Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance

Abstract

Background 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 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. Results The 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. Conclusion This 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.

Ornamental plant breeding: entering a new era?

“…Now, markers and their associated genes can be more accurately identified in the specific chromosome and deployed in the breeding program. Genome reduction techniques like transcriptome sequencing and genotyping by sequencing have facilitated identification of genes and SNPs and SSRs in multiple ornamental crops like gerbera, hydrangea, impatiens, caladium, and others (Bhattarai et al, 2020, Wu et al, 2021Bhattarai et al, 2018;Cao et al, 2017). Techniques like genome resequencing help to compare genomic regions of the individuals across the species and identify the markers applicable in the respective germplasm at the global level.…”

Recent Progress in Enhancing Fungal Disease Resistance in Ornamental Plants

“…SNP markers for linkage mapping and the transcripts that may be involved in Botrytis resistance have been recently identified in gerbera, and these findings may be useful for further studies of disease resistance [66]. Moreover, transcriptomic analyses performed in gerbera revealed candidate genes for resistance to powdery mildew, and these could provide valuable resources for developing powdery mildew-resistant gerbera cultivars [136]. Recent reports detailing the enhancement of fungal disease resistance in various ornamental plants are listed in Table 2.…”

Cytological and transcriptomic analysis to unveil the mechanism of web blotch resistance in Peanut

“…In an earlier study on the interaction between rice and the fungus responsible for rice blast, 58 candidate effectors were screened [ 20 ]. Many genes related to disease resistance have been identified in wheat [ 21 ], maize [ 22 ], cucumber [ 23 ], Gastrodia [ 24 ], Gerbera [ 25 ], and other species. Furthermore, key metabolic pathways in plant responses to pathogen infections have been determined, providing the theoretical basis for research on plant disease resistance mechanisms [ 26 ].…”