Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress

Abstract

Spring frost is a major limiting abiotic stress for the cultivation of almonds [Prunus dulcis (Mill.)] in Mediterranean areas or the Middle East. Spring frost, in particular, damages almond fully open flowers, resulting to significant reduction in yield. Little is known about the genetic factors expressed after frost stress in Prunus spp. as well as in almond fully open flowers. Here, we provide the molecular signature of pistils of fully open flowers from a frost-tolerant almond genotype. The level of frost tolerance in this genotype was determined for all three flowering stages and was confirmed by comparing it to two other cultivars using several physiological analyses. Afterwards, comprehensive expression profiling of genes expressed in fully open flowers was performed after being exposed to frost temperatures (during post-thaw period). Clean reads, 27,104,070 and 32,730,772, were obtained for non-frost-treated and frost-treated (FT) libraries, respectively. A total of 62.24 Mb was assembled, generating 50,896 unigenes and 66,906 transcripts. Therefore, 863 upregulated genes and 555 downregulated genes were identified in the FT library. Functional annotation showed that most of the upregulated genes were related to various biological processes involved in responding to abiotic stress. For the first time, a highly expressed cold-shock protein was identified in the reproductive organ of fruit trees. The expression of six genes was validated by RT-PCR. As the first comprehensive analysis of open flowers in a frost-tolerant almond genotype, this study represents a key step toward the molecular breeding of fruit tree species for frost tolerance.

Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

“…Primers for the IGT family members were designed using the respective QUIAGEN CLC Genomics Workbench tool (QUIAGEN, https://digitalinsights.qiagen.com/). Actin primers were used as an internal control to normalize expression [56]. The reactions were performed using a 7900 DNA sequence detector (Thermo Fisher Scientific, https://www.thermofisher.com).…”

Advances in biotechnology and propagation of nut trees in Iran

“…In another study, transcriptome analysis of a frost-tolerant genotype in response to freezing stress using RNA-Seq method revealed 863 upregulated genes and 555 downregulated genes in the frost-treated library. In this study, a highly expressed cold-shock protein was identified which can be used as a marker in future studies [17].…”

Transcriptome profiling in Camellia japonica var. decumbens for the discovery of genes involved in chilling tolerance under cold stress

“…decumbens in response to cold stress -cold sensor or signal transduction genes GeneID and expression patterns of DEGs in C. japonica var. decumbens in response to cold stress -genes related to the stabilization of the plasma membrane and osmosensing response acclimation-related transcriptome of C. japonica (Li et al 2016), and in cold-related transcriptome studies with other woody species such as Hevea brasiliensis (Cheng et al 2018), Eucalyptus nitens (Gaete-Loyola et al 2017), or Prunus dulcis (Hosseinpour et al 2018). Dozens of cold related genes with known function in other model plants were found in this differential expression list, including cold sensor or signal transduction genes, cold responsive transcription factor genes, plasma membrane stabilization related genes and osmosensing-responsive genes.…”