Transcriptomic basis for salt tolerance and disease resistance of silverleaf sunflower revealed by Iso-seq and RNA-seq

Abstract

Background Silverleaf sunflower, Helianthus argophyllus , is one of the most important wild species that have been usually used for the improvement of cultivated sunflower. Although a reference genome is now available for the cultivated species, H. annuus , its effect in helping understanding the mechanisms underlying the traits of H. argophyllus is limited by the substantial genomic variance between these two species.Results In this study, we generated a high-quality reference transcriptome of H. argophyllus using Iso-seq strategy. This assembly contains 50,153 unique genes covering more than 91% of the whole genes. Among them, we find 205 genes that are absent in the cultivated species and 475 fusion genes containing components of coding or non-coding sequences from the genome of H. annuus . It is interesting that in line with the strong disease resistance observed for H. argophyllus , these H. argophyllus -specific genes are predominantly related to functions of resistance. We have also profiled the gene expressions in leaf and root under normal or salt stressed conditions and, as a result, find distinct transcriptomic responses to salt stress in leaf and root. Particularly, genes involved in several critical processes including the synthesis and metabolism of glutamate and carbohydrate transport are reversely regulated in leaf and root.Conclusions Overall, this study provided insights into the genomic mechanisms underlying the disease resistance and salt tolerance of silverleaf sunflower and the transcriptome assembly and the genes identified in this study can serve as a complement data resources for future research and breeding programs of sunflowers.

Genetic Improvement in Sunflower Breeding—Integrated Omics Approach

“…Authors assembled a high quality reference transcriptome for H. argophyllus with over 50,000 genes and found that 205 of them are not present in cultivated sunflower. Transcriptomic response to salt stress revealed more than double the number of genes (3930) that were significantly regulated in root compared to leaf (1885), which is understandable considering the higher sensitivity of root, as it is more exposed to this type of stress [68]. Transcriptomic analysis can be very useful for distinguishing gene expression in drought-sensitive and drought-tolerant genotypes [69], which is of great help for the development of drought-tolerant genotypes as one of the main goals in sunflower breeding.…”

“…The significance of transcriptomic study is also reflected in the fact that it can be used for comparative analysis of genome differences between cultivated crops and wild relatives, thus revealing specific genes that can be important for improvement in the breeding process. Using a long read technique (Iso-seq) as well as RNA sequencing (RNA-seq), transcriptomic basis for salt tolerance and disease resistance of wild sunflower species (Helianthus argophyllus) was studied [68]. Authors assembled a high quality reference transcriptome for H. argophyllus with over 50,000 genes and found that 205 of them are not present in cultivated sunflower.…”