Antisense Phenotypes Reveal a Functional Expression of OsARF1 , an Auxin Response Factor, in Transgenic Rice

Attia, Kotb A.; Abdelkhalik, A. F.; Ammar, Megahed H.; Wei, Chun; Yang, Jinshui; Lightfoot, David A.; El-Sayed, Wagih M.; El‐Shemy, Hany A.

doi:10.21775/9781912530069.04

Cited by 47 publications

(59 citation statements)

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“…Recent studies showed that PIN1-mediated auxin transport was related to cellular differentiation during maize embryogenesis and endosperm development [46] and essential role of OsARF1 in rice seed development [47]. Altered auxin signaling in seeds may cause abnormal development, proposing an “autonomous” mechanism of auxin signaling in seeds.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

2012

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BackgroundThe development of rice (Oryza sativa) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement.Principal FindingsOur analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of Arabidopsis seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant cultivar Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development.ConclusionsThese results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

2012

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“…Closely related AtARF genes appear to have somewhat redundant roles in Arabidopsis. In rice, an antisense mutation of the OsARF1 gene resulted in a phenotype exhibiting low vigor, stunted growth, curled leaves, and sterility, which suggests that OsARF1 is vital for vegetative and reproductive development (Attia et al 2009). …”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii

Sun

Wang

Guo

et al. 2015

Funct Integr Genomics

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Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In this study, a total of 35 ARF genes, named as GrARFs, were identified in a diploid cotton species Gossypium raimondii. The 35 ARF genes were located in 12 of the 13 cotton chromosomes; the intron/exon distribution of the GrARF genes was similar among sister pairs, whereas the divergence of some GrARF genes suggests the possibility of functional diversification. Our results show that the middle domains of nine GrARF proteins rich in glutamine (Q) are activators, while 26 other GrARF proteins rich in proline (P), serine (S), and threonine (T) are repressors. Our results also show that the expression of GrARF genes is diverse in different tissues. The expression of GrARF1 was significantly higher in leaves, whereas GrARF2a had higher expression level in shoots, which implicates different roles in the tested tissues. The GrARF11 has a higher expression level in buds than that in leaves, while GrARF19.2 shows contrasting expression patterns, having higher expression in leaves than that in buds. This suggests that they play different roles in leaves and buds. During long-term evolution of G. raimondii, some ARF genes were lost and some arose. The identification and characterization of the ARF genes in G. raimondii elucidate its important role in cotton that ARF genes regulate the development of flower buds, sepals, shoots, and leaves.

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“…Those three phytochromes are involved in regulating flowering time (Takano et al, 2005;Kiyota et al, 2012), while the other TFs function primarily in developmental processes or stress responses. For example, OsARF1 regulates root and shoot lengths (Attia et al, 2009); rice indoleacetic acid1 (OsIAA1) controls leaf angle and root lengths (Song et al, 2009); SLR1 modulates cell division and expansion (UeguchiTanaka et al, 2007); homeodomain transcription factor 1a (HOX1a) regulates elongation of the uppermost internode (Wen et al, 2011); an OsHOX4 mutation causes dwarfism (Dai et al, 2008); outcurved leaf1 (OUL1) regulates leaf rolling (Zou et al, 2011); OsWRKY78 controls cell elongation ; rice histone associated protein 3A (OsHAP3A) and OsHAP3B influence chloroplast development (Miyoshi et al, 2003); rice P-deficiency responsive transcription factor 1 (OsPTF1) and…”

Section: Discussion Go Enrichment Reveals Essential Biological Procesmentioning

confidence: 99%

“…In three cases (Os11g32110, Os02g05840, and Os02g50550), expression levels were higher only in certain organs ( Figure 5A). Mutations in Os11g32110 (auxin response factor 1 [OsARF1]) affected root and shoot lengths (Attia et al, 2009); expression of that gene was higher when compared with its counterpart, Os12g29520. Mutations in Os02g05840 (rice leaf inclination2) affected leaf angles through brassinosteroid signaling (Zhao et al, 2010).…”

Section: Evaluation Of Functional Dominancy For Phenomic Analysis Usimentioning

confidence: 99%

Genome-Wide Identification and Functional Analysis of Genes Expressed Ubiquitously in Rice

et al. 2015

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Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.

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Antisense Phenotypes Reveal a Functional Expression of OsARF1 , an Auxin Response Factor, in Transgenic Rice

Cited by 47 publications

References 0 publications

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii

Genome-Wide Identification and Functional Analysis of Genes Expressed Ubiquitously in Rice

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