Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes.

Abstract:

BACKGROUND:Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. RESULTS:RNA-Seq-derived transcriptome profiles of fungal- and mock-inoculated developing kernel tissues of two maize inbred lines were used to identify differentially expressed transcripts and propose candidate genes mapping within GER resistance quantitative trait loci (QTL). A total of 1255 transcripts were significantly (P ≤ 0.05) up regulated due to fungal infection in both susceptible and resistant inbreds. A greater number of transcripts were up regulated in the former (1174) than the latter (497) and increased as the infection progressed from 1 to 2 days after inoculation. Focusing on differentially expressed genes located within QTL regions for GER resistance, we identified 81 genes involved in membrane transport, hormone regulation, cell wall modification, cell detoxification, and biosynthesis of pathogenesis related proteins and phytoalexins as candidate genes contributing to resistance. Applying droplet digital PCR, we validated the expression profiles of a subset of these candidate genes from QTL regions contributed by the resistant inbred on chromosomes 1, 2 and 9. CONCLUSION:By screening global gene expression profiles for differentially expressed genes mapping within resistance QTL regions, we have identified candidate genes for gibberella ear rot resistance on several maize chromosomes which could potentially lead to a better understanding of Fusarium resistance mechanisms.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Kebede AZ,Johnston A,Schneiderman D,Bosnich W,Harris LJ

doi

10.1186/s12864-018-4513-4

subject

Has Abstract

pub_date

2018-02-09 00:00:00

pages

131

issue

1

issn

1471-2164

pii

10.1186/s12864-018-4513-4

journal_volume

19

pub_type

杂志文章
  • Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats.

    abstract:BACKGROUND:Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on trans...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6244-6

    authors: Zeng H,Yu BF,Liu N,Yang YY,Xing HY,Liu XX,Zhou MW

    更新日期:2019-11-14 00:00:00

  • Diet, gonadal sex, and sex chromosome complement influence white adipose tissue miRNA expression.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adipogenesis, and are expressed at different levels in adipose tissue from lean and obese mice. The deg...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3484-1

    authors: Link JC,Hasin-Brumshtein Y,Cantor RM,Chen X,Arnold AP,Lusis AJ,Reue K

    更新日期:2017-01-17 00:00:00

  • Pseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity.

    abstract:BACKGROUND:Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-318

    authors: Grosso-Becerra MV,Santos-Medellín C,González-Valdez A,Méndez JL,Delgado G,Morales-Espinosa R,Servín-González L,Alcaraz LD,Soberón-Chávez G

    更新日期:2014-04-28 00:00:00

  • Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis.

    abstract:BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2209-6

    authors: Baksa I,Nagy T,Barta E,Havelda Z,Várallyay É,Silhavy D,Burgyán J,Szittya G

    更新日期:2015-12-01 00:00:00

  • Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome.

    abstract:BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-632

    authors: Tremblay DC,Alexander G Jr,Moseley S,Chadwick BP

    更新日期:2010-11-15 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

    doi:10.1186/1471-2164-13-560

    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

  • Comparison of leaf transcriptome in response to Rhizoctonia solani infection between resistant and susceptible rice cultivars.

    abstract:BACKGROUND:Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular breeding of R. solani-resistant rice cultivars, the changes of transcriptome profiles in response to ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6645-6

    authors: Shi W,Zhao SL,Liu K,Sun YB,Ni ZB,Zhang GY,Tang HS,Zhu JW,Wan BJ,Sun HQ,Dai JY,Sun MF,Yan GH,Wang AM,Zhu GY

    更新日期:2020-03-19 00:00:00

  • Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes.

    abstract:BACKGROUND:Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS:We identified orthologous...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3880-6

    authors: Onishi K,Yamane M,Yamaji N,Tokui M,Kanamori H,Wu J,Komatsuda T,Sato K

    更新日期:2017-06-29 00:00:00

  • Analysis of qPCR reference gene stability determination methods and a practical approach for efficiency calculation on a turbot (Scophthalmus maximus) gonad dataset.

    abstract:BACKGROUND:Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray results. Several issues are crucial for a successful qPCR study, particularly the selection of internal...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-648

    authors: Robledo D,Hernández-Urcera J,Cal RM,Pardo BG,Sánchez L,Martínez P,Viñas A

    更新日期:2014-08-04 00:00:00

  • Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity.

    abstract:BACKGROUND:Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant g...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2104-1

    authors: Ariff A,Wise MJ,Kahler CM,Tay CY,Peters F,Perkins TT,Chang BJ

    更新日期:2015-10-24 00:00:00

  • Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine.

    abstract:BACKGROUND:Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). RESULT:Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6111-5

    authors: Wang P,Yang Y,Shi H,Wang Y,Ren F

    更新日期:2019-10-15 00:00:00

  • Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

    abstract:BACKGROUND:Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regio...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-683

    authors: Ramos E,Levinson BT,Chasnoff S,Hughes A,Young AL,Thornton K,Li A,Vallania FL,Province M,Druley TE

    更新日期:2012-12-06 00:00:00

  • Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection.

    abstract:BACKGROUND:The obligate intracellular parasite Toxoplasma gondii establishes a life-long chronic infection within any warm-blooded host. After ingestion of an encysted parasite, T. gondii disseminates throughout the body as a rapidly replicating form during acute infection. Over time and after stimulation of the host i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-806

    authors: Pittman KJ,Aliota MT,Knoll LJ

    更新日期:2014-09-20 00:00:00

  • Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain.

    abstract:BACKGROUND:Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5121-z

    authors: Zamora-Lagos MA,Eckstein S,Langer A,Gazanis A,Pfeiffer F,Habermann B,Heermann R

    更新日期:2018-11-29 00:00:00

  • Mapping a quantitative trait locus (QTL) conferring pyrethroid resistance in the African malaria vector Anopheles funestus.

    abstract:BACKGROUND:Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were use...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-34

    authors: Wondji CS,Morgan J,Coetzee M,Hunt RH,Steen K,Black WC 4th,Hemingway J,Ranson H

    更新日期:2007-01-29 00:00:00

  • In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.

    abstract:BACKGROUND:Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-86

    authors: Pao SY,Lin WL,Hwang MJ

    更新日期:2006-04-21 00:00:00

  • Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

    abstract:BACKGROUND:A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. RESULTS:In this study, we performed a u...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S8-S16

    authors: Zhao Z,Guo AY,van den Oord EJ,Aliev F,Jia P,Edenberg HJ,Riley BP,Dick DM,Bettinger JC,Davies AG,Grotewiel MS,Schuckit MA,Agrawal A,Kramer J,Nurnberger JI Jr,Kendler KS,Webb BT,Miles MF

    更新日期:2012-01-01 00:00:00

  • Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.

    abstract:BACKGROUND:The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-888

    authors: Pfeifer-Sancar K,Mentz A,Rückert C,Kalinowski J

    更新日期:2013-12-17 00:00:00

  • σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

    abstract:BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2176-y

    authors: Kazakov AE,Rajeev L,Chen A,Luning EG,Dubchak I,Mukhopadhyay A,Novichkov PS

    更新日期:2015-11-10 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

    doi:10.1186/s12864-018-4837-0

    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

  • The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage.

    abstract:BACKGROUND:Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. To date, PAL genes have been less extensively studied in gymnosperms than in angiosperms. Ou...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S3-S1

    authors: Bagal UR,Leebens-Mack JH,Lorenz WW,Dean JF

    更新日期:2012-06-11 00:00:00

  • A platform independent RNA-Seq protocol for the detection of transcriptome complexity.

    abstract:BACKGROUND:Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein coding genes and their splice variants. Indeed, most transcripts are the result of antisense, overlapping...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-855

    authors: Calabrese C,Mangiulli M,Manzari C,Paluscio AM,Caratozzolo MF,Marzano F,Kurelac I,D'Erchia AM,D'Elia D,Licciulli F,Liuni S,Picardi E,Attimonelli M,Gasparre G,Porcelli AM,Pesole G,Sbisà E,Tullo A

    更新日期:2013-12-05 00:00:00

  • Activation of metabolic and stress responses during subtoxic expression of the type I toxin hok in Erwinia amylovora.

    abstract:BACKGROUND:Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia am...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-021-07376-w

    authors: Peng J,Triplett LR,Sundin GW

    更新日期:2021-01-22 00:00:00

  • Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data.

    abstract:BACKGROUND:Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-732

    authors: Feng C,Xu CJ,Wang Y,Liu WL,Yin XR,Li X,Chen M,Chen KS

    更新日期:2013-10-25 00:00:00

  • High burden of private mutations due to explosive human population growth and purifying selection.

    abstract:BACKGROUND:Recent studies have shown that human populations have experienced a complex demographic history, including a recent epoch of rapid population growth that led to an excess in the proportion of rare genetic variants in humans today. This excess can impact the burden of private mutations for each individual, de...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-S4-S3

    authors: Gao F,Keinan A

    更新日期:2014-01-01 00:00:00

  • Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease.

    abstract:BACKGROUND:Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT:We have studied gene co...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4098-3

    authors: Chatterjee P,Roy D,Bhattacharyya M,Bandyopadhyay S

    更新日期:2017-09-12 00:00:00

  • Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats.

    abstract:BACKGROUND:Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several hu...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-608

    authors: Greenberger S,Levanon EY,Paz-Yaacov N,Barzilai A,Safran M,Osenberg S,Amariglio N,Rechavi G,Eisenberg E

    更新日期:2010-10-28 00:00:00

  • Characterization of the transcriptome and temperature-induced differential gene expression in QPX, the thraustochytrid parasite of hard clams.

    abstract:BACKGROUND:The hard clam or northern quahog, Mercenaria mercenaria, is one of the most valuable seafood products in the United States representing the first marine resource in some Northeastern states. Severe episodes of hard clam mortality have been consistently associated with infections caused by a thraustochytrid p...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-245

    authors: Rubin E,Tanguy A,Perrigault M,Pales Espinosa E,Allam B

    更新日期:2014-03-28 00:00:00

  • Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomes.

    abstract:BACKGROUND:Many gram-negative bacteria use type III secretion systems (T3SSs) to translocate effector proteins into host cells. T3SS effectors can give some bacteria a competitive edge over others within the same environment and can help bacteria to invade the host cells and allow them to multiply rapidly within the ho...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3363-1

    authors: Hobbs CK,Porter VL,Stow ML,Siame BA,Tsang HH,Leung KY

    更新日期:2016-12-19 00:00:00

  • Population and sex differences in Drosophila melanogaster brain gene expression.

    abstract:BACKGROUND:Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-654

    authors: Catalán A,Hutter S,Parsch J

    更新日期:2012-11-21 00:00:00