Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens

Journal of Advanced Research, Journal Year: 2023, Volume and Issue: 55, P. 1 - 16

Published: March 5, 2023

Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern breeding technology systems. Chicken is one of most efficient environmentally friendly livestock, especially fast-growing white-feathered (broiler), which well known for high yield, but underlying basis poorly understood. We generated whole-genome resequencing three purebred broilers (n = 748) six local breeds/lines 114), sequencing data twelve breeds 199) were obtained from NCBI database. Additionally, transcriptome tissues two 129) at developmental stages was performed. A genome-wide association study combined with cis-eQTL mapping Mendelian randomization applied. identified > 17 million high-quality SNPs, 21.74% newly identified, based on 21 breeds/lines. total 163 protein-coding genes underwent positive selection in broilers, 83 differentially expressed between chickens. Notably, muscle development proven be major difference chickens, or ancestors, transcriptomic evidence multiple stages. The MYH1 gene family showed top muscle-specific expression broilers. Furthermore, we found that causal SOX6 influenced breast yield also myopathy occurrences. refined haplotype provided, had a significant effect phenotypic changes. Our provides comprehensive atlas comprising typical variants transcriptional characteristics suggests regulatory target (SOX6–MYH1s axis) myopathy, aid genome-scale selective aimed broiler

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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Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: March 29, 2022

Abstract Background A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding their biological functions. We performed a large-scale and generated high-resolution atlas the transcriptome in beef cattle. Results Our was from 135 bovine adult cattle, covering 51 tissue types major organ systems (e.g., muscular system, digestive immune reproductive system). Approximately 94.76% sequencing reads were successfully mapped to reference genome assembly ARS-UCD1.2. detected total 60,488 transcripts, 32% them not reported before. identified 2654 housekeeping genes (HKGs) 477 tissue-specific (TSGs) tissues. Using weighted co-expression network analysis, we obtained 24 modules with 237 hub (HUBGs). Functional enrichment showed that HKGs mainly maintain basic activities cells, while TSGs involved differentiation specific physiological processes. more conserved terms pattern as compared HUBGs among multiple species. Finally, subset differentially expressed (DEGs) between dairy cattle several functional pathways, which may be production health traits. Conclusions providing valuable enhancing annotation. HKGs, TSGs, further contribute better biology evolution DEGs also fill knowledge gaps about differential regulation underlying economically important

Language: Английский

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The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 11, 2023

A detailed understanding of genetic variants that affect beef merit helps maximize the efficiency breeding for improved production in cattle. To prioritize putative and genes, we ran a comprehensive genome-wide association studies (GWAS) analysis 21 agronomic traits using imputed whole-genome Simmental Then, applied expression quantitative trait loci (eQTL) mapping between genotype transcriptome three tissues (longissimus dorsi muscle, backfat, liver) 120 cattle.We identified 1,580 signals GWAS. We then illuminated 854,498 cis-eQTLs 6,017 genes 46,970 trans-eQTLs 1,903 built synergistic network by integrating transcriptomics with traits. These were preferentially close to transcription start site enriched functional regulatory regions. observed an average 43.5% improvement cis-eQTL discovery multi-tissue eQTL mapping. Fine-mapping revealed 111, 192, 194 most likely be causative regulate gene liver, respectively. The transcriptome-wide 722 significantly associated 11 Via colocalization Mendelian randomization analyses, found eQTLs several GWAS tissues, which included such as NADSYN1, NDUFS3, LTF KIFC2 GRAMD1C, TMTC2 ZNF613 well TIGAR, NDUFS3 L3HYPDH muscle could serve candidate economic traits.The extensive atlas GWAS, eQTL, fine-mapping, aid suggestion potentially cattle will invaluable source genomics

Language: Английский

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An overview of recent technological developments in bovine genomics

Veterinary and Animal Science, Journal Year: 2024, Volume and Issue: 25, P. 100382 - 100382

Published: July 23, 2024

Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number strategies improve the genetic makeup bovine germplasm. To ensure higher returns for dairy beef industries, researchers face greatest challenge in improving commercially important traits. One biggest developments last few decades creation instruments cattle improvement is discovery genome. Breeding livestock being revolutionized by genomic selection made possible availability medium- high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It becoming easier access high-dimensional data cattle. Continuously declining genotyping costs an increase services that use return on investment have both significant contribution this. field genomics come long way thanks groundbreaking discoveries such radiation-hybrid mapping, situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing genome editing. These advancements had positive impact genomics. This manuscript aimed review recent advances technologies breeding future prospects this field.

Language: Английский

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A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle

Gene, Journal Year: 2024, Volume and Issue: 908, P. 148295 - 148295

Published: Feb. 21, 2024

Language: Английский

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Genetic parameters and genome-wide association studies including the X chromosome for various reproduction and semen quality traits in Nellore cattle

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

Published: Jan. 10, 2025

Abstract Background The profitability of the beef industry is directly influenced by fertility rate and reproductive performance both males females, which can be improved through selective breeding. When performing genomic analyses, genetic markers located on X chromosome have been commonly ignored despite being one largest chromosomes in cattle genome. Therefore, primary objectives this study were to: (1) estimate variance components parameters for eighteen male five female traits Nellore including analyses; (2) perform genome-wide association studies functional analyses to better understand background cattle. Results percentage total direct heritability (h 2 ) explained x ranged from 3 32% (average: 16.4%) 9 67% 25.61%) traits, respectively. Among related breeding soundness evaluation, overall bull semen evaluation quality accounted highest proportion h relative with an average 39.5% 38.75%, number significant per trait 7 (seminal vesicle width) 43 (total major defects). zero five. A 683, 252, 694, 382, 61, 77 genes overlapped regions identified performance, quality, morphology, defects, bulls’ key candidate are PRR32 , STK26 TMSB4X TLR7 PRPS2 SMS SMARCA1 UTP14A BCORL1 . main gene ontology terms “Oocyte Meiosis”, “Progesterone Mediated Oocyte Maturation”, “Thermogenesis”, “Sperm Flagellum”, “Innate Immune Response”. Conclusions Our findings indicate role phenotypic variability reproduction Breeding programs aiming improve these should consider adding information their analyses.

Language: Английский

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The HTIRDB: A resource containing a transcriptional atlas for 105 different tissues from each of seven species of domestic herbivore

iMeta, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 28, 2025

Here, we describe the Herbivore Transcriptome Integrated Resource Database (HTIRDB, https://yanglab.hzau.edu.cn/HTIRDB#/). The HTIRDB comprises self-generated transcriptomic data from 100 to 105 tissues two female domestic herbivores six species (cattle, donkey, goat, horse, rabbit, and sika deer) breeds of sheep, an extra 28,710 related published datasets. user-friendly interface provides tools functionalities that facilitate exploration gene expression between species. for comparative transcriptomics can be used identify housekeeping genes, tissue-specific species-specific species-conserved genes. To date, is most extensive transcriptome resource freely available. Amongst herbivores, ruminants are essential sustainable agriculture because they well-adapted environments utilize low-quality feedstuff [1, 2]. further integrate into practices, it understand how their genotypes interact with environment affect phenotype. A cross-species atlas in organs or different herbivore would help uncover fundamental biological processes. Several transcriptional atlases some herbivore, such as cattle, donkeys, water buffalo, goats, available [3-6]. However, comparison these datasets difficult, if not impossible, separate databases, sample collection, RNA sequencing, processing were standardized across databases. Moreover, databases relatively small numbers always common all Here report creation https://yanglab.hzau.edu.cn/HTIRDB#/), a public database facilitates profiles large number seven high economic value (Figure 1A). includes deer, sheep. Both Hu small-tail Han sheep included relevance China. hosts 100–105 females each was collected using standard protocol [7], have close relationship herbivores. In addition, nine bioinformatics tools, publicly available, use by biologists. On homepage 1A), "Species" "Tissue Samples" panels link information on tissue samples. "Sample Information" module displays anatomical distribution coding system tables diagrams. offers four retrieval visualization: electronic fluorescent pictographic (eFP), expression, transcriptomics, co-expression analysis. suite bioinformatic 1B). 30,352 datasets, comprising 1642 RNA-sequences (RNA-Seq) (mapping rate 93.9 ± 4.0%, Table S1), RNA-Seq 94.8 5.5%, S2) contributing approximately 638 billion high-quality sequencing reads. eFP panel built Python Imaging Library Build (www.python.org). corresponding location presented representation animal colors 2A). "Single Species" enables user visualize absolute relative any target within Additionally, users compare ratio primary reference same "Two compares genes breeds. "Multiple one other "Expression" panel, three modules, comprehensive platform access mRNA lncRNA 2B). "Multi-genes Single analyses single multiple species/breed species/breeds. "LncRNA Expression Profile" queries tissues. visualized table, heatmap, broken line chart, box plot. unique called "Query Sample," which presents table so select "Comparative Transcriptomics" modules allow Species." selected compared 2C). differentially expressed (DEGs) outputs volcano plots, tables, bar plots 20 largest differences expression. (TSGs) (HKGs) retrieved section, while (SSGs) (SCGs) identified defaults user-defined parameters [8]. "Co-expression" creates networks visualizing similar patterns 2D). Once interest, species, selected, visual interactions generated together Pearson's correlation coefficients. "Variation Alternative Splicing" genomic variation specified region structure plot, annotation details those variations pie chart. "Alternative model options types index values splicing events "Tools" additional tools. For example, "JBrowser" viewer generates graphical overview newly RNA-seq illustrate profile samples entire sequences 2E). "Blast" tool interrogate download sequences, including genome protein specific 2F). "Gene Ontology Kyoto Encyclopedia Genes Genomes (GO&KEGG) Enrichment" function allows analysis explore roles pathways associated 2G). "Pathway" integrates KEGG visualizes involved pathway given "Novel Gene" "Download" identifies, compares, new data. main goal research focus website created offer obtained sampling protocol, (as shown Figure S1 case study 1 Supporting Information). Compared transcriptome, primarily genetic foundations economically significant traits novel improvement 2 Information, S2 Tables S3–S5). Secondarily, could understanding evolutionary processes taken place during domestication interaction genetics phenotypes (see 3 S3 S6). user-friendly. Users easily functional annotations, range first levels body hierarchical both comprehension avoiding linguistic ambiguity. It's important acknowledge current iteration has limitations. First, focuses mainly systems (cattle sheep) more benefits limits interpretation HTIRDB. Second, lacks tissues, male reproduction. Third, might genomes annotation. living will include become If funding permits, added ensure its over time. stored follows. dissected healthy juvenile individuals (details experimental animals S7). Sample total extraction, described previous publication [7]. mined RNA-Seqs ILLUMINA (read length > 50 bp, depth (clean read number) million) National Center Biotechnology Information Sequence Read Archive (NCBI SRA) [9-13]. Public closely yak, cattle-yak, hares, also (the codes grouping listed S8). quality control reported S9. calculated either mixture MySQL (https://www.mysql.com). Apache 2.4 (http://www.apache.org), PHP 7.4 (http://www.php.net), ThinkPHP 5.0 (http://www.thinkphp.cn/) create content database. web pages constructed HTML5 rendered Element (https://element.eleme.cn/) based Vue 2.0 (https://cn.vuejs.org). JavaScript framework Vue.js improve experience. Plotly.js, D3.js, ECharts (https://echarts.apache.org/) level results transcriptomics. combination visualizations, heatmaps, charts, boxplots, histograms Nine integrated webpage enhance functionality utility Diamond v0.9.14 acquisition positions eight [14]. Jbrowser structural genomics visualization [15]. Blast through Sequenceserver sequence alignment Fetch tool, powered Samtools v1.15 bedtools [16], easy like DNA, We GO/KEGG enrichment utilizing ClusterProfiler [17], eggNOG-mapper v2 eggNOG [18], DIAMOND [19] support Data2heatmap Echarts intuitive interactive heatmap tissues/species, retained than ten reads mapped at least Next, R package "DESeq.2" DEGs cut-off criteria: (i) false discovery (FDR) < 0.05, (ii) |log2 fold change| [20]. An specificity τ TSGs, HKGs, SSGs, SCGs rMATs BAM files nucleotide polymorphisms insertion-deletion annotated GATK's snpEff (v5.2a), respectively StringTie (v2.1.4) employed assemble transcripts RNA-Seq. TACO (v0.7.3), gffcompare (v0.12.6), gffread, Rfam (v14.9), blastn (v2.9.0+), CPC2 (v1.01), PLEK (v2.1), CNCI, TransDecoder (v5.5.0) subsequently lncRNAs network Cytoscape (https://js.cytoscape.org/). computing Pearson coefficient pair Luoyang Ding Yifan Wang: Methodology; investigation; writing—original draft; writing—review editing. Linna Zhang Chengfang Luo: Formal analysis; curation; software; Feifan Wu: Investigation; methodology; Yiming Huang: Software; curation. Yongkang Zhen Kelsey Pool: Ning Chen: project administration. Limin Wang, Li Song, Chuang Li, Xiang Yu, Zhenbin Zhang, Chun Xue, Yalan Gu, Weidong Huang, Lu Yan, Wenjun Wei, Yusu Jinying Yiquan Sun: methodology. Dominique Blache: Writing—review editing; investigation. Shane K. Maloney: Dongxu Liu: Zhiquan Yang: visualization. Xiaoyan Software. Rui Dai: Shengbo Wang Xinle Zhao: Validation; Haodong Ping Zhou Mengzhi Conceptualization; acquisition; supervision; Qing-Yong formal software. This supported grants State Key Laboratory Sheep Genetic Improvement Healthy Production (Nos. 2021ZD01, 2021ZD04, 2021ZD07, NCG202232, NCG202221), 14th 5-Year Plan Research Development Program 2023YFD1301705 2021YFD1600702), Priority Academic Jiangsu Higher Education Institutions (PAPD), authors declare no conflicts interest. All experiments carried out accordance ARRIVE guidelines, ethics application (No. RA202203046) approved Animal Ethics Committee Yangzhou University. open database, https://yanglab.hzau.edu.cn/HTIRDB#/download. raw RNA-Sequence been deposited NCBI SRA (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1017964). Supplementary materials (methods, figures, abstract, slides, videos, Chinese translated version, update materials) may found online DOI iMeta Science http://www.imeta.science/. S1. example showing paxillin S2. Comparison longissimus dorsi goats. S3. pattern enrichments herbivore. Haimen white goat. S4. S5. S6. House-keeping S7. Details S8. List organ codes. Codes construction. Please note: publisher responsible supporting supplied authors. Any (other missing content) should directed author article.

Language: Английский

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Flavor, Lipid, and Transcriptomic Profiles of Chinese Wagyu Beef Cuts: Insights into Meat Quality Differences

Foods, Journal Year: 2025, Volume and Issue: 14(5), P. 716 - 716

Published: Feb. 20, 2025

This study aimed to investigate the flavor formation and meat quality differences among different beef cuts in Chinese Wagyu cattle. The metabolites gene expression profiles of chuck, neck, rump, tenderloin, longissimus lumborum were analyzed. results revealed that a total 240 volatile organic compounds 779 lipid molecules detected cuts, with hydrocarbons (accounting for 29.71%) triglycerides (representing 41.21%) emerging as most prominent compounds, respectively. sensory-directed analysis highlighted significance sweet fruity aroma which contributed distinct cuts. Additionally, 60 key molecular markers, including FA(18:1), PC(40:5), TG(18:0_16:1_18:1), TG(36:0_18:1), etc., identified playing crucial roles generation essential across five Integrative multi-omics data pinpointed cluster differentially expressed genes (e.g., DLD, ACADM, PCCA, SCD), involved regulation valine, leucine, isoleucine degradation pathways metabolism. Taken together, this has candidate influencing providing valuable resource breeding high-quality traits

Language: Английский

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Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken

Poultry Science, Journal Year: 2025, Volume and Issue: 104(4), P. 104986 - 104986

Published: March 4, 2025

Systematically constructing a gene expression atlas of poultry tissues is critically important for advancing research and production. In this study, the profiles 9 major Lueyang black-bone chicken were successfully constructed by transcriptome sequencing technology. Through in-depth analysis data, total 10 housekeeping genes (HKGs) 87 marker (MGs) identified. Furthermore, applying weighted co-expression network (WGCNA), we delineated nine tissue-specific modules 90 hub genes, offering novel insights into regulatory networks underlying expression. Kyoto Encyclopedia Genes Genomes (KEGG) enrichment showed that HKGs predominantly involved in maintaining fundamental cellular functions, with significant pathways related to oxidative phosphorylation, cell cycle regulation, DNA replication. MGs closely associated physiological providing valuable molecular mechanisms governing tissue functionality. Notably, through multidimensional validation, EEF1A1 FTH1 confirmed exhibit cross-tissue stability, establishing them as ideal reference multi-tissue qPCR experiments chickens. Additionally, identified including TNNT2, PIT54, SFTPC, PGM1, which are specific heart, liver, lung, breast muscle, respectively. The results study have scientific value expanding selection elucidating mechanisms, provide solid theoretical support technical guidance breeding improvement production practice optimization.

Language: Английский

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