An inferred functional impact map of genetic variants in rice

Zhao, Hu; Li, Jiacheng; Yang, Ling; Qin, Gang; Xia, Chen; Xu, Xichen; Yangmeng, SU; Liu, Yinmeng; Ming, Luchang; Xiong, Lizhong; Xie, Weibo

doi:10.1016/j.molp.2021.06.025

Cited by 55 publications

(51 citation statements)

References 77 publications

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“…The variations (SNPs and Indels) in the MIR408 precursor and its 1kb upstream regulatory regions were detected in 4726 accessions using the 'variations by region tool' of RiceVarMap v2.0 (http://ricevarmap.ncpgr.cn; Zhao et al 2021 [40]). The variation IDs were then used as an input haplotype analysis using the 'Haplotype Network analysis' tool of RiceVarMap2.…”

Section: Identification Of Variation Haplotype Evaluation In 4726 Ric...mentioning

confidence: 99%

“…The precursor and 1 Kb upstream cis-regulatory region (Ch01: 12300661 to 12301873) was analyzed for sequence variations (SNP and Indels) across 4726 rice accessions using the RiceVarMap2(http://ricevarmap.ncpgr.cn; Zhao et al 2021 [40]) database. As a result, a total of 22 sequence variants were detected, out of which 15 lies within the promoter while 7 lie in the putative precursor region downstream of mature (Figure 2a-b).…”

Section: Comparative Analysis Of Variations and Haplotype Evaluation ...mentioning

confidence: 99%

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Delineating the Tissue-Mediated Drought Stress Governed Tuning of Conserved miR408 and Its Targets in Rice

Balyan¹,

Kansal²,

Jajo³

et al. 2022

Preprint

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MicroRNAs act as the cardinal post-transcriptional monitors of gene regulatory networks sculpturing the developmental plasticity and stress responses in plants. Single miRNA target several genes and how the transcriptional regulation of miRNA impacts its pool of targets in different tissues and stress conditions is still elusive. The present study investigated the highly conserved and evolving MIR408 family comprehensively by redefining its evolutionary conservation and diversification in plants followed by detailed functional analysis in rice. MIR408 family comprises three dominant mature forms (21 nt) including a distinct monocot variant. Plant MIR408 family can be divided into six groups. miR408 majorly cleave genes belonging to blue copper protein in addition to several other species-specific targets in plants. Screening of 4726 rice accessions identified 22 sequence variants in 1 Kb upstream (15) and MIR408 region leading to the identification of 8 haplotypes (3: Japonica-specific and 5: Indica-specific). miR408-3p follows flag leaf preferential and drought upregulated expression profile in flag leaf and roots of N22 which seems to be regulated by differential fraction of mCs in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice. Twelve high confidence targets including 4 plantacyanins (OsUCL6, 7, 9 and 30), pirin, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine rich cell wall, deoxyuridine 5-triphosphate nucleotidohydrolaseand OsERF7 with antagonistic expression under most conditions. Further, over-expression of osa-MIR408 in drought sensitive rice cultivar leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced the dehydration stress tolerance at seedling stage.

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Section: Identification Of Variation Haplotype Evaluation In 4726 Ric...mentioning

confidence: 99%

Section: Comparative Analysis Of Variations and Haplotype Evaluation ...mentioning

confidence: 99%

Delineating the Tissue-Mediated Drought Stress Governed Tuning of Conserved miR408 and Its Targets in Rice

Balyan¹,

Kansal²,

Jajo³

et al. 2022

Preprint

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“…Haplotypes were deduced for sequence variations in the selected genes using the RiceVarMap v2.0 tool [ 29 ]. Sequence variations were retrieved within the gene along with 1 kb upstream and downstream of the gene’s open reading frame (ORF).…”

Section: Methodsmentioning

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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“…In addition, Wei et al (2021b) generated a rice gene encyclopedia "RiceNavi" containing hundreds of known trait-related causative variants. Recently, Zhao et al (2021) quantitatively inferred the millions of variants in both coding and regulatory regions across the rice genome. The constructed rice functional impact map was integrated into "RiceVarMap2," which greatly assisted in pinpointing the causal variants and genes within GWAS signatures.…”

Section: Genome-wide Association Studiesmentioning

confidence: 99%

Rice functional genomics: decades’ efforts and roads ahead

Chen

Deng

Ding

et al. 2021

Sci. China Life Sci.

120

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Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

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An inferred functional impact map of genetic variants in rice

Cited by 55 publications

References 77 publications

Delineating the Tissue-Mediated Drought Stress Governed Tuning of Conserved miR408 and Its Targets in Rice

Delineating the Tissue-Mediated Drought Stress Governed Tuning of Conserved miR408 and Its Targets in Rice

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

Rice functional genomics: decades’ efforts and roads ahead

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