Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

BBSRC Waugh BarleyRNAseq

ABSTRACT: Eight tissues of cultivar Morex (three biological replications each) earmarking stages of the barley life cycle from germinating grain to maturing caryopsis were selected for deep RNA sequencing (RNA-seq)

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Hordeum vulgare subsp. vulgare

SUBMITTER: Robert Davey

PROVIDER: E-MTAB-2809 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A physical, genetic and functional sequence assembly of the barley genome.

Mayer Klaus F X KF Waugh Robbie R Brown John W S JW Schulman Alan A Langridge Peter P Platzer Matthias M Fincher Geoffrey B GB Muehlbauer Gary J GJ Sato Kazuhiro K Close Timothy J TJ Wise Roger P RP Stein Nils N

Nature 20121017 7426

Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complemen ...[more]

PMID: 23075845

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Project description:Water soluble carbohydrates (WSC, composed of mainly fructans, sucrose, glucose and fructose) deposited in wheat stems are important carbon sources for grain filling. Variation in stem WSC concentrations among wheat genotypes is one of the genetic factors influencing grain weight and yield under water-limited environments. Here, we describe the molecular dissection of carbohydrate metabolism in stems, at the WSC accumulation phase, of recombinant inbred SB (Seri/Babax) lines of Triticum aestivum differing in stem WSC concentrations. Affymetrix GeneChip analysis of carbohydrate metabolic enzymes revealed that the mRNA levels of two fructan synthetic enzyme families (sucrose:sucrose 1-fructosyltransferase and sucrose:fructan 6-fructosyltransferase) in the stem were positively correlated with stem WSC and fructan concentrations, while the mRNA levels of enzyme families involved in sucrose hydrolysis (sucrose synthase and soluble acid invertase) were inversely correlated with WSC concentrations. Differential regulation of the mRNA levels of these sucrose hydrolytic enzymes in SB lines resulted in genotypic differences in these enzyme activities. Down-regulation of sucrose synthase and soluble acid invertase in high WSC lines was accompanied by significant decreases in the mRNA levels of enzyme families related to sugar catabolic pathways (fructokinase and mitochondrion pyruvate dehydrogenase complex) and enzyme families involved in diverting UDP-glucose to cell wall synthesis (UDP-glucose 6-dehydrogenase, UDP-glucuronate decarboxylase and cellulose synthase), resulting in a reduction in cell wall polysaccharide contents (mainly hemicellulose) in the stem of high WSC lines. These data suggest that differential carbon partitioning in the wheat stem is one mechanism that contributes to genotypic variation in WSC accumulation. We used Affymetrix GeneChip to dissect genotypic variation in carbohydrate metabolism related to water soluble carbohydrate accumulation in stems of wheat. Experiment Overall Design: 8 genotypes of recombinant inbred lines Seri M82 x Babax with 2 biological replicates per genotype. Grown in the field under rain-fed conditions

Dataset Information

BBSRC Waugh BarleyRNAseq

Publications

A physical, genetic and functional sequence assembly of the barley genome.

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