Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data

Animal Bioscience, Journal Year: 2024, Volume and Issue: 37(3), P. 461 - 470

Published: Jan. 20, 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures Luxi cattle reveal its genomic characteristics in terms meat carcass traits, skeletal muscle development, body size, other traits.Methods: To further analyze cattle, sequenced 16 individuals from core conservation farm Shandong region, collected 174 published genomes for conjoint analysis. Furthermore, three different statistics (<i>pi</i>, <i>F</i>_st, XP-EHH) were used detect potential positive related cattle. Moreover, gene ontology Kyoto encyclopedia genes pathway enrichment analyses performed biological function candidate harbored selected regions.Results: results showed that had high diversity low inbreeding levels. Using complementary methods genome, there 2,941, 2,221 1,304 potentially identified, respectively. 45 annotated common overlapping regions covered 0.723 Mb, including PLAG1 zinc finger (<i>PLAG1</i>), dedicator cytokinesis 3 (<i>DOCK3</i>), ephrin A2 (<i>EFNA2</i>), DAZ associated protein 1 (<i>DAZAP1</i>), Ral GTPase activating catalytic subunit alpha (<i>RALGAPA1</i>), mediator complex 13 (<i>MED13</i>), decaprenyl diphosphate synthase 2 (<i>PDSS2</i>), most which enriched pathways growth differentiation immunity.Conclusion: In study, we provided a series with important economic traits found regions, scientific basis improvement

Language: Английский

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Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits

Genetics Selection Evolution, Journal Year: 2024, Volume and Issue: 56(1)

Published: May 21, 2024

Abstract Background Livestock populations are under constant selective pressure for higher productivity levels different purposes. This results in the selection of animals with unique adaptive and production traits. The study genomic regions associated these characteristics has potential to improve biological knowledge regarding process how it is connected resilience, which ability an animal adapt stress or imbalance homeostasis. Sheep a species that been subjected several natural artificial pressures during its history, resulting highly specialized adaptation challenging environments. Here, data from multiple studies aim at mapping sweeps across sheep genome traits were integrated identify confirmed (CSS). Results In total, 37 used 518 CSS genome, classified as (147 prodCSS) (219 adapCSS) based on frequency each type study. genes within relevant processes production. For example, adapCSS, related control seasonality, circadian rhythm, thermoregulation. On other hand, prodCSS feeding behaviour, reproduction, cellular differentiation. addition, harbouring both adapCSS showed interesting association lipid metabolism, suggesting role this regulation pleiotropic effects between classes Conclusions findings contribute deeper understanding genetic link adaptability breeds. information may provide insights into mechanisms underlie undesirable correlations two groups pave way better resilience positive respond environmental stressors, where negative level minimized.

Language: Английский

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Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection

Animals, Journal Year: 2024, Volume and Issue: 14(13), P. 1928 - 1928

Published: June 29, 2024

The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for regional economy have a cultural traditional importance inhabitants. aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) PS 2637) based on genome wide SNPs. Estimates linkage disequilibrium effective size (Ne) evidenced more variability (Ne 838) compared 197), regardless historical time (both recent ancient variability). discrepancy between these additionally confirmed by estimates genomic inbreeding (FROH), estimated be notably higher (FROH>2 0.062) than 0.029). average FROH2–4, FROH4–8, FROH8–16, FROH>16 were 0.26, 1.65, 2.14, 3.72 0.22, 0.61, 0.75, 1.58 PS, thus evidencing high contribution overall inbreeding. One ROH island with > 30% SNP incidence ROHs detected (OAR6; 34,253,440–38,238,124 bp) while there no islands PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, SPP1) involved growth, feed intake, milk production, immune responses, resistance associated found autozygosity. results represent first comprehensive insight into two will serve as baseline setting up most promising strategy Optimum Contribution Selection.

Language: Английский

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Comparative proteomics reveals genetic mechanisms of body weight in Hu sheep and Dorper sheep

Journal of Proteomics, Journal Year: 2022, Volume and Issue: 267, P. 104699 - 104699

Published: Aug. 20, 2022

Language: Английский

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Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(6), P. 1220 - 1235

Published: June 1, 2023

Nile tilapia (

Language: Английский

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Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information

Animals, Journal Year: 2023, Volume and Issue: 13(22), P. 3516 - 3516

Published: Nov. 14, 2023

Alpine Merino Sheep is a novel breed reared from Australian as the father and Gansu Fine-Wool mother, living all year in cold arid alpine areas with exceptional wool quality meat performance. Body weight an important economic trait of Sheep, but there limited research on identifying genes associated live 14th month for improving accuracy genomic prediction this trait. Therefore, study's sample comprised 1310 ewes, Fine Wool 50K Panel was used genome-wide association study (GWAS) analysis to identify candidate genes. Moreover, trial population (1310 ewes) randomly divided into two groups. One group GWAS screened most significant top 5%, 10%, 15%, 20% SNPs obtain prior marker information. The other estimate genetic parameters based assigned by heritability combined different aim compare breeding value estimation when information optimal linear unbiased method genome selection (GBLUP) target traits. Finally, evaluated using five-fold cross-validation method. This provides theoretical technical support improve sheep better guide breeding. results demonstrated that eight were analysis, gene function query literature search suggested FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, SYN3 affecting (WT), which regulated growth muscle bone sheep. In GBLUP calculate WT 0.335-0.374, after cross-verification 0.154-0.190, assigning weights accordance previous construct G matrix, model improved 2.59-7.79%.

Language: Английский

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Whole-genome sequencing reveals patterns of runs of homozygosity underlying genetic diversity and selection in domestic rabbits

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

Published: April 29, 2025

Runs of homozygosity (ROH) are continuous segments homozygous genotypes inherited from both parental lineages. These arise due to the transmission identical haplotypes. The genome-wide patterns and hotspot regions ROH provide valuable insights into genetic diversity, demographic history, selection trends. In this study, we analyzed whole-genome resequencing data 117 rabbits identify inbreeding level across eleven rabbit breeds, including seven Chinese indigenous breeds four exotic uncover selective signatures based on islands. We detected a total 31,429 ROHs autosomes all with number (NROH) per breed ranging 1316 7476. mean sum length (SROH) individual was 493.84 Mb, covering approximately 22.79% autosomal genome. majority ranged 1 2 Mb in length, an average (LROH) 1.84 Mb. longer than 6 constituted only 0.83% ROHs. coefficient derived (FROH) 0.23, FROH values 0.14 0.38 breeds. Among Jiuyishan exhibited highest NROH, SROH, LROH, FROH, whereas Fujian Yellow had lowest values. Japanese White displayed for while Flemish Giant these metrics. Additionally, identified 17 islands 22 encompassing 124 186 genes, respectively. prominent genes associated reproduction, CFAP206, RNF133, CPNE4, ASTE1, ATP2C1, as well related adaptation, namely CADPS2, FEZF1, EPHA7. contrast, prevalence fat deposition, such ELOVL3 NPM3, growth body weight FAM184B, NSMCE2, TWNK. This study enhances our understanding diversity pressures domestic rabbits, offering implications breeding management conservation strategies.

Language: Английский

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Genetic diversity and population structure of four Anatolian sheep revealed by genome-wide ddRADseq data

Small Ruminant Research, Journal Year: 2024, Volume and Issue: 235, P. 107285 - 107285

Published: May 9, 2024

Language: Английский

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Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

Genetics Selection Evolution, Journal Year: 2024, Volume and Issue: 56(1)

Published: July 30, 2024

Abstract Background Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of can have detrimental effects on reproduction and production performance a breed. Analysis facilitate identification signatures selection which may contribute to specific characteristics regarding health, physical appearance breed or population. In this study, breeds with well-characterized traits such as fine wool (Rambouillet, N = 745), parasite resistance (Katahdin, 581) environmental hardiness (Dorper, 265) were evaluated inbreeding, effective population size ( e ), runs (ROH) Wright’s fixation index (F ST ) outlier approach identify differential at 36,113 autosomal single nucleotide polymorphisms (SNPs). Results Katahdin sheep had largest current most recent generation estimated both GONe NeEstimator software. The highly conserved ROH Island was identified in Rambouillet signature chromosome 6 containing 202 SNPs called an 50 94% individuals. This region contained DCAF16 , LCORL NCAPG genes that been previously reported be under biological roles related milk growth traits. regions through F comparisons Dorper known mastitis susceptibility, growth, suggesting these natural artificial pressure populations. Genes involved cytokine-cytokine receptor interaction pathways all comparisons, indicates presence allelic between genomic controlling cytokine signaling mechanisms. Conclusions paper, we describe within diverse economically U.S. breeds. are proposed further study understand their relevance improve understanding diversity.

Language: Английский

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Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 4, 2023

Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They often reared as pure or used in crossbreeding common component synthetic development. This study evaluated genetic diversity, population structure, divergence 279 animals Merino-based breeds South Africa using Illumina Ovine SNP 50K BeadChip. The analysed included three Merino-derived Dohne ( n = 50); Meatmaster 47); Afrino 52) five presumed ancestral populations Merinos (Merino 46); African 10); Mutton 8)); non-Merino founding Damara 20); Ronderib Afrikaner 17); Nguni 29). Highest diversity values were observed (DM), with H o 0.39 ± 0.01, followed by (SAM), 0.37 0.03. level inbreeding ranged from 0.0 0.02 (DM) to 0.27 0.05 (Nguni). Analysis molecular variance (AMOVA) showed high within-population (&gt;80%) all categories. first principal (PC1) separated Merino, (SAMM), DM, (AFR) Meatmaster, Damara, Nguni, (RDA). PC2 aligned each its ancestors SAMM SAM. iHS analysis yielded selection sweeps AFR (12 sweeps), (four DM (29 sweeps). Hair/wool trait genes such FGF12 ; metabolic ICA1 , NXPH1 GPR171 immune response IL22 IL26 IFNAR1 IL10RB reported. Other include HMGA which was signatures other populations; WNT5A important development skeleton mammary glands; ANTXR2 associated adaptation variation climatic conditions; BMP2 has been reported strongly selected both fat-tailed thin-tailed sheep. vs. shared six sweep regions on chromosomes 1, 10, 11 SAMM. Genes OAR 1:191.3–194.7 Mb MAP2K4 11:28.6–31.3 observed. chromosome 10 region 28.6–30.3 harbouring RXFP2 polledness between Nguni. also an Rsb-based 1 268.5–269.9 Calpain gene, CAPN7. demonstrated some similarities emanating driven breed-specific goals. Overall, information regarding evolution these composite will guide future improvement programs management conservation efforts.

Language: Английский

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