Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

Tello-Ruiz, Marcela K.; Jaiswal, Pankaj; Ware, Doreen

doi:10.1007/978-1-0716-2067-0_5

Cited by 38 publications

(26 citation statements)

References 94 publications

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“…For determining the genes underlying the identified MQTLs for rice grain chalkiness, the physical locations of confidence interval (CI) flanking markers were retrieved from the Gramene Marker Database ( http://archive.gramene.org/qtl/ ) ( Tello-Ruiz et al, 2022 ). In case the physical position of a particular marker was not available, the position of the adjacent genetic marker was utilized for identifying the genomic coordinates.…”

Section: Methodsmentioning

confidence: 99%

Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice

Kumari

Sharma²,

Sharma³

et al. 2023

Front. Plant Sci.

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Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.

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Section: Methodsmentioning

confidence: 99%

Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice

Kumari

Sharma²,

Sharma³

et al. 2023

Front. Plant Sci.

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“…The hidden Markov model (HMM) profile (PF00743) search was done against the Gramene [ 74 ] database for different Oryza species ( Oryza brachyantha , Oryza punctata , Oryza meridionalis , Oryza glumaepatula , Oryza glaberrima , Oryza barthii , Oryza nivara , Oryza sativa subsp. indica , Oryza rufipogon and Oryza sativa subsp.…”

Section: Resultsmentioning

confidence: 99%

“…The HMM (hidden Markov model) search of the FMO domain (PF00743) was retrieved from the Pfam database, ( ; EMBL-EBI, UK; accessed on 12 July 2022), which was used to identify the full-length protein sequences of FMO in the Gramene [ 74 ] database ( , accessed on 12 July 2022) for the identification of homologous sequences in 10 Oryza species: Oryza sativa subsp. japonica , O. sativa subsp.…”

Section: Methodsmentioning

confidence: 99%

Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities

Gaba

Bhowal

Pareek

et al. 2023

IJMS

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The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N′-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types.

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“…To understand the biologic functions of the 20 DASE genes that were significantly associated with elevation in both continents, we searched their annotation from the Gramene database ( Tello-ruiz et al 2022 )⁠ and their characterized function from maizeGDB ( Woodhouse et al 2021 )⁠. Five of them have gene names from the maizeGDB, and at least three of them are transcription factors ( table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize

Crow

Nojoomi

et al. 2022

Molecular Biology and Evolution

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Maize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggests the maize’s adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.

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Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

Cited by 38 publications

References 94 publications

Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice

Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice

Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities

Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize

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