairwise FST, Nei's GST distances Yorkshire Landrace breeds are genetically closest, with distance 2.242, 0.029, 0.033, respectively. Conversely, Duroc showed highest divergence, 2.815, 0.048, 0.052, We identified 28 significant phenotypic traits were able differentiate accuracy. Functional Enrichment Analysis highlighted biological functions DNA packaging, chromatin integrity, preparation higher-order structures. Conclusion: study sheds light on underpinnings breeds, offering potential driving differentiation. prioritizing breed-specific SNPs, our approach enables more focused specific genomic regions relevant research question compared analyzing entire genome.

Language: Английский

Citations

2
Classification of breed combinations for slaughter pigs based on genotypes—modeling DNA samples of crossbreeds as fuzzy sets from purebred founders DOI Creative Commons
Hilde Vinje,

Hilde Kjelgaard Brustad,

Andrew Heggli

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: Dec. 4, 2023

In pig production, the production animals are generally three- or four-way crossbreeds. Reliable information regarding breed of origin slaughtered pigs is useful, even a prerequisite, for number purposes, e.g., evaluating potential effects on carcass grading. Genetic data from can easily be extracted and used crossbreed classification. current study, four classification methods, namely, random forest (RF), ADMIXTURE, partial least squares regression (PLSR), together with quadratic discriminant analysis (PLS-QDA) were evaluated simulated (

Language: Английский

Citations

2
SNP-based genetic signatures revealed breeding effects in indigenous Livni compared with Landrace and Large White breeds DOI Creative Commons
И. М. Чернуха, Elena Kotenkova, Liliya Fedulova

et al.

Foods and raw materials, Journal Year: 2023, Volume and Issue: 12(2), P. 283 - 307

Published: Nov. 17, 2023

Livni is one of the Russian local pig breeds. We previously reported that this breed was more distinct from Duroc than Landrace and Large White breeds, which participated in creation. The aim study to determine SNP-based genetic signatures fat-type shared with commercial ones are affected by putative selection. genome-wide SNP genotyping carried out using Porcine GGP HD BeadChip, contains ~ 80 000 SNPs. Obtained relationship admixture results indicated insignificant participation breeds formation modern allelofund pigs. 238 candidate genes were found genomic regions selection signatures, 182 described functions identified. In 35 common detected formed cluster enrichment coefficient = 4.94 predominant HOXD genes. largest amounts (62 average), two clusters. Cluster 1, 2.11, characterized involved glucose metabolism. 2, 1.60, demonstrated helicase Annotated clusters not determined for breed. However, 50 specific pigs associated various growth, carcass reproductive traits, essential thermoregulation. Results revealed breeding effects indigenous compared

Language: Английский

Citations

0
Functional and evolutionary analysis of host Synaptogyrin-2 in porcine circovirus type 2 susceptibility DOI Creative Commons

Lianna R. Walker,

Hiep L. X. Vu, Kristi L. Montooth

et al.

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(11), P. e1011029 - e1011029

Published: Nov. 27, 2023

Mammalian evolution has been influenced by viruses for millions of years, leaving signatures adaptive within genes encoding viral interacting proteins. Synaptogyrin-2 ( SYNGR2 ) is a transmembrane protein implicated in promoting bacterial and infections. A genome-wide association study pigs experimentally infected with porcine circovirus type 2b (PCV2b) uncovered missense mutation p . Arg63Cys associated load. In this study, CRISPR/Cas9-mediated gene editing the kidney 15 (PK15, wtSYNGR2 +p 63Arg cell line generated clones homozygous favorable 63Cys allele emSYNGR2 ). Infection edited resulted decreased PCV2 replication compared to wildtype PK15 (P<0.05), consistent effects across genetically distinct PCV2b PCV2d isolates. Sequence analyses wild domestic (n>700) revealed unique more predominant European than Asian breeds. haplotype defined was likely derived from an ancestral nearly fixed (0.977) but absent boar. We hypothesize that arose post-domestication swine. Decreased genetic diversity homozygotes , corroborates rapid increase frequency SYGNR2 via positive selection. Signatures mammalian species were also identified intraluminal loop domains, coinciding location Therefore, may reflect novel component host-virus evolutionary arms race mammals representing species-specific example putative evolution.

Language: Английский

Citations

0