Evidence map›Paper›PMID 36597029›Full record

ArticleBMC plant biology2023

Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation.

Meredith T Hanlon, Phanchita Vejchasarn, Jenna E Fonta, Hannah M Schneider, Susan R McCouch, Kathleen M Brown

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC plant biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
3.6field-weighted citation impact, top 8% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 9 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 3 countries.

Meredith T HanlonDepartment of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA.ORCID http://orcid.org/0000-0002-5616-8203
Phanchita VejchasarnDepartment of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA.
Jenna E FontaDepartment of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA.ORCID http://orcid.org/0000-0002-9292-8433
Hannah M SchneiderDepartment of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA.ORCID http://orcid.org/0000-0003-4655-6250
Susan R McCouchSection of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA.ORCID http://orcid.org/0000-0001-9246-3106
Kathleen M BrownDepartment of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA. kbe@psu.edu.ORCID http://orcid.org/0000-0002-4960-5292
Pennsylvania State University · USCornell University · US

Funding

Division of Graduate Education DGE1255832National Science Foundation 1444511
6 · The paper itself

Abstract

backgroundGenome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus, indica, temperate japonica, and tropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets.

resultsWe identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and Arabidopsis.

conclusionsRoot hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.

Indexed as

Genome-Wide Association StudyOryzaCell DifferentiationGenomicsPhenotypePolymorphism, Single NucleotideQuantitative Trait LociCandidate geneGWASRiceRoot biologyRoot hairsSubpopulation

Identifiers

PMID36597029
PMCPMC9811729
OpenAlexW4313456685

What Socratic holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.