Regulatory roles of small non-coding RNAs in sugar beet resistance against beet curly top virus

Authors: Majumdar, Raj; Galewski, Paul; Eujayl, Imad; MINOCHA, RAKESH - US Department Of Agriculture (USDA); Vincill, Eric; Strausbaugh, Carl

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2021
Publication Date: 1/10/2022
Citation: Majumdar, R., Galewski, P.J., Eujayl, I.A., Minocha, R., Vincill, E.D., Strausbaugh, C.A. 2022. Regulatory roles of small non-coding RNAs in sugar beet resistance against beet curly top virus. Frontiers in Plant Science. 12. Article 780877. https://doi.org/10.3389/fpls.2021.780877.
DOI: https://doi.org/10.3389/fpls.2021.780877

Interpretive Summary: Sugar beet is highly susceptible to beet curly top virus (BCTV) and the virus significantly impacts sugar beet yield and reduces sugar content. Sources of genetic resistance to BCTV are highly limited and even commercial cultivars possess only low to moderate resistance. We have developed sugar beet germplasm through selection and breeding that show strong resistance against BCTV strains. Among different factors that contribute to host plant resistance against stress, small non-coding RNAs (sncRNAs) have been shown to play an important role in biotic and abiotic stress tolerance. No information is available on how sncRNAs contribute to sugar beet resistance against pathogens especially against viruses. In this work we demonstrate molecular mechanisms by which sncRNAs in the BCTV resistant sugar beet lines contribute to BCTV resistance through modulating metabolic pathways and/or key resistant genes. We also demonstrate the role of BCTV derived sncRNAs, their potential targets in sugar beet, and differential regulation in the resistant versus susceptible lines. In addition, we demonstrate potential host plant derived miRNAs that target key genes related to BCTV pathogenesis during early stages of plant infection. The knowledge obtained from this work will be highly valuable in future designing of virus resistant plants not only in sugar beets but also in other crops such as tomatoes, peppers, beans etc. where BCTV causes significant damage and yield losses.

Technical Abstract: Beet curly top virus (BCTV) mediated yield loss in sugar beets is a major problem worldwide. The circular single-stranded DNA virus is transmitted by the beet leafhopper. Genetic sources of BCTV resistance in sugar beet are limited and commercial cultivars rely on chemical treatments versus durable genetic resistance. Phenotypic selection and double haploid production have resulted in sugar beet germplasm (KDH13-13 and KDH4-9-4) that are highly resistant to BCTV. The molecular mechanism of resistance to the virus is unknown, especially the role of small noncoding RNAs (sncRNAs) during early plant-viral interaction. Using the resistant lines along with a susceptible line (KDH19-17; 19), we demonstrate the role of sugar beet miRNAs in BCTV resistance during early infection stages when symptoms are not yet visible. The differentially expressed miRNAs altered the expression of their corresponding target genes such as pyruvate dehydrogenase (EL10Ac1g02046), carboxylesterase (EL10Ac1g01087), serine/threonine protein phosphatase (EL10Ac1g01374), and LRR receptor-like (EL10Ac7g17778), that were highly expressed in the resistant lines versus susceptible lines. Pathway enrichment analysis of the miRNA target genes showed an enrichment of genes involved in glycolysis/gluconeogenesis, galactose metabolism, starch, and sucrose metabolism to name a few. Carbohydrate analysis revealed altered glucose, galactose, fructose, and sucrose concentration in the infected leaves of resistant versus susceptible lines. We also demonstrate differential regulation of BCTV derived sncRNAs in the resistant versus susceptible lines that target sugar beet genes such as LRR (EL10Ac1g01206), 7-deoxyloganetic acid glucosyltransferase (EL10Ac5g12605), and transmembrane emp24 domain containing (EL10Ac6g14074) and altered their expression. In response to viral infection, we found that plant derived miRNAs targeted BCTV capsid protein/replication related genes and showed differences in expression among resistant and susceptible lines. The data presented here demonstrate the contribution of miRNA mediated regulation of metabolic pathways and cross-kingdom RNAi in sugar beet BCTV resistance.