Abstract:Fine-tuning of flowering timing is crucial for plants to survive and leave offspring and depends on various endogenous and environmental factors. Here we report the identification of a vascular transcription factor, ANAC075, a putative regulator of VASCULAR-RELATED NAC-DOMAIN7 (VND7), as a negative regulator of flowering in Arabidopsis. Loss of function of ANAC075 causes the upregulation of floral integrator genes and early flowering under both long-and short-day conditions. ANAC075 promoter activity was detec… Show more
“…These regions contained 1220 genes (Additional file 2 : Table S13) with functions relating to binding, metabolic process, cellular process, biological regulation, localization, and response to stimulus (Additional file 2 : Table S14). Many well-studied genes involved in the regulation of flowering, cell wall synthesis, and adaptation were identified, such as Rc10G022330 encoding a putative orthologue of TERMINAL FLOWER 1 (TFL1) that plays a critical role in the regulation of inflorescence meristem identity, flowering time, and plant height in Arabidopsis [ 32 , 33 ]; Rc03G005883 encoding a putative SNW/SKI-interacting protein (SKIP) that involved into the regulation of environmental fitness and floral transition in Arabidopsis [ 34 ]; Rc03G005826 encoding a NAC transcription factor, homologous to Arabidopsis ANAC075 that functions as a repressor of flowering and involved in secondary cell wall formation [ 35 , 36 ]; Rc04G007260 encoding a member of the R2R3 gene family (MYB46), which involved in the control of secondary cell wall thickening [ 37 ]; Rc05G010832 encoding a gibberellin 2-oxidase (GA2OX2) which had a functional role in the control of plant growth and height by regulating GA concentrations in aspen trees [ 38 ]; and two genes, Rc02G003752 and Rc02G003753, putatively encoding gibberellin-regulated proteins (Additional file 2 : Table S13). …”
Background
Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean.
Results
Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size.
Conclusions
This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.
“…These regions contained 1220 genes (Additional file 2 : Table S13) with functions relating to binding, metabolic process, cellular process, biological regulation, localization, and response to stimulus (Additional file 2 : Table S14). Many well-studied genes involved in the regulation of flowering, cell wall synthesis, and adaptation were identified, such as Rc10G022330 encoding a putative orthologue of TERMINAL FLOWER 1 (TFL1) that plays a critical role in the regulation of inflorescence meristem identity, flowering time, and plant height in Arabidopsis [ 32 , 33 ]; Rc03G005883 encoding a putative SNW/SKI-interacting protein (SKIP) that involved into the regulation of environmental fitness and floral transition in Arabidopsis [ 34 ]; Rc03G005826 encoding a NAC transcription factor, homologous to Arabidopsis ANAC075 that functions as a repressor of flowering and involved in secondary cell wall formation [ 35 , 36 ]; Rc04G007260 encoding a member of the R2R3 gene family (MYB46), which involved in the control of secondary cell wall thickening [ 37 ]; Rc05G010832 encoding a gibberellin 2-oxidase (GA2OX2) which had a functional role in the control of plant growth and height by regulating GA concentrations in aspen trees [ 38 ]; and two genes, Rc02G003752 and Rc02G003753, putatively encoding gibberellin-regulated proteins (Additional file 2 : Table S13). …”
Background
Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean.
Results
Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size.
Conclusions
This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.
“…1a; Zhong et al ., 2011b). Although expression of SND4/ANAC075 fused with the VP16 activation domain in nst1/3 fiber cells was able to reinstate their secondary wall thickening (Sakamoto & Mitsuda, 2015), a recent study concluded that SND4/ANAC075 was not involved in secondary wall formation and instead, it was a negative regulator of flowering based on the findings that the GUS reporter gene driven by its promoter was mainly expressed in the phloem and its mutation resulted in early flowering but no phenotypes associated with secondary walls (Fujiwara & Mitsuda, 2016). Since the promoter of SND4/ANAC075 used in that study may not encompass all the cis‐elements dictating its bona fide expression, we set out to re‐examine its expression pattern.…”
Section: Resultsmentioning
confidence: 99%
“…While the function of ANAC099 has not yet been studied, ANAC075 was shown to activate the VND7 promoter (Endo et al ., 2015) and expression of VP16‐fused ANAC075 in nst1/3 fiber cells was able to reinstate their secondary wall thickening (Sakamoto & Mitsuda, 2015). However, one study reported that the ANAC075 gene was mainly expressed in the phloem and suggested that it was not involved in secondary wall formation (Fujiwara & Mitsuda, 2016). Although it is uncertain whether ANAC075 plays a role in regulating secondary wall biosynthesis, it has been shown that its poplar orthologs, PtrNAC150 and PtrNAC151, are wood‐associated, PtrWND2B‐regulated transcription factors that can activate the promoters of several biosynthesis genes for secondary wall cellulose, xylan and lignin (Zhong et al ., 2011b).…”
Secondary cell wall biosynthesis has been shown to be regulated by a suite of transcription factors. Here, we identified a new xylem vessel-specific NAC domain transcription factor, secondary wall-associated NAC domain protein5 (SND5), in Arabidopsis thaliana and studied its role in regulating secondary wall biosynthesis.We showed that the expression of SND5 and its close homolog, SND4/ANAC075, was specifically associated with secondary wall-containing cells and dominant repression of their functions severely reduced secondary wall thickening in these cells. Overexpression of SND4/ 5 as well as their homologs SND2/3 fused with the activation domain of the viral protein VP16 led to ectopic secondary wall deposition in cells that are normally parenchymatous. SND2/3/ 4/5 regulated the expression of the same downstream target genes as do the secondary wall NAC master switches (SWNs) by binding to and activating the secondary wall NAC binding elements (SNBEs).Furthermore, we demonstrated that the poplar (Populus trichocarpa) orthologs of SND2/ 3/4/5 also activated SNBEs and regulated secondary wall biosynthesis during wood formation.Together, these findings indicate that SND2/3/4/5 and their poplar orthologs regulate the expression of secondary wall-associated genes through activating SNBEs and they are positioned at an upper level in the SWN-mediated transcriptional network.
“…There are one additional NAC gene and one additional MYB gene in the top 10 genes of the pink module but they are not annotated with the TF GO term. Sobic.003G035100 (SbNAC75a) is a close homolog of NAC075, a putative regulator of VASCULAR RELATED NAC-DOMAIN PROTEIN 7 (VND7, Supplementary Figure S4B) which is a master regulator of vessel SCW deposition in Arabidopsis (Endo et al, 2015;Fujiwara and Mitsuda, 2016). Sobic.001G110900 is a homolog of AtMYB52/54, another regulator of SCW (Zhong et al, 2008).…”
Section: Identification Of Hub Genes In the Cell Wall Enriched Modulesmentioning
Regulation of Sorghum Stem Composition unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
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