ATL54, a ubiquitin ligase gene related to secondary cell wall formation, is transcriptionally regulated by MYB46

Noda, Soichiro; Yamaguchi, Masatoshi; Tsurumaki, Yuta; Takahashi, Yoshinori; Nishikubo, Nobuyuki; Hattori, Takefumi; Demura, Taku; Suzuki, Shiro; Umezawa, Toshiaki

doi:10.5511/plantbiotechnology.13.0905b

Cited by 6 publications

(4 citation statements)

References 39 publications

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“…We identified the gene HanXRQChr14g0445121 located 1.4 Mb upstream of one of the markers. This product of this gene shared 47.71% of the sequence of the Arabidopsis protein RING-H2 FINGER PROTEIN ATL54, which is involved in the formation of the secondary cell wall (Noda et al, 2013). The second gene identified on chromosome 14 was HanXRQChr14g0459681, situated 20 kb upstream of the other marker.…”

Section: Resultsmentioning

confidence: 99%

Heliaphen, an Outdoor High-Throughput Phenotyping Platform for Genetic Studies and Crop Modeling

et al. 2019

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Heliaphen is an outdoor platform designed for high-throughput phenotyping. It allows the automated management of drought scenarios and monitoring of plants throughout their lifecycles. A robot moving between plants growing in 15-L pots monitors the plant water status and phenotypes the leaf or whole-plant morphology. From these measurements, we can compute more complex traits, such as leaf expansion (LE) or transpiration rate (TR) in response to water deficit. Here, we illustrate the capabilities of the platform with two practical cases in sunflower (Helianthus annuus): a genetic and genomic study of the response of yield-related traits to drought, and a modeling study using measured parameters as inputs for a crop simulation. For the genetic study, classical measurements of thousand-kernel weight (TKW) were performed on a biparental population under automatically managed drought stress and control conditions. These data were used for an association study, which identified five genetic markers of the TKW drought response. A complementary transcriptomic analysis identified candidate genes associated with these markers that were differentially expressed in the parental backgrounds in drought conditions. For the simulation study, we used a crop simulation model to predict the impact on crop yield of two traits measured on the platform (LE and TR) for a large number of environments. We conducted simulations in 42 contrasting locations across Europe using 21 years of climate data. We defined the pattern of abiotic stresses occurring at the continental scale and identified ideotypes (i.e., genotypes with specific trait values) that are more adapted to specific environment types. This study exemplifies how phenotyping platforms can assist the identification of the genetic architecture controlling complex response traits and facilitate the estimation of ecophysiological model parameters to define ideotypes adapted to different environmental conditions.

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Section: Resultsmentioning

confidence: 99%

Heliaphen, an Outdoor High-Throughput Phenotyping Platform for Genetic Studies and Crop Modeling

et al. 2019

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“…Borah and Khurana (2018) found that E3 ligase subunit F-box Kelch 1 (FBK1) was involved in root secondary cell wall thickening and lignin biosynthesis in rice. Another ubiquitin ligase protein, Arabidopsis Tóxicosen Levadura54 (ATL54) identified in Arabidopsis, participated in programmed cell death and secondary cell wall formation, although no significant variance on lignin content and composition in whole mature stem was observed by altering the expression level of ATL54 (Noda et al, 2013). TTNDFD associated marker MtChr4_32514187 was encompassed by a gene encoding sulfurtransferase (Str).…”

Section: Putative Candidate Genes With Functions Involved In Forage Qualitymentioning

confidence: 99%

Genome-Wide Association Studies Identifying Multiple Loci Associated With Alfalfa Forage Quality

et al. 2021

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Autotetraploid alfalfa is a major hay crop planted all over the world due to its adaptation in different environments and high quality for animal feed. However, the genetic basis of alfalfa quality is not fully understood. In this study, a diverse panel of 200 alfalfa accessions were planted in field trials using augmented experimental design at three locations in 2018 and 2019. Thirty-four quality traits were evaluated by Near Infrared Reflectance Spectroscopy (NIRS). The plants were genotyped using a genotyping by sequencing (GBS) approach and over 46,000 single nucleotide polymorphisms (SNPs) were obtained after variant calling and filtering. Genome-wide association studies (GWAS) identified 28 SNP markers associated with 16 quality traits. Among them, most of the markers were associated with fiber digestibility and protein content. Phenotypic variations were analyzed from three locations and different sets of markers were identified by GWAS when using phenotypic data from different locations, indicating that alfalfa quality traits were also affected by environmental factors. Among different sets of markers identified by location, two markers were associated with nine traits of fiber digestibility. One marker associated with lignin content was identified consistently in multiple environments. Putative candidate genes underlying fiber-related loci were identified and they are involved in the lignin and cell wall biosynthesis. The DNA markers and associated genes identified in this study will be useful for the genetic improvement of forage quality in alfalfa after the validation of the markers.

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“…The annealed doublestranded oligonucleotides were purified with a QIAquick Nucleotide Removal Kit (Qiagen). The electrophoresis of recombinant protein and probes, electroblotting, and probe detection were performed as described previously (Noda et al 2013b). …”

Section: Electrophoretic Mobility Shift Assay (Emsa)mentioning

confidence: 99%

The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63

Noda

Koshiba

Hattori

et al. 2015

Planta

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A rice MYB transcription factor, OsMYB58/63, was found to directly upregulate the expression of a rice secondary wall-specific cellulose synthase gene, cellulose synthase A7 ( OsCesA7 ); in contrast, the Arabidopsis putative orthologs AtMYB58 and AtMYB63 have been shown to specifically activate lignin biosynthesis. Although indirect evidence has shown that grass plants are similar to but partially different from dicotyledonous ones in transcriptional regulation of lignocellulose biosynthesis, little is known about the differences. This study showed that a rice MYB transcription factor, OsMYB58/63, directly upregulated the expression of a rice secondary wall-specific cellulose synthase gene, cellulose synthase A7 (OsCesA7). Gene co-expression analysis showed that, in rice, OsMYB58/63 and several rice MYB genes were co-expressed with genes encoding lignocellulose biosynthetic enzymes. The expression levels of OsMYB55/61, OsMYB55/61-L, OsMYB58/63, and OsMYB42/85 were commonly found to be high in culm internodes and nodes. All four MYB transcription factors functioned as transcriptional activators in yeast cells. OsMYB58/63 most strongly transactivated the expression of OsCesA7 in rice protoplasts. Moreover, recombinant OsMYB58/63 protein was bound to two distinct cis-regulatory elements, AC-II and SMRE3, in the OsCesA7 promoter. This is in sharp contrast to the role of Arabidopsis orthologs, AtMYB58 and AtMYB63, which had been reported to specifically activate lignin biosynthesis. The promoter analysis revealed that AC elements, which are the binding sites for MYB58 and MYB63, were lacking in cellulose and xylan biosynthetic genes in Arabidopsis, but present in cellulose, xylan, and lignin biosynthetic genes in rice, implying that the difference of transcriptional regulation between rice and Arabidopsis is due to the distinct composition of promoters. Our results provide a new insight into transcriptional regulation in grass lignocellulose biosynthesis.

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ATL54, a ubiquitin ligase gene related to secondary cell wall formation, is transcriptionally regulated by MYB46

Cited by 6 publications

References 39 publications

Heliaphen, an Outdoor High-Throughput Phenotyping Platform for Genetic Studies and Crop Modeling

Heliaphen, an Outdoor High-Throughput Phenotyping Platform for Genetic Studies and Crop Modeling

Genome-Wide Association Studies Identifying Multiple Loci Associated With Alfalfa Forage Quality

The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63

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