LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

  • [H. vulgare (gene)]
  • Detail of Experiment mapped on Hordeum vulgare vulgare L Hvulgare462r1

Details

NameTranscriptome analysis of pre-anthesis development in barley
DescriptionThe timing of reproductive development determines spike architecture and thus yield in temperate grasses such as barley (Hordeum vulgare L.). Reproductive development in barley is controlled by the photoperiod response gene Ppd-H1 which accelerates flowering time under long-day (LD) conditions. A natural mutation in Ppd-H1 prevalent in spring barley causes a reduced photoperiod response, and thus, late flowering under LD. However, it is not very well understood how LD and Ppd-H1 control pre-anthesis development, and thus spike architecture and yield in barley. We performed a detailed morphological analysis of the pre-anthesis development in the spring barley cultivar Scarlett and its wild barley derived introgression line S42-IL107, carrying the photoperiod responsive Ppd-H1 allele. Characterization of shoot apex development in these genotypes indicated that floral transition and initiation of floral primordia occurred under LD (16h light/ 8h dark) and short day (SD, 8h light/ 16h dark) conditions, while inflorescence and seed development strictly required LDs. Additionally, a fast photoperiod response in the presence of the dominant Ppd-H1 allele promoted floret fertility under LDs. To characterize the effects of the photoperiod and allelic variation at Ppd-H1 on gene expression during pre-anthesis development we performed RNA sequencing of leaves and developing main shoot apices during the vegetative phase and early stages of inflorescence development in Scarlett and S42-IL107 grown under SD and LD conditions. Main shoot apices of both genotypes were sampled at defined developmental stages, i.e. Waddington stage W0.5, W1.0, W2.0 and W3.5, respectively. Leaf samples were harvested from plants before (W1.0) and after floral transition (W2.0). We identified genes that were specifically regulated at floral transition independent of day-length and Ppd-H1 and thus may serve as markers for the staging of floral transition. Furthermore, we identified transcripts differentially expressed between photoperiods and between genotypes in leaves and in shoot apices. This set of transcripts might act as candidates downstream of Ppd-H1 and are correlated with the promotion of shoot apex development and higher floret fertility under LD and in the presence of the photoperiod responsive Ppd-H1 allele.
ContactHHU (Heinrich Heine University)
XrefPRJEB8748
Reference
Conditions16
SpeciesHordeum vulgare
Metadata export .CSV   .JSON

Analysis

Mapped Genomes Hvulgare462r1    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
Apex_LD_S42-IL017_W1_3DAS S42-IL107 W1.0 Apex Long Day
  • Apex_LD_S42-IL017_W1_3DAS_1
  • Apex_LD_S42-IL017_W1_3DAS_2
  • Apex_LD_S42-IL017_W1_3DAS_3
  • ERR781045 
  • ERR781046 
  • ERR781047 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_LD_S42-IL017_W2_6DAS S42-IL107 W2.0 Apex Long Day
  • Apex_LD_S42-IL017_W2_6DAS_1
  • Apex_LD_S42-IL017_W2_6DAS_2
  • ERR781048 
  • ERR781049 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Apex_LD_S42-IL107_W3.5_14DAS S42-IL107 W3.5 Apex Long Day
  • Apex_LD_S42-IL107_W3.5_14DAS_1
  • Apex_LD_S42-IL107_W3.5_14DAS_2
  • Apex_LD_S42-IL107_W3.5_14DAS_3
  • ERR781071 
  • ERR781072 
  • ERR781073 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_LD_Scarlett_W1_3DAS Scarlett W1.0 Apex Long Day
  • Apex_LD_Scarlett_W1_3DAS_1
  • Apex_LD_Scarlett_W1_3DAS_2
  • Apex_LD_Scarlett_W1_3DAS_3
  • ERR781042 
  • ERR781043 
  • ERR781044 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_LD_Scarlett_W2_9DAS Scarlett W2.0 Apex Long Day
  • Apex_LD_Scarlett_W2_9DAS_1
  • Apex_LD_Scarlett_W2_9DAS_2
  • Apex_LD_Scarlett_W2_9DAS_3
  • ERR781053 
  • ERR781054 
  • ERR781055 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_LD_Scarlett_W3.5_20DAS Scarlett W3.5 Apex Long Day
  • Apex_LD_Scarlett_W3.5_20DAS_1
  • Apex_LD_Scarlett_W3.5_20DAS_2
  • Apex_LD_Scarlett_W3.5_20DAS_3
  • ERR781077 
  • ERR781078 
  • ERR781079 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_SD_S42-IL017_W0.5_0DAS S42-IL107 W0.5 Apex Short Day
  • Apex_SD_S42-IL017_W0.5_0DAS_1
  • Apex_SD_S42-IL017_W0.5_0DAS_2
  • Apex_SD_S42-IL017_W0.5_0DAS_3
  • ERR781039 
  • ERR781040 
  • ERR781041 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_SD_S42-IL017_W1_7DAS S42-IL107 W1.0 Apex Short Day
  • Apex_SD_S42-IL017_W1_7DAS_1
  • Apex_SD_S42-IL017_W1_7DAS_2
  • Apex_SD_S42-IL017_W1_7DAS_3
  • ERR781059 
  • ERR781060 
  • ERR781061 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_SD_S42-IL017_W2_16DAS S42-IL017 W2.0 Apex Short Day
  • Apex_SD_S42-IL017_W2_16DAS_1
  • Apex_SD_S42-IL017_W2_16DAS_2
  • Apex_SD_S42-IL017_W2_16DAS_3
  • ERR781056 
  • ERR781057 
  • ERR781058 
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.bam    .bai    .csi   
.bam    .bai    .csi   
Apex_SD_S42-IL107_W3.5_50DAS S42-IL107 W3.5 Apex Short Day
  • Apex_SD_S42-IL107_W3.5_50DAS_1
  • Apex_SD_S42-IL107_W3.5_50DAS_2
  • Apex_SD_S42-IL107_W3.5_50DAS_3
  • ERR781083 
  • ERR781084 
  • ERR781085 
 .bam    .bai    .csi   
.bam    .bai    .csi   
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Leaf_LD_S42-IL017_W2_6DAS S42-IL107 W2.0 Leaf Long Day
  • Leaf_LD_S42-IL017_W2_6DAS_1
  • Leaf_LD_S42-IL017_W2_6DAS_2
  • Leaf_LD_S42-IL017_W2_6DAS_3
  • ERR781050 
  • ERR781051 
  • ERR781052 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Leaf_LD_S42-IL107_W1_3DAS S42-IL107 W1.0 Leaf Long Day
  • Leaf_LD_S42-IL107_W1_3DAS_1
  • Leaf_LD_S42-IL107_W1_3DAS_2
  • Leaf_LD_S42-IL107_W1_3DAS_3
  • ERR781065 
  • ERR781066 
  • ERR781067 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Leaf_LD_Scarlett_W1_3DAS Scarlett W1.0 Leaf Long Day
  • Leaf_LD_Scarlett_W1_3DAS_1
  • Leaf_LD_Scarlett_W1_3DAS_2
  • Leaf_LD_Scarlett_W1_3DAS_3
  • ERR781062 
  • ERR781063 
  • ERR781064 
 .bam    .bai    .csi   
.bam    .bai    .csi   
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Leaf_LD_Scarlett_W2_9DAS Scarlett W2.0 Leaf Long Day
  • Leaf_LD_Scarlett_W2_9DAS_1
  • Leaf_LD_Scarlett_W2_9DAS_2
  • Leaf_LD_Scarlett_W2_9DAS_3
  • ERR781068 
  • ERR781069 
  • ERR781070 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Leaf_SD_S42-IL107_W1_7DAS S42-IL107 W1.0 Leaf Short Day
  • Leaf_SD_S42-IL107_W1_7DAS_1
  • Leaf_SD_S42-IL107_W1_7DAS_2
  • Leaf_SD_S42-IL107_W1_7DAS_3
  • ERR781080 
  • ERR781081 
  • ERR781082 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
Leaf_SD_S42-IL107_W2_16DAS S42-IL107 W2.0 Leaf Short Day
  • Leaf_SD_S42-IL107_W2_16DAS_1
  • Leaf_SD_S42-IL107_W2_16DAS_2
  • Leaf_SD_S42-IL107_W2_16DAS_3
  • ERR781074 
  • ERR781075 
  • ERR781076 
 .bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi