Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers

Sun, Shiyu; Wang, Duoxiang; Li, Jingbin; Lei, Yaqi; Li, Gang; Cai, Wenguo; Zhao, Xiangxiang; Liang, Wanqi; Zhang, Dabing

doi:10.3389/fpls.2021.621561

Cited by 20 publications

(6 citation statements)

References 93 publications

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“…Additionally, a co-expression network developed in rice identified modules associated with temperature-inducible and photoperiod sensitive genes, which are important for the sterility transition [ 50 ]. Similarly, 496 hub genes and four modules showed a significant correlation with photo-sensitive differentially expressed genes in rice [ 51 ]. Furthermore, weighted gene co-expression analysis has identified differentially expressed genes such as OsHSPs, OsHSFC2A, and OsDJA5 upon cadmium treatment in stem nodes of different rice genotypes [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

Rana

Kumawat

Kumar

et al. 2022

Cells

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Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.

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Section: Discussionmentioning

confidence: 99%

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

Rana

Kumawat

Kumar

et al. 2022

Cells

View full text Add to dashboard Cite

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“…In our study, we have pooled the samples in two replications to have a representation of five data points. Two biological replicates have been used and cited widely ( Xu et al., 2015 ; Yang et al., 2015 ; Ding et al., 2017 ; Sun et al., 2021 ; Li et al., 2022 ) for transcriptome analysis especially when it is a reference-based transcriptome like that of rice.…”

Section: Discussionmentioning

confidence: 99%

Understanding plant–microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis

et al. 2022

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Understanding the beneficial plant–microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, “Plant pathogen interaction” and “MAPK signaling,” were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant–diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant–diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant–diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., no apical meristem, Petunia (NAC), abscisic acid (ABA), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.

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“…A few studies have aimed to better understand the dynamics of key genes and regulatory mechanisms in rice associated with morphology [ 22 ], physiology [ 23 ], abiotic and biotic stress mechanisms [ 24 , 25 , 26 ]. Transcriptional control of nutrients during grain filling in rice has been studied by designing a GeneChip microarray covering half of the rice genome to understand the effect of genes participating in nutrient partitioning on starch quality [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

Gene Expression in the Developing Seed of Wild and Domesticated Rice

Hasan

Furtado

Henry

2022

IJMS

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The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value.

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Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers

Cited by 20 publications

References 93 publications

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

Understanding plant–microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis

Gene Expression in the Developing Seed of Wild and Domesticated Rice

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