Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

Zhang, Zhonghui; Zhang, Feng; Deng, Yuan; Sun, Lisong; Mao, Mengdi; Chen, Ridong; Qiang, Qi; Zhou, Junjie; Long, Tuan; Zhao, Xuecheng; Liu, Xianqing; Wang, Shouchuang; Yang, Jun; Luo, Jie

doi:10.3390/metabo12050384

Cited by 8 publications

(8 citation statements)

References 59 publications

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“…As a result, the classification in this study based on morphological features concurs with the earlier report. The formation of different numbers of clusters using morphological characters in diverse rice genotypes was also reported [16, [20][21][22][23][24][25]. The dendrogram tends to cluster various landraces with related morphological features together can seen in Figure 2.…”

Section: Cluster Analysis Of Landraces Rice Phenotypic In West Javasupporting

confidence: 60%

Phenotypic variation of local rice in West Java, Indonesia

Ishaq,

Priani,

Haziman

et al. 2023

IOP Conf. Ser.: Earth Environ. Sci.

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Rice is the leading staple food in Indonesia and one of the largest production centers in West Java Province. Of the wide local varieties of rice in West Java, only a few have been inventoried and characterized for their morphological characteristics. This study aims to determine West Java’s phenotypic diversity of rice plants. Inventory and morphological characterization of local rice plants was carried out from 2018 to 2021 in seven districts in West Java (Sukabumi, Subang, Cianjur, Sumedang, Bogor, Tasikmalaya, and Bandung). A total of 30 accessions of local rice were observed based on Rice Descriptors. Data analysis used Principal Component Analysis (PCA) and Cluster Analysis with Minitab 21. The results showed that the seven main components contributed to the proportion of diversity of 83.7%. The local rice varieties in the five groups had a degree of similarity of 30%. The characters of leaf blade length, ligule length, ligule color, stem diameter, panicle extrusion, and the presence of awn contributed the most to the total diversity.

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Section: Cluster Analysis Of Landraces Rice Phenotypic In West Javasupporting

confidence: 60%

Phenotypic variation of local rice in West Java, Indonesia

Ishaq,

Priani,

Haziman

et al. 2023

IOP Conf. Ser.: Earth Environ. Sci.

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“…Moreover, OsUGT88C3 was phylogenetically far from other UGTs known to be responsible for anthocyanin biosynthesis, such as AcUFGT3a [ 20 ], VvF3GT1 [ 26 ], LcUFGT1 [ 27 ], Os3GT [ 28 ], AgUCGalT1 [ 19 ], DcUCGalT1 [ 18 ], AcGaT [ 17 ], and AtF3GlcT [ 29 ] in the 3GT clade; PfA5GlcT [ 30 ], VhA5GT [ 30 ], and AtF5GlcT [ 29 ] in the 5GT clade; OsGT1 [ 22 ] and OsGT5 [ 22 ] in the 7GT-5GT-3GT clade; OsGT4 [ 22 ] in the CGT clade; and OsGT2 [ 22 ], VpA3Glc2″GlcT [ 31 ], InA3Glc2″GlcT [ 32 ], AtA3Glc2″XylT [ 33 ], and AtF3Glc″GlcT [ 34 ] in the GGT clade. These results indicated that OsUGT88C3 is phylogenetically closer to flavonoid glycosyltransferase than anthocyanidin glycosyltransferase.…”

Section: Resultsmentioning

confidence: 99%

“…To explore other UGTs responsible for anthocyanin biosynthesis, the transcriptome of leaves of the three varieties were sequenced, and nine UGTs genes coexpressed with Os3GT and all the other ABGs were screened out ( Table 1 and Table S6 ). Among the nine genes, OsGT1 , OsGT2 , OsGT4 , and OsGT5 had been demonstrated to possess glycosyltransferase activities towards cyanidin and other anthocyanidin during germination [ 22 ]. OsUGT90A1 had been shown to function in the protection of plasma membranes during chilling stress in rice [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

OsUGT88C3 Encodes a UDP-Glycosyltransferase Responsible for Biosynthesis of Malvidin 3-O-Galactoside in Rice

Zhao,

Fu,

Cao

et al. 2024

Plants

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The diversity of anthocyanins is largely due to the action of glycosyltransferases, which add sugar moieties to anthocyanidins. Although a number of glycosyltransferases have been identified to glycosylate anthocyanidin in plants, the enzyme that catalyzes malvidin galactosylation remains unclear. In this study, we identified three rice varieties with different leaf color patterns, different anthocyanin accumulation patterns, and different expression patterns of anthocyanin biosynthesis genes (ABGs) to explore uridine diphosphate (UDP)-glycosyltransferases (UGTs) responsible for biosynthesis of galactosylated malvidin. Based on correlation analysis of transcriptome data, nine candidate UGT genes coexpressed with 12 ABGs were identified (r values range from 0.27 to 1.00). Further analysis showed that the expression levels of one candidate gene, OsUGT88C3, were highly correlated with the contents of malvidin 3-O-galactoside, and recombinant OsUGT88C3 catalyzed production of malvidin 3-O-galactoside using UDP-galactose and malvidin as substrates. OsUGT88C3 was closely related to UGTs with flavone and flavonol glycosylation activities in phylogeny. Its plant secondary product glycosyltransferase (PSPG) motif ended with glutamine. Haplotype analysis suggested that the malvidin galactosylation function of OsUGT88C3 was conserved among most of the rice germplasms. OsUGT88C3 was highly expressed in the leaf, pistil, and embryo, and its protein was located in the endoplasmic reticulum and nucleus. Our findings indicate that OsUGT88C3 is responsible for the biosynthesis of malvidin 3-O-galactoside in rice and provide insight into the biosynthesis of anthocyanin in plants.

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“…The genus Haliangium known for producing haliangicin a compound responsible for controlling many phytopathogenic fungi has been reported as a core genus in wheat landraces ( Fudou et al., 2001 ; Fudou et al., 2002 ; Rossmann et al., 2022 ). Landraces are generally resistant to diseases and are an important source of breeding material for resistance breeding ( Wang et al., 2022 ; Zhang et al., 2022 ). A high abundance of these potential biocontrol genera Haliangium and Gemmatimonas allows for exploring them as biocontrol agents in future studies.…”

Section: Discussionmentioning

confidence: 99%

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties

et al. 2023

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Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

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Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

Cited by 8 publications

References 59 publications

Phenotypic variation of local rice in West Java, Indonesia

Phenotypic variation of local rice in West Java, Indonesia

OsUGT88C3 Encodes a UDP-Glycosyltransferase Responsible for Biosynthesis of Malvidin 3-O-Galactoside in Rice

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties

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