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Related Concept Videos

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Related Experiment Video

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Lateral Root Inducible System in Arabidopsis and Maize
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Genome-wide association mapping for root cone angle in rice.

Mathilde Bettembourg1, Audrey Dardou1, Alain Audebert1,2

  • 1Cirad, UMR AGAP, F34398, Montpellier Cedex 5, France.

Rice (New York, N.Y.)
|October 4, 2017
PubMed
Summary

Researchers identified new quantitative trait loci (QTLs) for rice root cone angle using genome-wide association mapping. This study advances understanding of root system architecture and identifies candidate genes for future investigation.

Keywords:
Rice, Oryza sativa, Indica, Japonica, root cone angle, hydroponics, association mapping, GWAS

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Area of Science:

  • Genetics
  • Plant Biology
  • Agronomy

Background:

  • Root system architecture is crucial for plant anchorage and nutrient/water uptake.
  • Root cone angle, alongside root depth, dictates the soil volume explored by plants.
  • Previous research identified two genes (DRO1, SOR1) and several QTLs for root cone angle.

Purpose of the Study:

  • To identify novel quantitative trait loci (QTLs) associated with root cone angle in rice.
  • To analyze candidate genes underlying detected QTLs, focusing on auxin-related and developmental genes.
  • To explore genetic variations contributing to wide root cone angle in rice accessions.

Main Methods:

  • Genome-wide association mapping was performed on indica and japonica rice panels (162 and 169 accessions, respectively).
  • Genotyping utilized two sets of SNP markers: a genotyping-by-sequencing set (~16,000 markers) and a high-density-rice-array set (~300,000 markers).
  • Root cone angle was measured using a screen protractor on images from the Rhizoscope phenotyping system after one month of growth.

Main Results:

  • Association mapping identified 15 QTLs in the indica panel and 40 QTLs in the japonica panel.
  • Several japonica rice accessions exhibited an unusually wide root cone angle, appearing as outliers.
  • Eight candidate genes, including auxin-related and kinase genes, were identified within QTL regions.

Conclusions:

  • The study discovered new genetic sources for wide root cone angle in rice.
  • It proposes methods to overcome association mapping limitations for trait genetics research.
  • Candidate genes identified warrant further investigation for their role in root development.