Effects of dietary physical or nutritional factors on morphology of rumen papillae and transcriptome changes in lactating dairy cows based on three different forage-based diets.


BACKGROUND:Rumen epithelial tissue plays an important role in nutrient absorption and rumen health. However, whether forage quality and particle size impact the rumen epithelial morphology is unclear. The current study was conducted to elucidate the effects of forage quality and forage particle size on rumen epithelial morphology and to identify potential underlying molecular mechanisms by analyzing the transcriptome of the rumen epithelium (RE). To achieve these objectives, 18 mid-lactation dairy cows were allocated to three groups (6 cows per group), and were fed with one of three different forage-based diets, alfalfa hay (AH), corn stover (CS), and rice straw (RS) for 14 weeks, respectively. Ruminal volatile fatty acids (VFAs) and epithelial thickness were determined, and RNA-sequencing was conducted to identify the transcriptomic changes of rumen epithelial under different forage-based diets. RESULTS:The RS diet exhibited greater particle size but low quality, the AH diet was high nutritional value but small particle size, and CS diet was low quality and small particle size. The ruminal total VFA concentration was greater in AH compared with those in CS or RS. The width of the rumen papillae was greater in RS-fed cows than in cows fed AH or CS. In total, 31, 40, and 28 differentially expressed (DE, fold change > 2, FDR < 0.05) genes were identified via pair-wise comparisons including AH vs. CS, AH vs. RS, and RS vs. CS, respectively. Functional classification analysis of DE genes revealed dynamic changes in ion binding (such as DSG1) between AH and CS, proliferation and apoptotic processes (such as BAG3, HLA-DQA1, and UGT2B17) and complement activation (such as C7) between AH or RS and CS. The expression of HLA-DQA1 was down-regulated in RS compared with AH and CS, and the expression of UGT2B17 was down-regulated in RS compared with CS, with positive (R = 0.94) and negative (R = -0.96) correlation with the width of rumen epithelial papillae (P < 0.05), respectively. CONCLUSION:Our results suggest that both nutrients (VFAs) and particle sizes can alter expression of genes involved in cell proliferation/apoptosis process and complement complex. Our results suggest that particle size may be more important in regulating rumen epithelial morphology when animals are fed with low-quality forage diets and the identified DE genes may affect the RE nutrient absorption or morphology of RE. Our findings provide insights into the effects of the dietary particle size in the future management of dairy cow feeding, that when cows were fed with low-quality forage (such as rice straw), smaller particle size may be beneficial for nutrients absorption and milk production.


BMC Genomics


BMC genomics


Wang B,Wang D,Wu X,Cai J,Liu M,Huang X,Wu J,Liu J,Guan L




Has Abstract


2017-05-06 00:00:00












  • Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

    abstract:BACKGROUND:HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen B,Zhong D,Monteiro A

    更新日期:2006-06-17 00:00:00

  • Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing.

    abstract:BACKGROUND:After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang JZ,Ai XY,Sun LM,Zhang DL,Guo WW,Deng XX,Hu CG

    更新日期:2011-01-26 00:00:00

  • Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.

    abstract:BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

    更新日期:2015-02-15 00:00:00

  • Parallel progressive multiple sequence alignment on reconfigurable meshes.

    abstract:BACKGROUND:One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Nguyen KD,Pan Y,Nong G

    更新日期:2011-12-23 00:00:00

  • Antennal transcriptome analysis of the chemosensory gene families in the tree killing bark beetles, Ips typographus and Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae).

    abstract:BACKGROUND:The European spruce bark beetle, Ips typographus, and the North American mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae), are severe pests of coniferous forests. Both bark beetle species utilize aggregation pheromones to coordinate mass-attacks on host trees, while odora...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Andersson MN,Grosse-Wilde E,Keeling CI,Bengtsson JM,Yuen MM,Li M,Hillbur Y,Bohlmann J,Hansson BS,Schlyter F

    更新日期:2013-03-21 00:00:00

  • Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae.

    abstract:BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Biryukova I,Ye T

    更新日期:2015-04-10 00:00:00

  • RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification.

    abstract:BACKGROUND:Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in m...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Arslan M,Devisetty UK,Porsch M,Große I,Müller JA,Michalski SG

    更新日期:2019-06-13 00:00:00

  • Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study.

    abstract:BACKGROUND:Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic archit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Du X,Liu S,Sun J,Zhang G,Jia Y,Pan Z,Xiang H,He S,Xia Q,Xiao S,Shi W,Quan Z,Liu J,Ma J,Pang B,Wang L,Sun G,Gong W,Jenkins JN,Lou X,Zhu J,Xu H

    更新日期:2018-06-13 00:00:00

  • Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

    abstract:BACKGROUND:Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. RESULTS:In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhou F,Olman V,Xu Y

    更新日期:2008-01-24 00:00:00

  • Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome.

    abstract:BACKGROUND:The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ambrosio AB,do Nascimento LC,Oliveira BV,Teixeira PJ,Tiburcio RA,Toledo Thomazella DP,Leme AF,Carazzolle MF,Vidal RO,Mieczkowski P,Meinhardt LW,Pereira GA,Cabrera OG

    更新日期:2013-02-11 00:00:00

  • Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx.

    abstract:BACKGROUND:The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kleinman-Ruiz D,Martínez-Cruz B,Soriano L,Lucena-Perez M,Cruz F,Villanueva B,Fernández J,Godoy JA

    更新日期:2017-07-21 00:00:00

  • Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea.

    abstract:BACKGROUND:Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Deulvot C,Charrel H,Marty A,Jacquin F,Donnadieu C,Lejeune-Hénaut I,Burstin J,Aubert G

    更新日期:2010-08-11 00:00:00

  • Mitochondrial lineage M1 traces an early human backflow to Africa.

    abstract:BACKGROUND:The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: González AM,Larruga JM,Abu-Amero KK,Shi Y,Pestano J,Cabrera VM

    更新日期:2007-07-09 00:00:00

  • Oocyte-somatic cells interactions, lessons from evolution.

    abstract:BACKGROUND:Despite the known importance of somatic cells for oocyte developmental competence acquisition, the overall mechanisms underlying the acquisition of full developmental competence are far from being understood, especially in non-mammalian species. The present work aimed at identifying key molecular signals fro...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Charlier C,Montfort J,Chabrol O,Brisard D,Nguyen T,Le Cam A,Richard-Parpaillon L,Moreews F,Pontarotti P,Uzbekova S,Chesnel F,Bobe J

    更新日期:2012-10-19 00:00:00

  • A transcriptome approach towards understanding the development of ripening capacity in 'Bartlett' pears (Pyrus communis L.).

    abstract:BACKGROUND:The capacity of European pear fruit (Pyrus communis L.) to ripen after harvest develops during the final stages of growth on the tree. The objective of this study was to characterize changes in 'Bartlett' pear fruit physico-chemical properties and transcription profiles during fruit maturation leading to att...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Nham NT,de Freitas ST,Macnish AJ,Carr KM,Kietikul T,Guilatco AJ,Jiang CZ,Zakharov F,Mitcham EJ

    更新日期:2015-10-09 00:00:00

  • The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum.

    abstract:BACKGROUND:Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA meth...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rogato A,Richard H,Sarazin A,Voss B,Cheminant Navarro S,Champeimont R,Navarro L,Carbone A,Hess WR,Falciatore A

    更新日期:2014-08-20 00:00:00

  • Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress.

    abstract:BACKGROUND:Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound ada...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang MQ,Bai ZY,Xiao YF,Li Y,Liu QL,Zhang L,Pan YZ,Jiang BB,Zhang F

    更新日期:2019-11-20 00:00:00

  • How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis.

    abstract:BACKGROUND:Prediction methods are increasingly used in biosciences to forecast diverse features and characteristics. Binary two-state classifiers are the most common applications. They are usually based on machine learning approaches. For the end user it is often problematic to evaluate the true performance and applica...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vihinen M

    更新日期:2012-06-18 00:00:00

  • De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

    abstract:BACKGROUND:Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, Toxoplasma gondii, are based on computer model predictions without cDNA sequence ver...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hassan MA,Melo MB,Haas B,Jensen KD,Saeij JP

    更新日期:2012-12-12 00:00:00

  • Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton.

    abstract:BACKGROUND:The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma Q,Wu M,Pei W,Li H,Li X,Zhang J,Yu J,Yu S

    更新日期:2014-06-12 00:00:00

  • Deep sequencing of transcriptomes from the nervous systems of two decapod crustaceans to characterize genes important for neural circuit function and modulation.

    abstract:BACKGROUND:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Northcutt AJ,Lett KM,Garcia VB,Diester CM,Lane BJ,Marder E,Schulz DJ

    更新日期:2016-11-04 00:00:00

  • Germline mutation within COL2A1 associated with lethal chondrodysplasia in a polled Holstein family.

    abstract:BACKGROUND:The bulldog calf syndrome is a lethal form of the inherited congenital chondrodysplasias. Among the progeny of the polled Holstein bull Energy P cases of lethal chondrodysplasia were observed. Pedigrees of the cases and the frequency of 3/8 cases among the offspring of Energy P at our teaching and experiment...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Reinartz S,Mohwinkel H,Sürie C,Hellige M,Feige K,Eikelberg D,Beineke A,Metzger J,Distl O

    更新日期:2017-10-10 00:00:00

  • A method for near full-length amplification and sequencing for six hepatitis C virus genotypes.

    abstract:BACKGROUND:Hepatitis C virus (HCV) is a rapidly evolving RNA virus that has been classified into seven genotypes. All HCV genotypes cause chronic hepatitis, which ultimately leads to liver diseases such as cirrhosis. The genotypes are unevenly distributed across the globe, with genotypes 1 and 3 being the most prevalen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bull RA,Eltahla AA,Rodrigo C,Koekkoek SM,Walker M,Pirozyan MR,Betz-Stablein B,Toepfer A,Laird M,Oh S,Heiner C,Maher L,Schinkel J,Lloyd AR,Luciani F

    更新日期:2016-03-17 00:00:00

  • Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus.

    abstract:BACKGROUND:Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Baeza JA

    更新日期:2020-12-09 00:00:00

  • Investigation of transmembrane proteins using a computational approach.

    abstract:BACKGROUND:An important subfamily of membrane proteins are the transmembrane alpha-helical proteins, in which the membrane-spanning regions are made up of alpha-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmem...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yang JY,Yang MQ,Dunker AK,Deng Y,Huang X

    更新日期:2008-01-01 00:00:00

  • RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection.

    abstract:BACKGROUND:The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wilk E,Pandey AK,Leist SR,Hatesuer B,Preusse M,Pommerenke C,Wang J,Schughart K

    更新日期:2015-09-02 00:00:00

  • Treatment-independent miRNA signature in blood of Wilms tumor patients.

    abstract:BACKGROUND:Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001. RESULTS:We did not find a significant difference between miRNA signature of both groups...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Schmitt J,Backes C,Nourkami-Tutdibi N,Leidinger P,Deutscher S,Beier M,Gessler M,Graf N,Lenhof HP,Keller A,Meese E

    更新日期:2012-08-07 00:00:00

  • The I2 resistance gene homologues in Solanum have complex evolutionary patterns and are targeted by miRNAs.

    abstract:BACKGROUND:Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. RESULTS:Comparative analysis showed that the structure and evolutionary patterns of the I...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wei C,Kuang H,Li F,Chen J

    更新日期:2014-08-30 00:00:00

  • Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

    abstract:BACKGROUND:Malaria, caused by the parasitic protist Plasmodium falciparum, represents a major public health problem in the developing world. The P. falciparum genome has been sequenced, which provides new opportunities for the identification of novel drug targets. Eukaryotic protein kinases (ePKs) form a large family o...

    journal_title:BMC genomics

    pub_type: 杂志文章,评审


    authors: Ward P,Equinet L,Packer J,Doerig C

    更新日期:2004-10-12 00:00:00

  • Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells.

    abstract:BACKGROUND:Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rengaraj D,Lee SI,Park TS,Lee HJ,Kim YM,Sohn YA,Jung M,Noh SJ,Jung H,Han JY

    更新日期:2014-09-04 00:00:00