Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds.

Abstract:

BACKGROUND:Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed. Together they form an ideal model system to study the biological mechanisms underlying broiler chicken selection responses in a natural system. The objective of this study was to study the biological mechanisms underlying differential phenotypes between the two breeds in muscle and liver tissues, and relate these to the growth rate and body development phenotypes of the two breeds. RESULTS:The muscle tissue in the Wuding breed showed higher expression of muscle development genes than muscle tissue in the Daweishan chicken breed. This expression was accompanied by higher expression of acute inflammatory response genes in Wuding chicken than in Daweishan chicken. The muscle tissue of the Daweishan mini chicken breed showed higher expression of genes involved in several metabolic mechanisms including endoplasmic reticulum, protein and lipid metabolism, energy metabolism, as well as specific immune traits than in the Wuding chicken. The liver tissue showed fewer differences between the two breeds. Genes displaying higher expression in the Wuding breed than in the Daweishan breed were not associated with a specific gene network or biological mechanism. Genes highly expressed in the Daweishan mini chicken breed compared to the Wuding breed were enriched for protein metabolism, ABC receptors, signal transduction, and IL6-related mechanisms. CONCLUSIONS:We conclude that faster growth rates and larger body size are related to increased expression of genes involved in muscle development and immune response in muscle, while slower growth rates and smaller body size are related to increased general cellular metabolism. The liver of the Daweishan breed displayed increased expression of metabolic genes.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Dou T,Zhao S,Rong H,Gu D,Li Q,Huang Y,Xu Z,Chu X,Tao L,Liu L,Ge C,Te Pas MFW,Jia J

doi

10.1186/s12864-017-3845-9

subject

Has Abstract

pub_date

2017-06-20 00:00:00

pages

469

issue

1

issn

1471-2164

pii

10.1186/s12864-017-3845-9

journal_volume

18

pub_type

杂志文章
  • Multiple genetic loci define Ca++ utilization by bloodstream malaria parasites.

    abstract:BACKGROUND:Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilization by genetically distinct lines of P. falciparum. These differences, if identified, may provide...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5418-y

    authors: Apolis L,Olivas J,Srinivasan P,Kushwaha AK,Desai SA

    更新日期:2019-01-16 00:00:00

  • A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men.

    abstract:BACKGROUND:Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically e...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6363-0

    authors: Hu Y,Tan A,Yu L,Hou C,Kuang H,Wu Q,Su J,Zhou Q,Zhu Y,Zhang C,Wei W,Li L,Li W,Huang Y,Huang H,Xie X,Lu T,Zhang H,Yang X,Gao Y,Li T,Jiang Y,Mo Z

    更新日期:2019-12-16 00:00:00

  • Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici).

    abstract:BACKGROUND:Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. This sophisticated biotrophic parasite infiltrates wheat leaves and develops infection structures inside host cells, appropriating nutrients while sup...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1895-4

    authors: Mueth NA,Ramachandran SR,Hulbert SH

    更新日期:2015-09-21 00:00:00

  • Tracing the genetic history of the 'Cañaris' from Ecuador and Peru using uniparental DNA markers.

    abstract:BACKGROUND:According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lam...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06834-1

    authors: Sandoval JR,Lacerda DR,Jota MMS,Robles-Ruiz P,Danos P,Paz-Y-Miño C,Wells S,Santos FR,Fujita R

    更新日期:2020-09-10 00:00:00

  • Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty.

    abstract:BACKGROUND:Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. RE...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5720-3

    authors: Hajiramezanali E,Imani M,Braga-Neto U,Qian X,Dougherty ER

    更新日期:2019-06-13 00:00:00

  • Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica.

    abstract:BACKGROUND:Oomycetes are a group of filamentous microorganisms that includes both animal and plant pathogens and causes major agricultural losses. Phytophthora species can infect most crops and plants from natural ecosystems. Despite their tremendous economic and ecologic importance, few effective methods exist for lim...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-538

    authors: Attard A,Evangelisti E,Kebdani-Minet N,Panabières F,Deleury E,Maggio C,Ponchet M,Gourgues M

    更新日期:2014-06-29 00:00:00

  • Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum.

    abstract:BACKGROUND:Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-260

    authors: Mbanefo EC,Chuanxin Y,Kikuchi M,Shuaibu MN,Boamah D,Kirinoki M,Hayashi N,Chigusa Y,Osada Y,Hamano S,Hirayama K

    更新日期:2012-06-20 00:00:00

  • Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci.

    abstract:BACKGROUND:Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are needed for certain light-activated genes in Neurospora crassa (Neurospora), including frequency (frq) and...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5729-7

    authors: Zhu Q,Ramakrishnan M,Park J,Belden WJ

    更新日期:2019-05-08 00:00:00

  • Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data.

    abstract:BACKGROUND:Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-16-S7-S3

    authors: Cui W,Qian Y,Zhou X,Lin Y,Jiang J,Chen J,Zhao Z,Shen B

    更新日期:2015-01-01 00:00:00

  • Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity.

    abstract:BACKGROUND:Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Sho...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-803

    authors: Lu S,Le S,Tan Y,Li M,Liu C,Zhang K,Huang J,Chen H,Rao X,Zhu J,Zou L,Ni Q,Li S,Wang J,Jin X,Hu Q,Yao X,Zhao X,Zhang L,Huang G,Hu F

    更新日期:2014-09-19 00:00:00

  • Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses.

    abstract:BACKGROUND:Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-218

    authors: Sánchez-Sevilla JF,Cruz-Rus E,Valpuesta V,Botella MA,Amaya I

    更新日期:2014-04-17 00:00:00

  • Generation and analysis of expression sequence tags from haustoria of the wheat stripe rust fungus Puccinia striiformis f. sp. Tritici.

    abstract:BACKGROUND:Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. In spite of its agricultural importance, the genomics and genetics of the pathogen are poorly characterized. Pst transcripts from urediniospores and germinated ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-626

    authors: Yin C,Chen X,Wang X,Han Q,Kang Z,Hulbert SH

    更新日期:2009-12-23 00:00:00

  • Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.

    abstract:BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4697-7

    authors: Jangid RK,Kelkar A,Muley VY,Galande S

    更新日期:2018-05-02 00:00:00

  • Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters.

    abstract:BACKGROUND:Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e.,...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-16-S13-S5

    authors: Arkova OV,Ponomarenko MP,Rasskazov DA,Drachkova IA,Arshinova TV,Ponomarenko PM,Savinkova LK,Kolchanov NA

    更新日期:2015-01-01 00:00:00

  • Bcheck: a wrapper tool for detecting RNase P RNA genes.

    abstract:BACKGROUND:Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily spec...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-432

    authors: Yusuf D,Marz M,Stadler PF,Hofacker IL

    更新日期:2010-07-13 00:00:00

  • In silico prediction and characterization of secondary metabolite biosynthetic gene clusters in the wheat pathogen Zymoseptoria tritici.

    abstract:BACKGROUND:Fungal pathogens of plants produce diverse repertoires of secondary metabolites, which have functions ranging from iron acquisition, defense against immune perturbation, to toxic assaults on the host. The wheat pathogen Zymoseptoria tritici causes Septoria tritici blotch, a foliar disease which is a signific...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3969-y

    authors: Cairns T,Meyer V

    更新日期:2017-08-17 00:00:00

  • Gene editing in the context of an increasingly complex genome.

    abstract::The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catal...

    journal_title:BMC genomics

    pub_type: 杂志文章,评审

    doi:10.1186/s12864-018-4963-8

    authors: Blighe K,DeDionisio L,Christie KA,Chawes B,Shareef S,Kakouli-Duarte T,Chao-Shern C,Harding V,Kelly RS,Castellano L,Stebbing J,Lasky-Su JA,Nesbit MA,Moore CBT

    更新日期:2018-08-08 00:00:00

  • Regulation of gene expression by FSP27 in white and brown adipose tissue.

    abstract:BACKGROUND:Brown and white adipose tissues (BAT and WAT) play critical roles in controlling energy homeostasis and in the development of obesity and diabetes. The mouse Fat-Specific protein 27 (FSP27), a member of the cell death-inducing DFF45-like effector (CIDE) family, is expressed in both BAT and WAT and is associa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-446

    authors: Li D,Zhang Y,Xu L,Zhou L,Wang Y,Xue B,Wen Z,Li P,Sang J

    更新日期:2010-07-22 00:00:00

  • H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast.

    abstract:BACKGROUND:The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. RESULTS:We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in bud...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1247-4

    authors: Gu M,Naiyachit Y,Wood TJ,Millar CB

    更新日期:2015-02-19 00:00:00

  • De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis.

    abstract:BACKGROUND:Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07113-9

    authors: Chiu YL,Shikina S,Yoshioka Y,Shinzato C,Chang CF

    更新日期:2020-10-21 00:00:00

  • Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression.

    abstract:BACKGROUND:On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. RESULTS:The mouse genome is shown to have a segmented structure defined by strand bias. Transcriptio...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-16

    authors: Evans KJ

    更新日期:2008-01-14 00:00:00

  • Genomic predictions combining SNP markers and copy number variations in Nellore cattle.

    abstract:BACKGROUND:Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach often cannot achieve high accuracy for some complex traits. It is possible that SNP markers are not suff...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4787-6

    authors: Hay EHA,Utsunomiya YT,Xu L,Zhou Y,Neves HHR,Carvalheiro R,Bickhart DM,Ma L,Garcia JF,Liu GE

    更新日期:2018-06-05 00:00:00

  • GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine.

    abstract:BACKGROUND:Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able t...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06996-y

    authors: Malagoli Tagliazucchi G,Taccioli C

    更新日期:2020-09-10 00:00:00

  • Differential gene expression and Hog1 interaction with osmoresponsive genes in the extremely halotolerant black yeast Hortaea werneckii.

    abstract:BACKGROUND:Fluctuations in external salinity force eukaryotic cells to respond by changes in the gene expression of proteins acting in protective biochemical processes, thus counteracting the changing osmotic pressure. The high-osmolarity glycerol (HOG) signaling pathway is essential for the efficient up-regulation of ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-280

    authors: Vaupotic T,Plemenitas A

    更新日期:2007-08-16 00:00:00

  • Exploring hierarchical and overlapping modular structure in the yeast protein interaction network.

    abstract:BACKGROUND:Developing effective strategies to reveal modular structures in protein interaction networks is crucial for better understanding of molecular mechanisms of underlying biological processes. In this paper, we propose a new density-based algorithm (ADHOC) for clustering vertices of a protein interaction network...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-S4-S17

    authors: Liu C,Li J,Zhao Y

    更新日期:2010-12-02 00:00:00

  • Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.).

    abstract:BACKGROUND:Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are freque...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-569

    authors: Cavagnaro PF,Senalik DA,Yang L,Simon PW,Harkins TT,Kodira CD,Huang S,Weng Y

    更新日期:2010-10-15 00:00:00

  • Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.).

    abstract:BACKGROUND:Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3000-z

    authors: Xu F,Bao J,He Q,Park YJ

    更新日期:2016-08-20 00:00:00

  • Uncovering molecular events associated with the chemosuppressive effects of flaxseed: a microarray analysis of the laying hen model of ovarian cancer.

    abstract:BACKGROUND:The laying hen model of spontaneous epithelial ovarian cancer (EOC) is unique in that it is the only model that enables observations of early events in disease progression and is therefore also uniquely suited for chemoprevention trials. Previous studies on the effect of dietary flaxseed in laying hens have ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-709

    authors: Hales KH,Speckman SC,Kurrey NK,Hales DB

    更新日期:2014-08-24 00:00:00

  • Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data.

    abstract:BACKGROUND:Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological experti...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6053-y

    authors: Feng D,Whitehurst CE,Shan D,Hill JD,Yue YG

    更新日期:2019-08-27 00:00:00

  • Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle.

    abstract:BACKGROUND:Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6099-x

    authors: Tao SQ,Cao B,Morin E,Liang YM,Duplessis S

    更新日期:2019-10-09 00:00:00