Identification of the soybean genes responsible for UV-B stress by genome and transcriptome analyses

Abstract

The depletion of the ozone layer in the stratosphere has led to a dramatic spike in ultraviolet B (UV-B) intensity and increased UV-B light levels. The direct absorption of high-intensity UV-B induces complex abiotic stresses in plants including excessive light exposure, heat, and dehydration. However, UV-B stress signaling mechanisms in plants including soybean (Glycine max [L.]) and quantitative loci (QTLs) responsible for UV-B resistance remain poorly understood. Therefore, we surveyed the overall transcriptional responses of two soybean genotypes, UV-B-sensitive Cheongja 3 and UV-B-resistant Buseok, to continuous UV-B irradiation for 0 (control), 0.5, and 6 h using RNA-seq analysis to identify signaling genes responsible for UV-B. Homology analysis using UV-B-related genes from Arabidopsis thaliana revealed differentially expressed genes (DEGs) likely involved in UV-B stress responses. Functional classification of the DEGs showed that the categories of immune response, stress defense signaling, and reactive oxygen species (ROS) metabolism were over-represented. UV-B-resistant Buseok utilized phosphatidic acid-dependent signaling pathways (based on subsequent reactions of phospholipase C and diacylglycerol kinase) rather than phospholipase D in response to UV-B exposure at high fluence rates, and genes involved in its downstream pathways, such as ABA signaling, mitogen-activated protein kinase cascades, and ROS overproduction, were upregulated in this genotype. In addition, the DEGs for TIR-NBS-LRR and heat shock proteins are positively activated. These results suggest that defense mechanisms against UV-B stress at high fluence rates are separate from the photomorphogenic responses utilized by plants to adapt to low-level UV light. Furthermore soybean (Glycine max [L.]) has evolved to survive under abiotic and biotic stress conditions by utilizing multiple signaling pathways. Although several studies have revealed shared defense signaling pathways in plants, the majority of components at the convergence points of signaling pathways triggered by both abiotic and biotic stress remain poorly understood. In chapter II, we profiled the overall transcriptional responses of soybean to two different types of stress using the UV-B-resistant cultivar, Buseok, and the UV-B-sensitive cultivar, Cheongja 3, as well as two near isogenic lines (NILs) carrying bacterial leaf pustule (BLP) disease-resistant and -susceptible alleles. We compared transcript abundance and identified genes that commonly respond to UV-B stress and BLP disease. In addition, we surveyed the co-localization of differentially expressed genes (DEGs) and their paralogs with abiotic and biotic stress-related quantitative trait loci (QTLs) on the soybean genome. Among 14 DEGs that respond to both stresses, five DEGs are involved in the jasmonic acid (JA) metabolic pathway, encoding Jasmonate ZIM (Zinc-finger protein expressed in Inflorescence Meristem) domain-containing protein 1 (JAZ 1), a negative regulator of JA signaling. Two DEGs for JAZ 1 were co-localized with biotic stress-related QTLs. One DEG encoding the stress-induced protein starvation-associated message 22 (SAM 22) and its two paralogs were co-localized with both abiotic and biotic stress-related QTLs. In Chapter III, we investigated phenotypic data of UV-B treated 174 F6 RIL population derived from Cheongja 3 and Buseok, and we tried to construct genetic map by genotype-by-sequencing to identify QTLs and candidate genes responsible for UV-B resistance. High degree of phenotypic variations was shown in response to UV-B irradiation. Frequency distribution of leaf damage degree for UV-B treatments were ranged between 10 and 100%. The mean range of damage leaf degree was 50.3%, paternal UV-B resistance Buseok showed 26.8% damage degree, and maternal UV-B sensitive Cheongja 3 exhibited 62.4 damage degrees (%).Total high quality 2,291 SNPs were obtained and used for construction of genetic map using Joinmap 4.1. The newly detected two QTLs in this study are UVBR14-1 and UVBR17-1. The one gene on chr 14 is K+ efflux antiporter 6 (KEA 6) (Glyma.14g093900) which may contribute towards K+ acquisition and homeostasis under saline conditions. The four candidate genes on chr 17 are Leucine rich repeat F-box/RNI-like superfamily protein (TIR1) (Glyma.17g247500), inositol polyphosphate 5-phosphatase 11 (Glyma.17g247600), Adaptor protein rnigma and related PDZ-LIM proteins (DA1) (Glyma.17g247700) and Leucine rich repeat receptor-like protein kinase (Glyma.17g247800). The biological function of KEA 6 on chr 14 and InsP5-ptase on chr 17 need to be examined more as UV-B responsible gene under UV-B light as multiple stressors including heat and hydration. Finally, the results of this comprehensive study elucidate not only soybean signaling mechanism under UV-B stress but also identification of the candidate genes responsible for UV-B resistance. These results will help develop high adoptable soybean breeding under UV-B irradiation.