Comprehensive Transcriptomic Analysis of Auxin Responses in Submerged Rice Coleoptile Growth

Abstract

Cultivating rice in wet or water direct seeding systems is simple and time and labor efficient. Rice (Oryza sativa) seeds are a unique cereal that can germinate not only when submerged, but also in anoxic conditions. Many complicated hormone signals interact in submerged seed germination. Ethylene is involved in rice coleoptile elongation, but little is known regarding the role of auxin signaling under submergence. This study demonstrated that the coleoptile is shorter and curlier when submerged with 2,3,5-triiodobenzoic acid (TIBA). In transcriptomic analysis, 3448 of the 31,860 genes were upregulated, and 4360 genes were downregulated with submergence and TIBA treatment. The Gene Ontology function classification results demonstrated that upregulated differentially expressed genes (DEGs) were mainly involved in redox, stress, and signal transduction, whereas the down-regulated DEGs were mainly involved in RNA transcription, stress, and development. Furthermore, auxin signaling involved in the carbohydrate metabolism pathway was demonstrated while using transcriptomic analysis and confirmed in a quantitative real-time polymerase chain reaction. In addition, the transcript levels of development-related genes and mitochondria-electron- transport-related genes were regulated by auxin signaling under submergence. Auxin signaling was not only involved in regulating rice coleoptile elongation and development, but also regulated secondary metabolism, carbohydrate metabolism, and mitochondria electron transport under submergence. Our results presented that auxin signaling plays an important role during rice coleoptile elongation upon the submergence condition and improving the advance of research of direct rice seeding system.

Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence

“…OsARF , a rice homolog of the ARF, was found to be positively correlated with auxin-dependent differential growth in rice coleoptiles ( Waller et al, 2002 ). Recently, Wu and Yang (2020) have revealed the involvement of auxin signaling in regulating rice coleoptile elongation as well as regulation of carbohydrate metabolism and secondary metabolism under submergence. Besides, auxin plays a key role in cell division during coleoptile elongation in the japonica rice under submergence ( Nghi et al, 2020 ).…”

“…ARF7 and ARF19 TFs are known to regulate the expression of LBD16 and LBD29 for lateral organ development in Arabidopsis ( Okushima et al, 2007 ). Recently, it has been shown that these TF genes could be regulated by auxin signaling under submergence ( Wu and Yang, 2020 ), although the function is not known yet. This element could be present in the upregulated genes of all groups for lateral organ development later once the coleoptile reaches the surface of water for O 2 availability.…”

“…A number of microarray and RNA-sequencing studies performed on rice germination under anoxia/hypoxia have shown the up-/downregulation of a number of stress-responsive genes ( Lasanthi-Kudahettige et al, 2007 ; Narsai et al, 2009 ; Shingaki-Wells et al, 2011 ; Narsai et al, 2015 ; Hsu and Tung, 2017 ; Wu and Yang, 2020 ). During such stress conditions, transcription factors (TFs) play a key role in regulating the expression of genes that support them to survive through tolerance mechanism.…”

“…These data favor the understanding that rice coleoptile elongation is promoted by ethylene during submerged conditions. Besides, it has been shown that auxin also plays a key role in coleoptile elongation during submergence ( Ishizawa and Esashi, 1983 ; Wu and Yang, 2020 ). Auxin-dependent differential growth in rice coleoptile is shown to be due to the effect of the TF auxin response factor 1 ( OsARF1 ) ( Waller et al, 2002 ).…”

“…These results support the importance of TFs in the regulation of tolerance of rice plants under submerged/flooding conditions. Recent studies of the roles of auxin in rice coleoptile elongation suggest that it plays a key role in the cell division and tropism of rice coleoptiles under submergence ( Wu and Yang, 2020 ).…”