Dataset features


Application: RNA-seq analysis
Number of samples: 8
Release date: Jan 13 2018
Last update date: Jan 24 2018
Access: Public
Diseases: Coinfection
Chemicals: Abscisic Acid
Dataset link RNA-Sequencing Analysis of Abscission-related Transcriptome in Citrus Calyx Abscission Zone Reveals Distinguishing Profile of Phytohormone Expression Associated with Abscission of HLB-affected Sweet Orange

Experimental Protocol

Six-year old ‘Hamlin’ orange trees (Citrus sinensis (L.) Osbeck), about 2.5-3.0 m tall, on 'Swingle' citrumelo (C. paradisi Macf. × Poncirus trifoliata (L) Raf.) rootstock, in a commercial grove located in Southern Florida. Thirty six trees were selected for the experiment, of which eighteen were CLas negative (healthy) and the other eighteen were CLas positive (HLB), as tested by qPCR using the method of Li et al. (2006). The selected trees were similar in size, and all were grown under similar agro-climatic conditions and received common cultural practices and the grower’s standard pest and disease management. Fruit were harvested on 1 Dec. 2014 (during commercial harvest season). The ground under the trees was cleaned just before shaking the trees, and trees were shaken manually. For HLB-diseased trees (d), many of the fruit dropped (Dd) upon shaking the trees. For healthy trees (h), the forces of shaking were strong enough to get enough number of dropped fruit (Dh) from the trees. The dropped fruit (Dd or Dh) were collected, and the retained fruit on HLB-diseased (Rd) or healthy trees (Rh) were hand-picked off the trees (Fig. 1A). The fruit from nine trees were pooled together as a group. There were two groups (biological replicates) for each of the Dd, Rd, Dh and Rh. Thirty fruit were randomly picked from each of the Dd, Rd, Dh and Rh groups, and the AZ-C were excised (Fig.1B) and immediately frozen in liquid nitrogen and stored at –80 ºC for RNA isolation. Another thirty fruit from each of the groups were transported to the laboratory where fruit ethylene production was measured.