RNA-Seq analysis reveals that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in curled-cotyledons mutant of soybean [Glycine max (L.) Merr.]

Abstract

BackgroundSoybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the genetic dissection of embryo patterning and seed development. However, the molecular mechanisms underlying soybean cotyledon development are largely unexplored.ResultsIn this study, we characterised a soybean curled-cotyledon (cco) mutant. Compared with wild-type (WT), anatomical analysis revealed that the cco cotyledons at the torpedo stage became more slender and grew outward. The entire embryos of cco mutant resembled the “tail of swallow”. In addition, cco seeds displayed reduced germination rate and gibberellic acid (GA3) level, whereas the abscisic acid (ABA) and auxin (IAA) levels were increased. RNA-seq identified 1,093 differentially expressed genes (DEGs) between WT and the cco mutant. The KEGG pathway analysis showed many DEGs were mapped to the hormone biosynthesis and signal transduction pathways. Consistent with assays of hormones in seeds, the results of RNA-seq indicated auxin and ABA biosynthesis and signal transduction in cco were more active than in WT, while an early step in GA biosynthesis was blocked, as well as conversion rate of inactive GAs to bioactive GAs in GA signaling. Furthermore, genes participated in other hormone biosynthesis and signalling pathways such as cytokinin (CK), ethylene (ET), brassinosteroid (BR), and jasmonate acid (JA) were also affected in the cco mutant.ConclusionsOur data suggest that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in cco, and changes in these pathways may partially contribute to the cco mutant phenotype, suggesting the involvement of multiple hormones in the coordination of soybean cotyledon development.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-510) contains supplementary material, which is available to authorized users.

Transcriptomic Profiling of the Maize (Zea mays L.) Leaf Response to Abiotic Stresses at the Seedling Stage

“…One of the most studied phytohormones is ABA, which has been described as a stress hormone, and crops have been shown to adjust ABA levels in response to adverse environmental conditions ( Tuteja, 2007 ). ABA biosynthesis and catabolism are regulated by BCH, ABA1, NCED, ABA2, AAO, and CYP707A ( Nambara and Marion-Poll, 2005 ; Peleg and Blumwald, 2011 ; Chan, 2012 ; Shan et al, 2013 ; Shi et al, 2014 ; Song et al, 2014 ; Miao et al, 2015 ; Shankar et al, 2016 ). Zeaxanthin is an important intermediate in the biosynthetic reaction of β-carotene to form ABA; β-carotene hydroxylases encoded by BCH can catalyze the biosynthesis of zeaxanthin ( Finkelstein, 2013 ); xanthophyll cleavage by NCED is the first committed, rate-limiting step in ABA biosynthesis; and CYP707As encode enzymes that can catalyze ABA catabolism.…”

“…Transcription factors regulate almost all aspects of plant growth and development and could orchestrate regulatory networks to improve resistance to abiotic and biotic stresses in plants ( Golldack et al, 2014 ). Major plant TF families such as NAC, AP2/ERF, bZIP, and MYB have been documented as important regulators in plant responses to various abiotic and biotic stresses ( Golldack et al, 2011 ; Shan et al, 2013 ; Shi et al, 2014 ; Song et al, 2014 ; Miao et al, 2015 ; Shankar et al, 2016 ; Wang H.Y. et al, 2016 ).…”

Genome‐Wide Analysis of Soybean LATERAL ORGAN BOUNDARIES Domain‐Containing Genes: A Functional Investigation of GmLBD12

“…S5B) (Yu et al, 2012;Shi et al, 2014). Analysis of RNA-Seq data (Shi et al, 2014) revealed three GmLBD members (GmLBD12, GmLBD55, and GmLBD59) were differentially expressed between CK and the cco mutant. In particular, the transcript levels of GmLBD12 were greatly reduced in the cco mutant compared with CK.…”

Balanced gene retention, transcription and methylation levels between subgenomes produced by soybean-specific paleo-tetraploidization

“…So far, the technology has been successfully applied in different plants, especially the model plants, such as Arabidopsis and rice [10][11][12][13][14][15][16][17]. With soybean, RNA-Seq datasets were produced to study plant response to seed and nodule development, dehydration stress, salinity stress, drought, flooding, or ozone damage, nematode resistance, phytohormone biosynthesis, signal transduction pathways, and the novel and alternatively spliced transcripts [18][19][20][21][22][23][24][25][26][27][28]. A report proposed that one subgenome has subject to lower levels of gene expression in maize, whereas none of these features was observed in soybean [29].…”