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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Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus)

Heredity, Journal Year: 2023, Volume and Issue: 130(4), P. 242 - 250

Published: Feb. 17, 2023

The distribution of runs homozygosity (ROH) may be shaped by a number interacting processes such as selection, recombination and population history, but little is known about the importance these mechanisms in shaping ROH wild populations. We combined an empirical dataset >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs evolutionary simulations to investigate influence each factors on ROH. assessed focal comparison effect history. investigated role using both physical map genetic linkage search for found differences between populations types indicating that history local rate have Finally, we ran forward with varying histories, rates levels allowing us further interpret our data. These showed has greater than either or selection. show selection can cause genomic regions where common, only when effective size (N

Language: Английский

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Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Animals, Journal Year: 2024, Volume and Issue: 14(8), P. 1246 - 1246

Published: April 22, 2024

Cashmere goats are valuable genetic resources which famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic levels examined candidate associated with trait using whole-genome resequencing data from 123 Herein, Inner Mongolia goat presented lowest coefficient 0.0263. In total, 57,224 ROHs. Seventy-four islands containing 50 were detected. Certain meat, fiber milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); body size growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus identified, found (FGF5, DVL3, NRAS, KIT) length color. These findings enhance our comprehension foundations traits influenced by selective breeding. This contributes significantly future breeding, reservation use other breeds.

Language: Английский

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Genetics underlying phenotypic diversity in South African sheep breeds

Small Ruminant Research, Journal Year: 2025, Volume and Issue: unknown, P. 107499 - 107499

Published: April 1, 2025

Language: Английский

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Genomic Tools for Effective Conservation of Livestock Breed Diversity

Diversity, Journal Year: 2019, Volume and Issue: 12(1), P. 8 - 8

Published: Dec. 20, 2019

Human concern about the status of genetic diversity in livestock breeds and their conservation has increased, as intense selection reduced population sizes many caused losses on global biodiversity. Traditionally, pedigree data provided by breeders were used to estimate parameters, but over past decades, technology made possible development genomic markers. The result been new opportunities more detail, improve well prioritizing animals for resources. aim review is summarize evolution markers explore potential newest high-throughput technologies estimation diversity. More accurate parameters are observed when information decisions instead traditional estimates using data. It also additional such linkage disequilibrium calculate effective size or minimize relatedness among selected individuals based runs homozygosity. For long-term perspectives, methods genome editing considered perspectives reach a balance.

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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Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds

Genes, Journal Year: 2019, Volume and Issue: 10(7), P. 491 - 491

Published: June 28, 2019

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total 1476 horses originating from 12 breeds for the loss diversity by runs homozygosity (ROH) utilizing 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures were identified breed similarities/dissimilarities between populations evaluated. In entire dataset, 180 ROH islands identified, whilst 100 specific, all other overlapped 36 genomic with at least one island another breed. Furthermore, two hot spots determined chromosome 3 (ECA3) ECA11. Besides confirmation previously documented target genes involved coat color (MC1R, STX17, ASIP), body size (LCORL/NCAPG, ZFAT, LASP1, HMGA2), racing ability (PPARGC1A), behavioral traits (GRIN2B, NTM/OPCML) gait patterns (DMRT3), several putative related embryonic morphogenesis (HOXB), energy metabolism (IGFBP-1, IGFBP-3), hair follicle (KRT25, KRT27, INTU) autophagy (RALB) highlighted. pinpointed which might be environmental adaptation habitats (UVSSA, STXBP4, COX11, HLF, MMD).

Language: Английский

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Comparative evaluation of genomic inbreeding parameters in seven commercial and autochthonous pig breeds

animal, Journal Year: 2020, Volume and Issue: 14(5), P. 910 - 920

Published: Jan. 1, 2020

Single nucleotide polymorphism (SNP) genotyping tools, which can analyse thousands of SNPs covering the whole genome, have opened new opportunities to estimate inbreeding level animals directly using genome information. One most commonly used genomic measures considers proportion autosomal covered by runs homozygosity (ROH), are defined as continuous and uninterrupted chromosome portions showing at all loci. In this study, we analysed distribution ROH in three commercial pig breeds (Italian Large White, n = 1968; Italian Duroc, 573; Landrace, 46) four autochthonous (Apulo-Calabrese, 90; Casertana, Cinta Senese, 38; Nero Siciliano, 48) raised Italy, SNP data generated from Illumina PorcineSNP60 BeadChip. We calculated ROH-based coefficients (FROH) different minimum length (1, 2, 4, 8, 16 Mbp) compared them with several other (including difference between observed expected number homozygous genotypes (FHOM)) correlated these genomic-based pedigree coefficient (FPED) for pigs some breeds. Autochthonous had larger mean size than FHOM was highly (0.671 0.985) FROH Apulo-Calabrese Casertana highest values considering lengths (ranging 0.273 0.189 0.226 0.152, moving 1 Mbp (FROH1) (FROH16)), whereas lowest were Siciliano (from 0.072 0.051) White 0.117 0.042). decreased increased Duroc correlations FPED 0.514 0.523) (0.485). Among breeds, Senese correlation FPED. This might be due imperfect measure FPED, which, mainly local extensive production systems, cannot consider a higher errors potential relatedness founder population. It appeared that better captured information could complement pedigree-based management genetic resources.

Language: Английский

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Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(6), P. e0209632 - e0209632

Published: June 14, 2019

Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data 373 animals belonging 23 sheep breeds different geographic origins using the Rsb (extended haplotype homozygosity) FST statistical approaches, identify loci associated with fat-tail phenotype. We also checked if these putative overlapped high-homozygosity (ROH). The analyses identified novel signals confirmed presence signature in genomic that harbor candidate genes known affect fat deposition. Several appeared ROH were within each breed, but only two islands signatures. results reported herein provide most complete genome-wide study for African Eurasian breeds; they contribute insights into genetic basis tail phenotype sheep, confirm great complexity mechanisms underlie quantitative traits, fat-tail.

Language: Английский

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Runs of Homozygosity in Modern Chicken Revealed by Sequence Data

G3 Genes Genomes Genetics, Journal Year: 2020, Volume and Issue: 10(12), P. 4615 - 4623

Published: Oct. 20, 2020

Abstract Runs of homozygosity (ROH) are chromosomal stretches that in a diploid genome appear homozygous state and display identical alleles at multiple contiguous loci. This study aimed to systematically compare the genomic distribution ROH islands among five populations wild vs. commercial chickens both layer broiler type. To this end, we analyzed whole sequences 115 birds including white (WL, n = 25), brown (BL, line A (BRA, 20), B (BRB, 20) Red Junglefowl (RJF, 25). The segments varied size markedly populations, ranging from 0.3 21.83 Mb reflecting their past genealogy. White layers contained largest portion with an average length 432.1 (±18.7) per bird, despite carrying it short (0.3-1 Mb). Population-wise inbreeding measures based on Wright’s (Fis) (FROH) metrics revealed highly inbred lines relative broilers Junglefowl. We further islands, overlapped QTL related limb development (GREM1, MEOX2), body weight (Meis2a.1, uc_338), eggshell color (GLCCI1, ICA1, UMAD1), antibody response Newcastle virus (ROBO2), feather pecking. Comparison landscape sequencing resolution demonstrated sizable segregates homozygote state, many generations assortative mating intensive selection recent history. In contrary, carry shorter segments, likely suggestive older evolutionary events.

Language: Английский

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