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Affy_zeawall_ril_maize - Expression studies in 5 early maize RIL with contracted allelic patterns at major QTL posititions

ABSTRACT: affy_zeawall_ril_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled. Keywords: genotype comparison, time course

ORGANISM(S): Zea mays

PROVIDER: GSE22439 | GEO | 2012/06/17

SECONDARY ACCESSION(S): PRJNA128637

REPOSITORIES: GEO

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affy_zeawall_ril2_maize: ZeaWall Project, defavorable parent F271

Project description:affy_zeawall_ril2_maize - affy_zeawall_ril2_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). The defavorable parent F271 was studied in complement and is the object of this last array. Expression studies will be investigated in ear internode at two stages (emerging tassel and early silking).-Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). The defavorable parent F271 was also studied in complement and is the object of this last array.Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled.

2012-08-30 | GSE27070 | GEO

affy_zeawall_ril_maize - Expression studies in 5 early maize RIL with contracted allelic patterns at major QTL posititions

Project description:affy_zeawall_ril_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled. Keywords: genotype comparison, time course 20 arrays - maize

2012-06-16 | E-GEOD-22439 | biostudies-arrayexpress

affy_zeawall_ril2_maize: ZeaWall Project, defavorable parent F271

2012-08-30 | E-GEOD-27070 | biostudies-arrayexpress

Expression analysis of circadian light response in Drosophila recombinant inbred lines (RIL)

Project description:The aim of this study was to identify quantitative trait loci (QTL) associated with variation in circadian photosensitivity in Drosophila, by measuring the locomotor response to early night light pulse (Zt15). We used QTL mapping of recombinant inbred lines (RIL), which was followed by microarrays expression comparison of two RI lines which differed significantly in their light response (RIL 104 shows a strong long phase delay response while RIL 58 shows a weak light response).

2016-02-09 | GSE77116 | GEO

Allelic variation at a major QTL for cell wall related traits and coordinated changes in gene expression in maize

Project description:ngs2015_12_zeawall2-zeawall2-Address the hypothesis that allelic variation at a major QTL for cell wall related traits gives rise to coordinated changes in gene expression in maize-Two pairs of BC2S2 maize lines carrying F271 or F288 alleles in an 18-20 Mb interval of chromosome 6 in an otherwise F271 genetic background were grown in the field at Mauguio (Hérault, France) in 2015 with two row replicates. Irrigation was applied during the summer to prevent water stress. The bottom third of upstream-ear internodes (without nodes) of three representative plants in each of the two replicates were harvested two days before silking. All samples were immediately frozen in liquid nitrogen and stored at -80°C.

2019-12-14 | GSE115157 | GEO

Expression analysis of circadian light response in Drosophila recombinant inbred lines (RIL)

2016-02-09 | E-GEOD-77116 | biostudies-arrayexpress

Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

2015-04-30 | GSE49805 | GEO

Whole genome transcriptome profiling of Pusa 1266 and Pusa Basmati 1 in panicle primordia stage

Project description:The aim of this study was to identify candidate genes responsible for grain number per panicle between a pair of rice varieties (Pusa 1266 and Pusa Basmati 1) by combining QTL analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 2741 differentially expressed genes. The differentially expressed genes were shortened to 18 on the basis of their occurance in the QTL region (responsible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1. RNA from the stage '0' panicle primordia of Pusa 1266 and Pusa Basmati 1 were analysed in two different biological replications (A and B) making total four samples

2010-04-28 | E-GEOD-15912 | biostudies-arrayexpress

Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

Project description:The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development. Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.

2015-04-30 | E-GEOD-49805 | biostudies-arrayexpress

Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton

Project description:Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding.

2022-06-23 | GSE186533 | GEO

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