Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia

Genetics Selection Evolution, Journal Year: 2022, Volume and Issue: 54(1)

Published: April 28, 2022

Abstract Background The importance of local breeds as genetic reservoirs valuable variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation several pig breeds. In present study, diversity parameters were analysed six autochthonous from Slovenia, Croatia Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka Krskopolje pig). Animals each these genotyped using microsatellites single nucleotide polymorphisms (SNPs). results obtained with two marker systems those based on pedigree data compared. addition, we estimated inbreeding levels distribution runs homozygosity (ROH) identified genomic regions under selection pressure ROH islands integrated haplotype score (iHS). Results lowest heterozygosity values calculated microsatellite SNP observed pig. was higher than expected Both types markers allowed us distinguish clusters individuals belonging breed. analysis admixture between revealed potential gene flow Mangalitsa Moravka, but no introgression events detected Banija spotted across genome not uniform. Analysis an extremely high frequency shared within which harboured genes associated cholesterol biosynthesis, fatty acid metabolism daily weight gain. iHS approach detect signatures candidate containing roles reproduction traits disease resistance. Conclusions Based estimation population three sets, showed existence relationships among here. estimate level extent homozygous potentially phenotypic detection pressure.

Language: Английский

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Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: May 5, 2022

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including production high-quality branded products, (ii) enrich animal biobanking (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer opportunity for whole-genome comparisons among individuals breeds. Animals from twenty European pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), three commercial (Duroc, Landrace Large White) were sampled genotyped with GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset 51 Wild Boars was also added, summing up 1186 (~ 49 pigs/breed). The aim to: investigate individual admixture ancestries assess breed traceability via discriminant analysis on principal components (DAPC). Albeit mosaic shared found Sarda indicated independent evolvement rest High prediction accuracy DAPC mark SNP data as reliable solution breed-specific products.

Language: Английский

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Merging metabolomics and genomics provides a catalog of genetic factors that influence molecular phenotypes in pigs linking relevant metabolic pathways

Genetics Selection Evolution, Journal Year: 2025, Volume and Issue: 57(1)

Published: March 6, 2025

Metabolomics opens novel avenues to study the basic biological mechanisms underlying complex traits, starting from characterization of metabolites. Metabolites and their levels in a biofluid represent simple molecular phenotypes (metabotypes) that are direct products enzyme activities relate all metabolic pathways, including catabolism anabolism nutrients. In this study, we demonstrated utility merging metabolomics genomics pigs uncover large list genetic factors influence mammalian metabolism. We obtained targeted plasma metabolome more than 1300 two populations Large White Duroc pig breeds. The metabolomic profiles these were used identify genetically influenced metabolites by estimating heritability level 188 Then, combining breed-specific genome-wide association studies single ratios across breed meta-analyses, identified total 97 metabolite quantitative trait loci (mQTL), associated with 126 Using results, constructed human-pig comparative catalog influencing profile. Whole genome resequencing data several putative causative mutations for mQTL. Additionally, based on major mQTL kynurenine level, designed nutrigenetic feeding piglets carried different genotypes at candidate gene 3-monooxygenase (KMO) varying tryptophan effect factor pathway. Furthermore, reconstruct pathways using Gaussian Graphical Models, which included perturbation This has provided first affecting describe blood metabolome, links important opening merge genetics nutrition livestock species. results relevant applied biology evaluate as biomedical model. Genetically can be further exploited approaches pigs. described useful dissect traits design feeding, breeding selection programs

Language: Английский

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Genome-Wide Runs of Homozygosity Reveal Inbreeding Levels and Trait-Associated Candidate Genes in Diverse Sheep Breeds

Genes, Journal Year: 2025, Volume and Issue: 16(3), P. 316 - 316

Published: March 7, 2025

Background: Quantifying and controlling the inbreeding level in livestock populations is crucial for long-term sustainability of animal husbandry. However, extent has not been fully understood sheep on a global scale. Methods: Here, we analyzed high-depth genomes 210 from 20 worldwide breeds to identify pattern distribution genome-wide runs homozygosity (ROH) detect candidate selected genes ROH islands agronomic phenotypic traits. Results: Leveraging whole-genome sequencing data, found large number short (e.g., <1.0 Mb) all observed overall higher values statistics coefficient European than Asian Dorper sheep. We identified some well-known CAMK4, HOXA gene family, ALOX12, FGF11, MTOR) 40 novel KLHL1, FGFRL1, WDR62, GDF6, KHDRBS2, PAX1) that are functionally associated with fecundity, body size, wool-related traits Based genes, revealed different genetic bases fecundity Conclusions: This study improves resolution detection provides new insights into genomic trait architecture as well useful markers future breeding practice.

Language: Английский

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Assessment of Heterozygosity in European Local and Cosmopolitan Pig Populations

Agriculture, Journal Year: 2025, Volume and Issue: 15(7), P. 761 - 761

Published: April 1, 2025

Researchers focused on assessing differences in gene diversity within and between populations, whether cosmopolitan or local. However, the identification of patterns variation non-random heterozygous genomic stretches, known as Heterozygosity-Rich regions (HRRs), has not yet been determined European local pig breeds. A total 23 breeds (20 3 cosmopolitan) were assessed compared terms heterozygosity-rich regions. The with highest number HRRs Large White, Lithuanian Old type, Landrace, followed by Native, Mora Romagnola, Duroc. lowest Alentejana, Iberian, Majorcan Black. No shared HRR islands found all breeds, but enrichment analysis performed most common revealed several biologically important genes that cluster together play significant roles, primarily related to immune system. Permutation indicated some serve true reservoirs genetic diversity, displaying distinct unique characteristics heterozygosity. This study suggests importance investigating heterozygosity develop a comprehensive picture regardless production system, country origin, population size.

Language: Английский

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Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Frontiers in Veterinary Science, Journal Year: 2022, Volume and Issue: 9

Published: March 8, 2022

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures livestock. Commercial breeds provide excellent materials reveal the landscape ROH shaped during intense process. Here, we GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data 3,770 American Duroc (AD) 2,096 Canadian (CD) pigs analyze genome-wide ROH. First, showed that AD had a moderate differentiation with CD pigs, more abundant diversity significantly lower level inbreeding than pigs. In addition, sows larger levels boars in These differences may be caused by selective intensity. Next, hotspots revealed many candidate genes putatively under for growth, sperm, muscle development two lines. Population-specific ROHs inferred have special female reproduction, while immunity. Moreover, overlapping populations, observed missense mutation (rs81216249) located growth fat deposition-related supergene (

Language: Английский

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Identification of population‐informative markers from high‐density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds

Animal Genetics, Journal Year: 2024, Volume and Issue: 55(2), P. 193 - 205

Published: Jan. 8, 2024

Abstract Large genotyping datasets, obtained from high‐density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied Boruta algorithm, wrapper machine learning random forest on database 23 European pig (20 autochthonous three cosmopolitan breeds) with 70k SNP chip, pre‐select informative SNPs. sets these pre‐selected were then ranked based their mean decrease accuracy gene indexes. We evaluated efficiency subsets breed classification usefulness approach detect candidate genes affecting breed‐specific phenotypes relevant production traits that might differ breeds. The lowest overall error (2.3%) was reached subpanel including only 398 SNPs (ranked accuracy), no in seven using up 49 Several selected subpanels genomic regions which previous studies had identified signatures selection associated morphological distinguish analysed Therefore, even if not originally designed selection, results showed they could potentially useful purpose.

Language: Английский

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Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

Journal of Dairy Science, Journal Year: 2021, Volume and Issue: 105(3), P. 2408 - 2425

Published: Dec. 23, 2021

Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas white with some pale gray shades). Almost all milk produced by these breeds transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive economic incomes needed sustainable conservation animal genetic resources. After setting up herd books 1960s, experienced a strong reduction population size was subsequently reverted starting 1990s (Reggiana) or more recently (Modenese) reaching at present total about 2,800 500 registered cows, respectively. Due to small inbreeding very important cause concern programs. Inbreeding traditionally estimated using pedigree data, summarized an coefficient calculated individual level (FPED). However, incompleteness information registration errors affect effectiveness strategies. High-throughput SNP genotyping platforms allow investigation genome overcome limits data. Several approaches have been proposed estimate genomic inbreeding, use runs homozygosity (ROH) considered appropriate. In this study, several parameters, whole book populations considering (GeneSeek GGP Bovine 150K) 1,684 323 cattle, were compared. Average values per year used calculate effective size. breed had generally lower than breed. The low correlation between pedigree-based genomic-based parameters (ranging 0.187 0.195 0.319 0.323 respectively) reflected common problems local records not complete. high proportion short ROH over number indicates no major recent events both breeds. islands spread (15 14 Modenese) identified signatures selection. Some included genes affecting production traits, stature, body conformation traits (with main island on BTA6 containing ABCG2, NCAPG, LCORL genes) (on BTA13 ASIP gene). conclusion, work provides extensive comparative analysis relevant will useful strategies iconic

Language: Английский

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Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity

Journal of Animal Breeding and Genetics, Journal Year: 2022, Volume and Issue: 139(3), P. 292 - 306

Published: Jan. 4, 2022

Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures at genome-wide level, runs homozygosity (ROH) getting increasing popularity. In this paper, ROH distribution features a sample 823 Sarda breed ewes farmed different levels altitude analysed investigate effect environment on patterns homozygosity. A total 46,829 (33,087 unique) were detected. OAR2 exhibited largest average number per animal. The most frequent (OAR27, 38.9-44.2 Mb) was shared by 327. length statistically affected (p < 0.001) both temperature place where flock located. highest probability SNP falling in observed for hill ewes, whereas smallest one mountain. 457 exceeded 99th percentile count considered significant. These markers mapped eight chromosomes they clustered into 17 islands, 80 candidate genes mapped. Results study highlighted differences among sheep flocks located altitude, confirming role environmental adaptability shaping breed.

Language: Английский

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Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

Animal Genetics, Journal Year: 2023, Volume and Issue: 54(5), P. 591 - 605

Published: June 28, 2023

Analysis of genomic data is becoming more and common for the effective management livestock breeding programmes, even in case local populations. In this work, genome-wide Nero Siciliano pig breed were compared to that wild boar, Italian cosmopolitan breeds investigate its genetic structure, runs homozygosity (ROH) heterozygosity patterns. The has been reported have highest rate diversity among breeds, a variability comparable breeds. Analyses structure relationships underlined proximity an internal substructure probably linked different family lines. showed low value inbreeding estimated from ROH, index if lower than cosmopolitans. Four ROH islands three chromosomes (SSC8, SSC11, SSC14) one heterozygosity-rich region (SSC1) identified Siciliano, highlighting regions related productive QTL. Across SSC8 SSC14 with most islands, Mora Romagnola boar showing level autozygosity. Chromosomes SSC2, SSC6, SSC13 majority regions, mainly found which several genes associated health-related outlined results can help better identify profile order plan matings, maintain adequate exploit production system.

Language: Английский

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