RESUMEN
BACKGROUND: Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms underlying inflorescence architecture is pivotal for improving crop yield potential. Quinoa (Chenopodium quinoa Willd), a pseudo cereal originated from Andean region of South America, has been widely recognized as a functional super food due to its excellent nutritional elements. Increasing worldwide consumption of this crop urgently calls for its yield improvement. However, dissection of the regulatory networks underlying quinoa inflorescence patterning is lacking. RESULTS: In this study, we performed RNA-seq analysis on quinoa inflorescence samples collected from six developmental stages, yielding a total of 138.8 GB data. We screened 21,610 differentially expressed genes (DEGs) among all the stages through comparative analysis. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to categorize the DEGs into ten different modules. Subsequently, we placed emphasis on investigating the modules associated with none branched and branched inflorescence samples. We manually refined the coexpression networks with stringent edge weight cutoffs, and generated core networks using transcription factors and key inflorescence architecture related genes as seed nodes. The core networks were visualized and analyzed by Cytoscape to obtain hub genes in each network. Our finding indicates that the specific occurrence of B3, TALE, WOX, LSH, LFY, GRAS, bHLH, EIL, DOF, G2-like and YABBY family members in early reproductive stage modules, and of TFL, ERF, bZIP, HD-ZIP, C2H2, LBD, NAC, C3H, Nin-like and FAR1 family members in late reproductive stage modules, as well as the several different MADS subfamily members identified in both stages may account for shaping quinoa inflorescence architecture. CONCLUSION: In this study we carried out comparative transcriptome analysis of six different stages quinoa inflorescences, and using WGCNA we obtained the most highly potential central hubs for shaping inflorescence. The data obtained from this study will enhance our understanding of the gene network regulating quinoa inflorescence architecture, as well will supply with valuable genetic resources for high-yield elite breeding in the future.
Asunto(s)
Chenopodium quinoa/genética , Regulación de la Expresión Génica de las Plantas , Inflorescencia/genética , Chenopodium quinoa/anatomía & histología , Chenopodium quinoa/metabolismo , Grano Comestible/genética , Redes Reguladoras de Genes/fisiología , Inflorescencia/anatomía & histología , Inflorescencia/metabolismo , Proteínas de Dominio MADS/genética , Proteínas de Dominio MADS/metabolismo , RNA-Seq , América del Sur , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
BACKGROUND: Common buckwheat (Fagopyrum esculentum) is an important staple food crop in southwest China, where drought stress is one of the largest limiting factors that lead to decreased crop production. To reveal the molecular mechanism of common buckwheat in response to drought stress, we performed a comprehensive transcriptomics study to evaluate gene expression profiles of common buckwheat during PEG-mediated drought treatment. RESULTS: In total, 45 million clean reads were assembled into 53,404 unigenes with an average length of 749 bp and N50 length of 1296 bp. A total of 1329 differentially expressed genes (DEGs) were identified by comparing wellwatered and drought-treated plants, out of which 666 were upregulated and 663 were downregulated. Furthermore, we defined the functional characteristics of DEGs using GO and KEGG classifications. GO enrichment analysis showed that the DEGs were significantly overrepresented in four categories, namely, "oxidoreductase activity," "oxidationreduction process," "xyloglucan:xyloglucosyl transferase activity," and "apoplast." Using KEGG pathway analysis, a large number of annotated genes were overrepresented in terms such as "plant hormone signal transduction," "phenylpropanoid biosynthesis," "photosynthesis," and "carbon metabolism." Conclusions: These results can be further exploited to investigate the molecular mechanism of common buckwheat in response to drought treatment and could supply with valuable molecular sources for abiotic-tolerant elite breeding programs in the future.