Transcriptome sequencing of transgenic poplar (Populus × euramericana 'Guariento') expressing multiple resistance genes.

Abstract:

BACKGROUND:Transgenic poplar (Populus × euramericana 'Guariento') plants harboring five exogenous, stress-related genes exhibit increased tolerance to multiple stresses including drought, salt, waterlogging, and insect feeding, but the complex mechanisms underlying stress tolerance in these plants have not been elucidated. Here, we analyzed the differences in the transcriptomes of the transgenic poplar line D5-20 and the non-transgenic line D5-0 using high-throughput transcriptome sequencing techniques and elucidated the functions of the differentially expressed genes using various functional annotation methods. RESULTS:We generated 11.80 Gb of sequencing data containing 63, 430, 901 sequences, with an average length of 200 bp. The processed sequences were mapped to reference genome sequences of Populus trichocarpa. An average of 62.30% and 61.48% sequences could be aligned with the reference genomes for D5-20 and D5-0, respectively. We detected 11,352 (D5-20) and 11,372 expressed genes (D5-0), 7,624 (56.61%; D5-20) and 7,453 (65.54%; D5-0) of which could be functionally annotated. A total of 782 differentially expressed genes in D5-20 were identified compared with D5-0, including 628 up-regulated and 154 down-regulated genes. In addition, 196 genes with putative functions related to stress responses were also annotated. Gene Ontology (GO) analysis revealed that 346 differentially expressed genes are mainly involved in 67 biological functions, such as DNA binding and nucleus. KEGG annotation revealed that 36 genes (21 up-regulated and 15 down-regulated) were enriched in 51 biological pathways, 9 of which are linked to glucose metabolism. KOG functional classification revealed that 475 genes were enriched in 23 types of KOG functions. CONCLUSION:These results suggest that the transferred exogenous genes altered the expression of stress (biotic and abiotic) response genes, which were distributed in different metabolic pathways and were linked to some extent. Our results provide a theoretic basis for investigating the functional mechanisms of exogenous genes in transgenic plants.

journal_name

BMC Genet

journal_title

BMC genetics

authors

Zhang W,Chu Y,Ding C,Zhang B,Huang Q,Hu Z,Huang R,Tian Y,Su X

doi

10.1186/1471-2156-15-S1-S7

subject

Has Abstract

pub_date

2014-01-01 00:00:00

pages

S7

issn

1471-2156

pii

1471-2156-15-S1-S7

journal_volume

15 Suppl 1

pub_type

杂志文章
  • Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs.

    abstract:BACKGROUND:Feed efficiency is one of the major components determining costs of animal production. Residual feed intake (RFI) is defined as the difference between the observed and the expected feed intake given a certain production. Residual feed intake 1 (RFI1) was calculated based on regression of individual daily fee...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-15-27

    authors: Do DN,Ostersen T,Strathe AB,Mark T,Jensen J,Kadarmideen HN

    更新日期:2014-02-17 00:00:00

  • Molecular basis of a new ovine model for human 3M syndrome-2.

    abstract:BACKGROUND:Brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS, OMIA 001595-9940 ) is a previously reported recessively inherited disorder in Australian Poll Merino/Merino sheep. Affected lambs are stillborn with various congenital defects as reflected in the name of the disease, as well as short stature, ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-00913-8

    authors: Woolley SA,Hayes SE,Shariflou MR,Nicholas FW,Willet CE,O'Rourke BA,Tammen I

    更新日期:2020-09-15 00:00:00

  • The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars.

    abstract:BACKGROUND:Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the ec...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-35

    authors: Ramos AM,Duijvesteijn N,Knol EF,Merks JW,Bovenhuis H,Crooijmans RP,Groenen MA,Harlizius B

    更新日期:2011-04-20 00:00:00

  • Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss).

    abstract:BACKGROUND:There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregu...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-46

    authors: Le Bras Y,Dechamp N,Krieg F,Filangi O,Guyomard R,Boussaha M,Bovenhuis H,Pottinger TG,Prunet P,Le Roy P,Quillet E

    更新日期:2011-05-14 00:00:00

  • Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon.

    abstract:BACKGROUND:Anopheles gambiae females are the world's most successful vectors of human malaria. However, a fraction of these mosquitoes is refractory to Plasmodium development. L3-5, a laboratory selected refractory strain, encapsulates transforming ookinetes/early oocysts of a wide variety of Plasmodium species. Previo...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-4-16

    authors: Zheng L,Wang S,Romans P,Zhao H,Luna C,Benedict MQ

    更新日期:2003-10-24 00:00:00

  • Bayesian shrinkage mapping of quantitative trait loci in variance component models.

    abstract:BACKGROUND:In this article, I propose a model-selection-free method to map multiple quantitative trait loci (QTL) in variance component model, which is useful in outbred populations. The new method can estimate the variance of zero-effect QTL infinitely to zero, but nearly unbiased for non-zero-effect QTL. It is analog...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-30

    authors: Fang M

    更新日期:2010-04-29 00:00:00

  • On different approximations to multilocus identity-by-descent calculations and the resulting power of variance component-based linkage analysis.

    abstract::An empirical comparison between three different methods for estimation of pair-wise identity-by-descent (IBD) sharing at marker loci was conducted in order to quantify the resulting differences in power and localization precision in variance components-based linkage analysis. On the examined simulated, error-free data...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-4-S1-S72

    authors: Göring HH,Williams JT,Dyer TD,Blangero J

    更新日期:2003-12-31 00:00:00

  • Family-based approaches: design, imputation, analysis, and beyond.

    abstract::Participants in the family-based analysis group at Genetic Analysis Workshop 19 addressed diverse topics, all of which used the family data. Topics addressed included questions of study design and data quality control (QC), genotype imputation to augment available sequence data, and linkage and/or association analyses...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0318-5

    authors: Wijsman EM

    更新日期:2016-02-03 00:00:00

  • Cytoplasm affects grain weight and filled-grain ratio in indica rice.

    abstract:BACKGROUND:Cytoplasmic effects on agronomic traits--involving cytoplasmic and nuclear genomes of either different species or different cultivars--are well documented in wheat but have seldom been demonstrated in rice (Oryza sativa L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three indica c...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-53

    authors: Tao D,Xu P,Zhou J,Deng X,Li J,Deng W,Yang J,Yang G,Li Q,Hu F

    更新日期:2011-06-01 00:00:00

  • Comparative mapping combined with homology-based cloning of the rice genome reveals candidate genes for grain zinc and iron concentration in maize.

    abstract:BACKGROUND:Grain zinc and iron concentration is a complex trait that is controlled by quantitative trait loci (QTL) and is important for maintaining body health. Despite the substantial effort that has been put into identifying QTL for grain zinc and iron concentration, the integration of independent QTL is useful for ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0176-1

    authors: Jin T,Chen J,Zhu L,Zhao Y,Guo J,Huang Y

    更新日期:2015-02-14 00:00:00

  • Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces.

    abstract:BACKGROUND:Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present st...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-019-0736-x

    authors: Yao F,Zhang X,Ye X,Li J,Long L,Yu C,Li J,Wang Y,Wu Y,Wang J,Jiang Q,Li W,Ma J,Wei Y,Zheng Y,Chen G

    更新日期:2019-03-26 00:00:00

  • Interval estimation of disease loci: development and applications of new linkage methods.

    abstract::Three variants of the confidence set inference (CSI) procedure were proposed and applied to both the simulated and the Collaborative Study on the Genetics of Alcoholism (COGA) data. For each of the two applications, we first performed a preliminary genome scan study based on the microsatellite markers using the GENEHU...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-6-S1-S21

    authors: Papachristou C,Lin S

    更新日期:2005-12-30 00:00:00

  • Genetic diversity among eight Dendrolimus species in Eurasia (Lepidoptera: Lasiocampidae) inferred from mitochondrial COI and COII, and nuclear ITS2 markers.

    abstract:BACKGROUND:Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the mo...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0463-5

    authors: Kononov A,Ustyantsev K,Wang B,Mastro VC,Fet V,Blinov A,Baranchikov Y

    更新日期:2016-12-22 00:00:00

  • Gene expression variations in high-altitude adaptation: a case study of the Asiatic toad (Bufo gargarizans).

    abstract:BACKGROUND:Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations to high-altitude adaptation in Asiatic toads (Bufo gargarizans), we implemented a reciprocal transpla...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-017-0529-z

    authors: Yang W,Qi Y,Lu B,Qiao L,Wu Y,Fu J

    更新日期:2017-07-03 00:00:00

  • A copy number variation in human NCF1 and its pseudogenes.

    abstract:BACKGROUND:Neutrophil cytosolic factor-1 (NCF1) is a component of NADPH oxidase. The NCF1 gene colocalizes with two pseudogenes (NCF1B and NCF1C). These two pseudogenes have a GT deletion in exon 2, resulting in a frameshift and an early stop codon. Here, we report a copy number variation (CNV) of the NCF1 pseudogenes ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-13

    authors: Brunson T,Wang Q,Chambers I,Song Q

    更新日期:2010-02-23 00:00:00

  • Detecting responses to treatment with fenofibrate in pedigrees.

    abstract:BACKGROUND:Fenofibrate (Fb) is a known treatment for elevated triglyceride (TG) levels. The Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study was designed to investigate potential contributors to the effects of Fb on TG levels. Here, we summarize the analyses of 8 papers whose authors had access to the GO...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0652-5

    authors: Cherlin S,Wang MH,Bickeböller H,Cantor RM

    更新日期:2018-09-17 00:00:00

  • A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism.

    abstract:BACKGROUND:Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with th...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0670-3

    authors: Velie BD,Fegraeus KJ,Solé M,Rosengren MK,Røed KH,Ihler CF,Strand E,Lindgren G

    更新日期:2018-08-29 00:00:00

  • Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves.

    abstract::Alcohol dependence is a serious public health problem. We studied data from families participating in the Collaborative Study on the Genetics of Alcoholism (COGA) and made available to participants in the Genetic Analysis Workshop 14 (GAW14) in order to search for genes predisposing to alcohol dependence. Using factor...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-6-S1-S15

    authors: Yu Y,Meng Y,Ma Q,Farrell J,Farrer LA,Wilcox MA

    更新日期:2005-12-30 00:00:00

  • Coronary risk in relation to genetic variation in MEOX2 and TCF15 in a Flemish population.

    abstract:BACKGROUND:In mice MEOX2/TCF15 heterodimers are highly expressed in heart endothelial cells and are involved in the transcriptional regulation of lipid transport. In a general population, we investigated whether genetic variation in these genes predicted coronary heart disease (CHD). RESULTS:In 2027 participants rando...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0272-2

    authors: Yang WY,Petit T,Thijs L,Zhang ZY,Jacobs L,Hara A,Wei FF,Salvi E,Citterio L,Delli Carpini S,Gu YM,Knez J,Cauwenberghs N,Barcella M,Barlassina C,Manunta P,Coppiello G,Aranguren XL,Kuznetsova T,Cusi D,Verhamme P,Lu

    更新日期:2015-10-01 00:00:00

  • Exome sequencing in one family with gastric- and rectal cancer.

    abstract:BACKGROUND:Heritable factors are well known to increase the risk of cancer in families. Known susceptibility genes account for a small proportion of all colorectal cancer cases. The aim of this study was to identify the genetic background in a family suggested to segregate a dominant cancer syndrome with a high risk of...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0351-z

    authors: Thutkawkorapin J,Picelli S,Kontham V,Liu T,Nilsson D,Lindblom A

    更新日期:2016-02-13 00:00:00

  • Epidermal growth factor receptor gene mutations in patients with lung adenocarcinoma differ by frequency and type between Uighur and Han ethnic groups in Xinjiang Autonomous Region.

    abstract:BACKGROUND:This study was designed to investigate epidermal growth factor receptor (EGFR) mutation types affecting lung cancer treatment in patients in Xinjiang, China. We detected and analyzed differences in the EGFR mutation points of Uighur and Han patients with lung adenocarcinoma. We examined 181 specimens of lung...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0181-4

    authors: Li X,Wang X,Zhu H,Liu C,Zhou X,Zhao B,Duan H,Yang J,Gu G,Zhan Y,Yuan J,Abuduwaili K,Qionglu S

    更新日期:2015-02-28 00:00:00

  • Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton.

    abstract:BACKGROUND:Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this rese...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-017-0596-1

    authors: Magwanga RO,Lu P,Kirungu JN,Lu H,Wang X,Cai X,Zhou Z,Zhang Z,Salih H,Wang K,Liu F

    更新日期:2018-01-15 00:00:00

  • Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source.

    abstract:BACKGROUND:The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS) samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-58

    authors: Hollegaard MV,Grove J,Grauholm J,Kreiner-Møller E,Bønnelykke K,Nørgaard M,Benfield TL,Nørgaard-Pedersen B,Mortensen PB,Mors O,Sørensen HT,Harboe ZB,Børglum AD,Demontis D,Ørntoft TF,Bisgaard H,Hougaard DM

    更新日期:2011-07-04 00:00:00

  • Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects.

    abstract:BACKGROUND:Hybrid breakdown has been well documented in various species. Relationships between genomic heterozygosity and traits-fitness have been extensively explored especially in the natural populations. But correlations between genomic heterozygosity and vegetative and reproductive traits in cotton interspecific po...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0366-5

    authors: Dai B,Guo H,Huang C,Zhang X,Lin Z

    更新日期:2016-04-12 00:00:00

  • MicroRNA-146a rs2910164 is associated with severe preeclampsia in Black South African women on HAART.

    abstract:BACKGROUND:South African (SA) Black women have a high prevalence of preeclampsia and HIV, both conditions associated with increased inflammation. miR-146a is an inflammatory-associated miR and a common single nucleotide polymorphism (rs2910164) has been associated with several disease conditions. To date, this SNP has ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0469-z

    authors: Maharaj NR,Ramkaran P,Pillay S,Chuturgoon AA

    更新日期:2017-01-19 00:00:00

  • Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa.

    abstract:BACKGROUND:Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0607-x

    authors: van Hooft P,Keet DF,Brebner DK,Bastos ADS

    更新日期:2018-04-03 00:00:00

  • Genetic structure of the gentle Africanized honey bee population (gAHB) in Puerto Rico.

    abstract:BACKGROUND:The Africanized honey bee is one of the most spectacular invasions in the Americas. African bees escaped from apiaries in Brazil in 1956, spread over Americas and by 1994 they were reported in Puerto Rico. In contrast to other places, the oceanic island conditions in Puerto Rico may mean a single introductio...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-14-65

    authors: Galindo-Cardona A,Acevedo-Gonzalez JP,Rivera-Marchand B,Giray T

    更新日期:2013-08-06 00:00:00

  • Clustering by genetic ancestry using genome-wide SNP data.

    abstract:BACKGROUND:Population stratification can cause spurious associations in a genome-wide association study (GWAS), and occurs when differences in allele frequencies of single nucleotide polymorphisms (SNPs) are due to ancestral differences between cases and controls rather than the trait of interest. Principal components ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-108

    authors: Solovieff N,Hartley SW,Baldwin CT,Perls TT,Steinberg MH,Sebastiani P

    更新日期:2010-12-09 00:00:00

  • Cattle phenotypes can disguise their maternal ancestry.

    abstract:BACKGROUND:Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (V...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-017-0523-5

    authors: Srirattana K,McCosker K,Schatz T,St John JC

    更新日期:2017-06-26 00:00:00

  • Truncating CHRNG mutations associated with interfamilial variability of the severity of the Escobar variant of multiple pterygium syndrome.

    abstract:BACKGROUND:In humans, muscle-specific nicotinergic acetylcholine receptor (AChR) is a transmembrane protein with five different subunits, coded by CHRNA1, CHRNB, CHRND and CHRNG/CHRNE. The gamma subunit of AChR encoded by CHRNG is expressed during early foetal development, whereas in the adult, the γ subunit is replace...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0382-5

    authors: Kariminejad A,Almadani N,Khoshaeen A,Olsson B,Moslemi AR,Tajsharghi H

    更新日期:2016-05-31 00:00:00