Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 2, 2024

Abstract Heterozygosity-rich regions (HRR) are genomic of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim work was inter-breed relationships HRR patterns using Sliding Window (SW) Consecutive Runs (CR) detection methods. Genetic highlighted a clear separation between non-European European breeds, well north–south geographic cline within latter. Pearson correlation coefficients descriptive parameters obtained SW CR methods were higher than 0.9. A total 166 islands detected. CHI1, CHI11, CHI12 CHI18 chromosomes harboring highest number islands. genes annotated in linked various factors productive, reproductive, immune, environmental adaptation mechanisms. Notably, Montecristo feral showed despite level inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying species-specific pattern could provide clearer view mechanisms regulating genome modelling following anthropogenic combined interaction.

Language: Английский

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Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Sept. 26, 2023

Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information scarce local goat breeds in Egypt. In current study, regions with selection signatures were identified as well runs homozygosity (ROH), inbreeding coefficients (FROH) fixation index (FST) detected Egyptian Nubian, Damascus, Barki Boer breeds. A total 46,268 SNP markers 337 animals available analyses. On average, 145.44, 42.02, 87.90 126.95 ROHs per individual autosomal genome respective The mean accumulative ROH lengths ranged from 46.5 Mb Damascus to 360 Nubian. short segments (< 2 Mb) most frequent all breeds, while longest (> 16 exclusively found highest average FROH was observed Nubian (~ 0.12) followed by 0.11), lowest 0.05) breed 0.03). estimated FST 0.14 (Egyptian Boer), 0.077 Barki), 0.075 Damascus), 0.071 (Barki 0.064 (Damascus 0.015 each pair Interestingly, multiple SNPs that accounted high values on chromosome 6 harboring ALPK1 KCNIP4. Genomic overlapping both harbor genes related immunity (IL4R, PHF23, GABARAP, GPS2, CD68), reproduction (SPATA2L, TNFSF12, TMEM95, RNF17), embryonic development (TCF25 SOX15) adaptation (MC1R, KDR, KIT), suggesting potential genetic adaptations environmental conditions. Our results contribute understanding architecture different may provide valuable effective preservation

Language: Английский

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Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 29, 2024

Abstract Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to remarkable adaptability diverse environmental and production systems. Differential selection pressures influenced by climate led variations in physical attributes, leaving genetic imprints within the genomes of goat breeds raised agroecological settings. In light this, our study pursued a comprehensive analysis, merging data with single nucleotide polymorphism (SNP) variations, unearth indications shaped climate-mediated forces goats. Through examination 43,300 SNPs from 51 indigenous adapting different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), spatial analysis method (SAM), A total 74 genes were revealed display clear signs selection, which are believed be conditions. Among these genes, 32 consistently identified at least two applied methods, three ( DENND1A , PLCB1 ITPR2 ) confirmed all approaches. Moreover, investigation yielded 148 Gene Ontology (GO) terms based on underlining pivotal biological pathways crucial for adaptation. These encompass functions like vascular smooth muscle contraction, cellular response heat, GTPase regulator activity, rhythmic processes, responses temperature stimuli. Of significance, GO about endocrine regulation energy metabolic responses, key local adaptation also uncovered, including such cell differentiation, peptide hormone secretion, lipid metabolism. findings contribute knowledge structure climate-triggered genome practical implications marker-assisted breeding

Language: Английский

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Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 16, 2024

Abstract Background Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation these modern breeds via admixture events. However, their confusing genetic backgrounds include genomic footprint regulating complex traits, which is not conducive animal breeding. Results To better evaluate candidate regions under domestication indigenous chickens, we considered both runs homozygosity (ROHs) selective signatures 13 chickens. The Silkie feather presented highest heterozygosity, whereas inbreeding status ROH number found Luhua Short (< 1 Mb), principal type all A total 291 islands detected, QTLdb mapping results indicated that body weight carcass traits most important traits. An on chromosome 2 covering VSTM2A gene was detected 12 populations. Combined analysis with Tajima’s D index revealed 18 genes (e.g., , BBOX1 RYR2 ) selection covered by islands. Transcriptional showed specifically expressed heart muscle tissue, respectively. Conclusion Based genome-wide scanning for signatures, evaluated characteristics significant signatures. findings this study facilitated understanding diversity provided valuable insights chicken breeding conservation strategies.

Language: Английский

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Genome-wide landscape of genetic diversity, runs of homozygosity, and runs of heterozygosity in five Alpine and Mediterranean goat breeds

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 3, 2025

Abstract Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection adaptability to harsh environments. Understanding their adaptive traits can aid breeding programs target enhanced resilience productivity, especially as we are facing important climate agriculture challenges. To this aim genomic architecture 480 goats belonging five (i.e., Saanen [SAA], Camosciata delle Alpi [CAM], Murciano-Granadina [MUR], Maltese [MAL], Sarda [SAR]) reared Sardinia Island were genotyped evaluated find molecular basis traits. Inbreeding, runs homozygosity (ROH) heterozygosity (ROHet) identified. Finally, candidate genes ROH ROHet regions explored through pathway analysis assess role. Results In total, detected 10,341 SAA genome, 11,063 CAM 12,250 MUR 8,939 MAL 18,441 SAR genome. Moreover, identified 4,087 for SAA, 3,360 CAM, 2,927 MUR, 3,701 MAL, 3,576 SAR, with having highest coefficient. Interestingly, when computing inbreeding coefficient using homozygous segment ( F ), showed lowest value while one, suggesting need improve selecting strategies preserve diversity within population. Among most significant genes, several ones linked different physiological functions, such milk production (e.g., DGAT1 , B4GALT1 immunity GABARAP GPS2 ) adaptation environment GJA3 GJB2 GJB6 ). Conclusions This study highlighted among goat breeds. The high levels some might indicate lack variation, which negatively impact animal Conversely, diversity, beneficial breed health resilience. Therefore, these findings could managing preserving diversity.

Language: Английский

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Investigation of selection signatures of dairy goats using whole-genome sequencing data

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 12, 2025

Dairy goats, a livestock species with long history of milk production, are essential for the economic advancement nations, particularly in regions experiencing growth. In this study, we gathered whole-genome resequencing data 58 including 34 dairy goats and 24 wild (Bezoar), to explore selection signatures linked production traits using ROH (Runs homozygosity), CLR (composite likelihood ratio), Fst (Fixation index), XP-EHH (Ex-tended haplotype homozygosity across populations) XP-CLR(Cross-population composite ratio test) methods. Analysis five tests revealed total 210 genes, genes consistently identified at least two approaches. These associated fat, protein, fat yield. Gene enrichment analysis highlighted important GO KEGG pathways related such as "acyl-CoA metabolic process", "glycerolipid biosynthetic "cellular response fatty ac-id", "hormone "Galactose metabolism". Additionally, repro-duction, immune response, environmental adaptation were goats. The findings from our study offer profound understanding into critical features practical guidance improvement development crossbreeding initiatives different goat breeds.

Language: Английский

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Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data

Animal Genetics, Journal Year: 2025, Volume and Issue: 56(3)

Published: May 14, 2025

Abstract The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province southern China and boasts a rich history. goats exhibit exceptional traits, including heat insect resistance, strong reproductive capabilities superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole‐genome resequencing on 21 goats. Additionally, performed joint analysis using published data from 119 goats, Chengdu goat, Matou Wuxue Xiangdong Black Qaidam Cashmere Ujumqin Shanbei goat. results revealed that genetically more pure than other Southern Chinese breeds. Furthermore, genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity inbreeding coefficient) goat's genome at low level among eight breeds, indicating need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide integrated haplotype score, fixation index cross‐population extended homozygosity, systematically scanned selective signals within genomic landscape outcomes underscore selection associated with genes implicated immune response, tolerance, performance quality. These findings make significant contribution our understanding genetics framework adaptive traits study explores which may contribute theoretical conserving its resources, while identified trait‐associated variations could inform future strategies optimize breeding programs.

Language: Английский

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A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array

animal, Journal Year: 2023, Volume and Issue: 17(3), P. 100706 - 100706

Published: Jan. 13, 2023

Tibetan goats, Taihang Jining grey and Meigu goats are the representative indigenous in China, found Qinghai-Tibet Plateau, Western pastoral area, Northern Southern agricultural regions. Very few studies have conducted a comprehensive analysis of genomic diversity selection these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, following breeds: (TG), (THG), (JGG), (MGG). A total 45 951 single nucleotide polymorphisms were filtered to estimate genetic signatures. All breeds had high proportion (over 95%) polymorphic loci. The observed excepted heterozygosity ranged from 0.338 (MGG) 0.402 (JGG) 0.339 0.395 respectively. Clustering displayed genetically distinct lineage for each breed, their Fst greater than 0.25, indicating that they higher differentiation between groups. Furthermore, effective population size reduced all four populations, loss diversity. In addition, runs homozygosity mainly distributed 5–10 Mb. Lastly, we identified signature genes, which closely related high-altitude adaptation (ADIRF) prolificity (CNTROB, SMC3, PTEN). This study provides valuable resource future on genome-wide perspectives signatures Chinese goats.

Language: Английский

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Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs

animal, Journal Year: 2024, Volume and Issue: 18(8), P. 101236 - 101236

Published: July 2, 2024

Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures humidity. Runs homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals selection signals that may reveal candidate genes associated with key functional traits. heterozygosity (ROHet) commonly balance selection, which help us understand adaptive evolutionary history domestic animals. In this study, we investigated ROHs ROHets 88 pigs. We also compared estimates coefficients calculated based on four methods. summary, detected a total 16 ROH islands our 100 were found within regions. These correlated economically important traits such as reproduction (e.g., SERPIND1, HIRA), quality PI4KA, TBX1), immunity ESS2, RANBP1), adaption heat stress (TXNRD2 DGCR8), food tolerance (TRPM6). Moreover, discovered 18 ROHet harbouring ARHGEF12, BMPR2), immune system BRD4, DNMT3B). findings design effective breeding conservation strategies unique breed.

Language: Английский

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Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Genes, Journal Year: 2024, Volume and Issue: 15(3), P. 313 - 313

Published: Feb. 28, 2024

Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits livestock. In this study, we analyzed resequencing data from 10 local goat breeds Yunnan province China five additional populations obtained a public database. The ROH analysis revealed 21,029 across 15 populations, an average length 1.27 Mb, pattern ROH, assessment coefficient indicating diversity varying levels inbreeding. iHS (integrated haplotype score) was analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) regions, related economic such as coat color weight variation. These candidate include OCA2 (OCA2 melanosomal transmembrane protein) MLPH (melanophilin) color, EPHA6 (EPH receptor A6) involved litter size, CDKAL1 (CDK5 regulatory subunit protein 1 like 1) POMC (proopiomelanocortin) linked variation some putative high-altitude adaptability immune. This study uncovers within province, China. identification provides actionable insights for utilization conservation efforts.

Language: Английский

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