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Defense mechanisms against herbivory: expression regulation of spruce gene family members representative of the phenylpropanoid pathway

ABSTRACT: A 21.8k spruce EST-spotted microarray was utilized to examine the genetic basis of constitutive defenses against herbivory. From twelve-year-old trees originating from partial diallel pedigree that segregates for resistance against Pissodes strobi, bark tissue of apical leaders was harvested at the onset of seasonal growth and natural weevil activity in the field. Our experimental design is based on a priori known genotype. We identified cross 26 from ♀PG87*♂PG165, cross 27 from ♀PG87*♂PG117, cross 29 from ♀PG21*♂PG165 and cross 32 from ♀PG21*♂PG117, respectively, forming a factorial diallel which showed widest segregation, based on a higher number of segregating SNP loci with genotypes significantly different between the most extreme resistance categories. The distant pair design introduced by ({Fu, 2006}) was modified for outbreds and maximized direct comparisons between different alleles at each locus. Our design resulted in 94 hybridisations profiling 48 individuals in cross 26, 36 in cross 27, and 50 in cross 29 as well as 54 individuals in cross 32. One criterion for identifying positional candidate genes involved that any association between trait variation and genotype variation had to be detected within 10 cM map distances; positional candidate genes for the studied phenotypic trait were then identified by strong collocations of transcript abundance variation and overlap of at least 40% of their expression quantitative trait loci (eQTLs) with phenotypic trait QTLs. 10,000 randomizations were run (p < 0.05).

ORGANISM(S): Picea engelmannii x Picea glauca Picea

PROVIDER: GSE22116 | GEO | 2011/01/01

SECONDARY ACCESSION(S): PRJNA127599

REPOSITORIES: GEO

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Defense mechanisms against herbivory: expression regulation of spruce gene family members representative of the phenylpropanoid pathway

Project description:A 21.8k spruce EST-spotted microarray was utilized to examine the genetic basis of constitutive defenses against herbivory. From twelve-year-old trees originating from partial diallel pedigree that segregates for resistance against Pissodes strobi, bark tissue of apical leaders was harvested at the onset of seasonal growth and natural weevil activity in the field. Our experimental design is based on a priori known genotype. We identified cross 26 from ♀PG87*♂PG165, cross 27 from ♀PG87*♂PG117, cross 29 from ♀PG21*♂PG165 and cross 32 from ♀PG21*♂PG117, respectively, forming a factorial diallel which showed widest segregation, based on a higher number of segregating SNP loci with genotypes significantly different between the most extreme resistance categories. The distant pair design introduced by ({Fu, 2006}) was modified for outbreds and maximized direct comparisons between different alleles at each locus. Our design resulted in 94 hybridisations profiling 48 individuals in cross 26, 36 in cross 27, and 50 in cross 29 as well as 54 individuals in cross 32. One criterion for identifying positional candidate genes involved that any association between trait variation and genotype variation had to be detected within 10 cM map distances; positional candidate genes for the studied phenotypic trait were then identified by strong collocations of transcript abundance variation and overlap of at least 40% of their expression quantitative trait loci (eQTLs) with phenotypic trait QTLs. 10,000 randomizations were run (p < 0.05). The experimental design optimized genetic distances between probe pairs on 94 two-color microarrays to profile 188 interior spruce F1-hybrids, independently grown and harvested.

2011-01-01 | E-GEOD-22116 | biostudies-arrayexpress

Identification of global copy number variations among diverse pig breeds by a CGH array

Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0). In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).

2013-08-09 | E-GEOD-41488 | biostudies-arrayexpress

Quantitative proteomes of Imp2 KO mouse 2-cell-stage embryos

Project description:Data showing the late 2-cell-stage, control embryos (Imp2♀+/♂+) and Imp2-knockout embryos (Imp2♀−/♂+) for HPLC MS/MS analysis. 3 replicates were performed using 330 embryos per group.

2019-11-12 | PXD010397 | Pride

Effects of sample size on differential gene expression, rank order and prediction accuracy of a gene signature

Project description:Gene expression profiles were generated from muscle biopsies from 134 individuals, and differences in expression based on sex were explored. Top differentially expressed gene lists are often inconsistent between studies and it has been suggested that small sample sizes contribute to lack of reproducibility and poor prediction accuracy in discriminative models. We considered sex differences (69♂, 65♀) in 134 human skeletal muscle biopsies using DNA microarray. The full dataset and subsamples (n= 10 (5♂, 5♀) to n=120 (60♂, 60♀)) thereof were used to assess the effect of sample size on the differential expression of single genes, gene rank order and prediction accuracy. Using our full dataset (n=134), we identified 717 differentially expressed transcripts (p-value < 0.0001; false discovery rate < 0.006) and we were able to predict sex with 92% accuracy, both within our dataset and on external datasets. Both p-values and rank order of top differentially expressed genes became more variable using smaller subsamples. For example, at n=10 (5♂, 5♀), no gene was considered differentially expressed at p<0.0001 and prediction accuracy was ~50% (no better than chance). We found that sample size clearly affects microarray analysis results; small sample sizes result in unstable gene lists and poor prediction accuracy. We anticipate this will apply to other phenotypes, in addition to sex.

2014-05-15 | GSE41726 | GEO

Inheritance Patterns of Leukocyte Gene Expression Under Heat Stress in F1 Hybrids Cattle and Their Parents

Project description:This study aimed to investigate the heat tolerance and inheritance patterns of leukocyte transcriptomics in F1 hybrid cattle (AN♂ × DR♀) and their parents Red Angus (AN) and Droughtmaster (DR) under heat stress.

2020-06-12 | GSE151817 | GEO

Cortical, hippocampal and thalamic whole genome transcriptome data from controls and G72 schizophrenia mice of both sexes

Project description:G72 transgenic (TG, transgenic mice carrying the G72/G30 locus) and wildtype (WT) mice with a CD1 background were used for transcriptome data acquisition. Importantly, three different brain regions, i.e., the retrosplenial cortex, the hippocampus and thalamus, of animals from both sexes were investigated. In total, eight WT control animals (four ♂, age: 23.14 ± 0.00 wks; four ♀, age: 23.46 ± 0.11 wks) and eight G72 transgenic mice (four ♂, age: 23.14 ± 0.00 wks; four ♀, age: 23.14 ± 0.00 wks) were used for dissection of the cortex, thalamus and hippocampus for subsequent transcriptome analysis. Our data allow new insight into relevant alterations in gene transcript levels in G72 mice and allow the reader/user to carry out additional complex analyses to characterize potential sex-, age- and brain-region-specific profiles in gene expression and related pathways. These analyses could trigger biomarker identification and drug research and development in schizophrenia research in the future.

2023-12-01 | E-MTAB-13547 | biostudies-arrayexpress

Fertile offspring derived from mouse spermatogonial stem cells cryopreserved for more than 14 years

Project description:To evaluate the possible deleterious affects prolonged cryopreservation and assisted reproductive technologies may have on the DNA of F0 progeny, we used array-based comparative genomic hybridization (CGH) for analysis of genomic DNA. ICSI-derived progeny were generated from ♂ (ZFLacZ sperm) x ♀ (DBA x C57BL/6 oocyte), where the ZFLazZ transgenic mice were originally generated from an SJL x C57BL/6 background.

2012-01-13 | E-GEOD-35056 | biostudies-arrayexpress

Developmental time-course study of Drosophila melanogaster, D. sechellia, D. simulans, and D. sim x D.s sec hybrids

Project description:In order to test the hypothesis that adult hybrid misexpression results from the cascading effect of earlier-expressed developmentally important improperly regulated genes, as well as address whether Von Baer’s 3rd law (suggesting that earlier stages of development should be more similar between species than later stages) holds at the level of gene expression, we conducted whole-transcriptome Drosophila melanogaster cDNA microarray-based expression profiling of males of D. melanogaster, D. sechellia, and D. simulans, at four synchronized developmental time-points (3rd instar larval [larval], early pupal, late pupal, and newly-emerged adult [adult]). D. simulans and D. sechellia shared a most recent common ancestor (MRCA) ~0.5 to 1.0 million years ago (MYA) and form a clade that shared an MRCA with D. melanogaster approximately 5.4 MYA. In addition, we also performed the same analysis on the male interspecific F1 hybrids of the D. simulans (♀) × D. sechellia (♂) cross.

2010-08-03 | GSE17535 | GEO

Mitral valve transcriptome analysis in thirty-four age-matched Cavalier King Charles Spaniels with or without congestive heart failure caused by myxomatous mitral valve disease

Project description:We here report the results of a mitral valve transcriptome study designed to identify genes and molecular pathways involved in development of congestive heart failure (CHF) following myxomatous mitral valve disease (MMVD) in dogs. The study is focused on a cohort of elderly age-matched dogs (n=34, age ~10 years) from a single breed – Cavalier King Charles Spaniels (CKCS) – with a high incidence of MMVD. The cohort comprises 19 dogs (10♀, 9♂) without MMVD-associated CHF, and 15 dogs (6♀, 9♂) with CHF caused by MMVD. I.e. we compare gene expression in breed and age matched groups of dogs, which only differ with respect to CHF status. We identify 56 genes, which are differentially expressed between the two groups. In this list of genes, we confirm an enrichment of genes related to the TNFβ signaling pathway, extracellular matrix organization, vascular development, and endothelium damage, which also have been identified in previous studies. However, the genes with the greatest difference in expression between the two groups are CNTN3 and MYH1. Both genes encode proteins, which are predicted to have an effect on the contractile activity of myocardial cells, which in turn may have an effect on valvular performance and hemodynamics across the mitral valve. This may result in shear forces with impact on MMVD progression.

2023-11-10 | GSE217750 | GEO

proteomics data of gonad tissue from crucian carp, common carp and allotetraploid

Project description:Allotetraploid Hybrids of Red Crucian Carp (Carassius auratus red var) (♀) and Common Carp (Cyprinus carpio L) (♂) is a species produced by distant hybridization. In this study, SWATH-MS were applied for quantitative proteomics profiling in gonad tissue of allotetraploid and its parents Red Crucian Carp (♀) and Common Carp (♂) respectively.

2020-04-02 | PXD018339 |

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