Population genomic analysis identifies the complex structural variation at the fibromelanosis (FM) locus in chicken

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 18, 2025

Abstract Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified complex structural variant involving both two large duplications (127.4 170.5 kb size) inversions associated upregulated expression of Endothelin 3 ( EDN3 ) gene. However, detailed organization arrangements have remained unclear. this study, we conducted comprehensive genomic survey 517 FM chickens representing 44 different populations. Our results elucidate arrangement at locus based on large-scale survey, population level genotyping, linkage disequilibrium analysis, providing conclusive support for one specific configuration duplications, resolving controversy that has been unresolved more than decade. show birth must involved an interchromosomal rearrangement creating fixed heterozygosity sequence differences between copies 127.4 duplication. This shows how genomics can be used understand variations underlie phenotypic variation.

Language: Английский

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Research progress and applications of genome‐wide association study in farm animals

Animal Research and One Health, Journal Year: 2023, Volume and Issue: 1(1), P. 56 - 77

Published: Aug. 1, 2023

Abstract Exploring the genetic loci underlying economic traits is foundational for innovation in modern animal breeding technology. Genome‐wide association studies (GWAS) have been valid and commonly used tools to dissect genomic variants associated with phenotypes past ∼20 years contributed our understanding of molecular bases various traits. Here, we comprehensively review recent research progress on GWAS methods. We highlight methodological advancements enabled by combination new proteome, transcriptome, epigenome, metagenome information multi‐omics analysis algorithms. The advances investigations chickens, pigs, cattle, other animals during last 5 are also described. Finally, discuss current applications cutting‐edge technologies overall future perspectives post‐GWAS era.

Language: Английский

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Danzhou chicken: a unique genetic resource revealed by genome-wide resequencing data

Poultry Science, Journal Year: 2024, Volume and Issue: 103(8), P. 103960 - 103960

Published: June 7, 2024

Danzhou chicken (DZ) is a local breed in China noted for its strong adaptability, roughage resistance, wildness, and delicious taste, thus containing important genetic resources. In this study, genome re-sequencing data was generated from 200 DZ chickens. Combined with previously 72 additional chickens across six other exotic breeds, these were used to systematically evaluate the germplasm characteristics of genomic perspective. Unlike both southern varieties exhibited high diversity, distance between smaller than A reconstructed Neighbor-Joining phylogenetic tree indicated that all sampled populations clustered into single independent populations, showing clear evidence intra-population differentiation, forming 2 subpopulations. Principal component analysis ADMIXTURE showed significantly different breeds. These results indicate unique resource native The study will improve our understanding structure current status breed, which great significance promoting conservation resources fostering innovations improvement.

Language: Английский

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Whole genome resequencing reveals the adaptability of native chickens to drought, tropical and frigid environments in Xinjiang

Poultry Science, Journal Year: 2024, Volume and Issue: 103(9), P. 103947 - 103947

Published: June 19, 2024

Chickens exhibit extensive genetic diversity and are distributed worldwide. Different chicken breeds have evolved to thrive in diverse environmental conditions. However, research on the mechanisms underlying adaptation extreme environments, such as tropical, frigid drought-prone regions, remains limited. In this study, we conducted whole-genome sequencing of 240 individuals from six native Xinjiang, China, well 4 publicly available inhabiting regions with varying annual precipitations, temperatures, altitudes. Our analysis revealed several variants among examined breeds. Furthermore, investigated population structure residing drought temperature environments by comparing them. Notably, exhibited different structures. Moreover, identified candidate genes associated adaptability environment, CORO2A, CTNNA3, AGMO, GRID2, BBOX1, COL3A1, INSR, SOX5, MAP2 PLPPR1. Additionally, pathways lysosome, cysteine methionine metabolism, glycosaminoglycan degradation, Wnt signaling may be play crucial roles regulating environments. Overall, these findings contribute our understanding governing also offer insights for enhancing resilience climatic

Language: Английский

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Genomic consequences of intensive inbreeding in miniature inbred pigs

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

Published: Feb. 17, 2025

Inbreeding, a central theme in evolutionary and conservation biology, is crucial practice breeding to stabilize enhance the specific traits or establish inbred lines. It also carries risk of inbreeding depression, reduced fitness, increased potential for extinction. Nevertheless, has been extensively studied small endangered populations but its effects large domesticated animals are poorly understood. Here, we aim investigate genomic consequences Banna miniature pig (BN), breed that over 40 years. We have sequenced 41 genomes BN Diannan (DN) at high-coverage (> 31×) combined them with published whole-genomes swine comprehensively genetic inbreeding. find genetically closely related DN, which consistent records. All families undergone an extreme bottleneck due intensive inbreeding, resulting higher coefficients, diversity, lower effective population size (Ne) compare non-inbred pigs. Furthermore, DN exhibit load relative Asian wild boars. Prolonged bottlenecks led some purging deleterious mutations compared conversion from masked realized load. present comprehensive analysis understand assess pigs perspective genomics. Utilizing measurements proves estimating especially when detailed accurate historical record pedigree lacking. Our results provide valuable resources on impacts potentially guiding efforts breeding, improvement, conservation.

Language: Английский

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Novel Candidate Genes Detection Using Bayesian Network‐Based Genome‐Wide Association Study of Latent Traits in F2 Chicken Population

Journal of Animal Breeding and Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

ABSTRACT In chickens, economically important traits are commonly controlled by multiple genes and often correlated. The genetic mechanisms underlying the correlated phenotypes likely involve pleiotropy or linkage disequilibrium, which is not handled properly in single‐trait genome‐wide association studies (GWAS). We employed factor analytical models to estimate value of latent reduce dimensionality adjusted phenotypes. dataset included from 369 F2 categorised into six observable classes, namely body weight (BW), feed intake (FI), efficiency (FE), immunity (IMU), blood metabolites (BMB), carcass (CC) traits. All birds were genotyped using a 60K SNP Beadchip. A Bayesian network (BN) algorithm was used discern recursive causal relationships among inferred Multi‐Trait (MT) Structural Equation Model (SEM) applied for analysis. Several candidate detected across phenotypic IPMK gene BW FI, and, MTERF2 FE. rs14565514 SNP, close , UBE2D1 CISD1 recognised as pleiotropic marker both models. NRG3 gene, located on chromosome 6, associated with FI. CRISP2 RHAG CYP2AC1 CENPQ genes, 3, BMB through MT‐ SEM‐GWAS. general, results indicated that SEM‐GWAS superior MT‐GWAS due considering traits, correcting effects each other, also leading identification markers.

Language: Английский

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Shennong 1 Chicken 40K Liquid Chip: Advancing Genetic Research in Chinese Indigenous Chickens

Animal Research and One Health, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

ABSTRACT China boasts an abundance of indigenous chicken genetic resources, where the exploitation whole‐genome single nucleotide polymorphism (SNP) information offers significant potential for their development. However, current SNP chips are primarily designed commercial chickens or a few local breeds. To address this gap, we have developed “Shennong 1 40K” liquid chip utilizing genotyping by targeted sequencing. This integrates SNPs and present/absent variants is specifically crafted Chinese chickens. It encompasses 44,849 target sites, selected through integration resequencing data, pan‐genome genome‐wide association study previously reported functional data economic traits. Compared to published gene chips, contains higher number polymorphic loci in chickens, demonstrating enhanced applicability. Our validation on 204 individuals from seven different breeds yielded mean capture ratio 99.474% with minor allele frequencies > 0.05 accounting 98.557% total sites. effectively classifies breeds, aligning clustering results population structure analysis actual breed groupings, thereby chip's excellent Additionally, identified genes associated production environmental adaptation selection signal ( IGF1, SOX5, CACNA1G, CXCR4 ). Importantly, sites allow precise evaluation, aiding understanding traits specific informed decision‐making. Overall, provides essential technical support conservation, breeding, identification, evaluation resources.

Language: Английский

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A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(19), P. 14550 - 14550

Published: Sept. 26, 2023

Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand meats from breeds has grown significantly, fueling the selection crossbreeding of (NXP). The latter raised concerns about conservation sustainable use as an important genetic resource. To address these concerns, we conducted comprehensive genomic study using 2242 geographically identified pigs. estimated composition (GBC) suggested 2077 purebred based on ≥94% NXP-GBC cut-off. remaining 165 were claimed to be crosses, including those between Duroc Shaziling pigs, non-Ningxiang Runs homozygosity (ROH) number length ROH varied individuals, with average 32.14 per animal total 202.4 Mb animal. Short (1-5 Mb) was most abundant, representing 66.5% all 32.6% coverage. inbreeding estimate low (0.089) compared imported western breeds. Nine islands identified, pinpointing candidate genes QTLs associated economic traits interest, such reproduction, carcass growth traits, lipid metabolism, fat deposition. Further investigation is anticipated better understand genomics

Language: Английский

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Comparative population genomics analysis uncovers genomic footprints and genes influencing body weight trait in Chinese indigenous chicken

Poultry Science, Journal Year: 2023, Volume and Issue: 102(11), P. 103031 - 103031

Published: Aug. 19, 2023

Body weight of chicken is a typical quantitative trait, which shows phenotypic variations due to selective breeding. Despite some QTL loci have been obtained, the body native breeds in different geographic regions varies greatly, its genetic basis remains unresolved questions. To address this issue, we analyzed 117 Chinese indigenous chickens from 10 (Huiyang Bearded, Xinhua, Hotan Black, Baicheng You, Liyang, Yunyang Da, Jining Bairi, Lindian, Beijing Tibetan). We applied fixation index (FST) analysis find selected genomic and genes associated with traits. Our study suggests that NELL1, XYLT1, NCAPG/LCORL are strongly trait breeds. In addition, IL1RAPL1 gene was large chickens, while PCDH17 CADM2 were small chickens. This result patterns variation commercial chicken, and/or distinct local may follow evolutionary mechanisms.

Language: Английский

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How mites influence cage-free egg production in the United States, mite management strategies, and the mitigating role of genomic selection

Animal Frontiers, Journal Year: 2024, Volume and Issue: 14(5), P. 24 - 31

Published: Oct. 1, 2024

Language: Английский

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