Abstract
BackgroundRNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants. Gerbera daisy is one of the most important flowers in the global floricultural trade, and powdery mildew (PM) is the most important disease of gerbera. Genetic improvement of gerbera PM resistance has become a crucial goal in gerbera breeding. A better understanding of the genetic control of gerbera resistance to PM can expedite the development of PM-resistant cultivars.ResultsThe objectives of this study were to identify gerbera genotypes with contrasting phenotypes in PM resistance and sequence and analyze their leaf transcriptomes to identify disease resistance and susceptibility genes differentially expressed and associated with PM resistance. An additional objective was to identify SNPs and SSRs for use in future genetic studies. We identified two gerbera genotypes, UFGE 4033 and 06–245-03, that were resistant and susceptible to PM, respectively. De novo assembly of their leaf transcriptomes using four complementary pipelines resulted in 145,348 transcripts with a N50 of 1124 bp, of which 67,312 transcripts contained open reading frames and 48,268 were expressed in both genotypes. A total of 494 transcripts were likely involved in disease resistance, and 17 and 24 transcripts were up- and down-regulated, respectively, in UFGE 4033 compared to 06–245-03. These gerbera disease resistance transcripts were most similar to the NBS-LRR class of plant resistance genes conferring resistance to various pathogens in plants. Four disease susceptibility transcripts (MLO-like) were expressed only or highly expressed in 06–245-03, offering excellent candidate targets for gene editing for PM resistance in gerbera. A total of 449,897 SNPs and 19,393 SSRs were revealed in the gerbera transcriptomes, which can be a valuable resource for developing new molecular markers.ConclusionThis study represents the first transcriptomic analysis of gerbera PM resistance, a highly important yet complex trait in a globally important floral crop. The differentially expressed disease resistance and susceptibility transcripts identified provide excellent targets for development of molecular markers and genetic maps, cloning of disease resistance genes, or targeted mutagenesis of disease susceptibility genes for PM resistance in gerbera.
Highlights
RNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants
Line 06–245-03 showed the highest level of powdery mildew (PM) susceptibility and was rated as the most susceptible among the selected lines with an Area under disease progress curve (AUDPC) (Area Under Disease Progress Curve) score of 21.67 per week, whereas UFGE 4033 consistently showed few or no PM symptoms with an AUDPC score of 4.25 per week during the study (Fig. 1)
Transcriptome sequencing was used to profile the leaf transcriptome of two gerbera breeding lines, UFGE 4033 and 06–245-03, that differed in resistance to powdery mildew and to analyze gene expression during the post-inoculation stage when most of the disease resistance (DR) genes are expressed in the breeding lines due to exposure to PM
Summary
RNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants. Gerbera daisy (Gerbera hybrida) is popular in the global floricultural trade for its wide array of bright colored flowers. It is predominantly grown as cut flower and increasingly as garden, bedding, patio and indoor plants. With an attractive and complex flower structure, gerbera has been used as a model plant to study flower development in the Asteraceae family. It has been used extensively in studies of plant secondary plant metabolism [5]
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