Genome-enabled analysis of Quercus rubra–ozone and Chenopodium quinoa-Cucumber mosaic virus interactions

Plants are exposed to a range of biotic and abiotic stresses, which could adversely affect growth, longevity, and yield. Advent of high-throughput sequencing have enabled holistic analyses of genes that are differentially expressed due to stress. Productivity of Northern red oak (Quercus rubra) (NRO), an economically important species in the forests of North America, is reduced by exposure to O3 and insect damage. However, limited information is available on its responses to exogenous stimuli at transcriptome level. Production and consumption of quinoa (Chenopodium quinoa Willd) have increased in recent years. Since quinoa seeds taste bitter due to high concentration of saponins in seed, low saponin (sweet) cultivars have been developed. Saponin has inhibitory role in several plant pathosystems. There is no knowledge regarding the influence of saponin content of quinoa cultivars on virus and nematode pathogenesis. Objectives of this research were to: 1) analyze NRO transcriptome to detect gene expression differences induced by ozone exposure and simulated insect wounding; 2) determine role of cultivars in quinoa-Cucumber mosaic virus (CMV) interactions using transcriptome and small RNA analyses; and 3) compare tolerance of sweet or bitter quinoa cultivars to Meloidogyne incognita (root-knot nematode [RKN]). Ozone exposure and mechanical wounding of NRO modulated primary biological pathways, terpenoid metabolism, and plant-pathogen interactions. This study provided the first reference transcriptome for NRO and initial insights into genomic responses of NRO to abiotic stresses. In quinoa, CMV-inoculated samples differed from mock-inoculated samples in translation, plant hormones, amino acid metabolism, plant-pathogen interaction, DNA repair, and terpenoid biosynthesis. In quinoa, gene silencing factors involved in biogenesis of sRNAs were: miRNA by DCL1 and AGO1; siRNA via DCL3, AGO4/6/9, and RDR2; and vsiRNA by DCL4/2 and RDR1/6. The bitter cultivar had higher tolerance to RKN as evidenced by fewer galls as compared to sweet cultivars; however, saponin was not the main factor in tolerance to RKN. In quinoa, cultivars appeared to be poor hosts for CMV and RKN. Knowledge generated in this study may prove useful in breeding programs to enhance resistance of NRO and quinoa cultivars to abiotic and biotic stressors, respectively.