PPubMed26 Dec 2023Cited 6×

Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome Et-GWAS for rare variants

Niranjani Gnanapragasam, Vinukonda Vishnu Prasanth, Krishna Tesman Sundaram, Ajay Kumar, Bandana Pahi, Anoop Gurjar, Challa Venkateshwarlu, Sanjay Kalia, Arvind Kumar, Shalabh Dixit, Ajay Kohli, Uma Maheshwer Singh, Vikas Kumar Singh, Pallavi Sinha

Abstract

'Krishna Tesman Sundaram' 'Ajay Kumar' 'Bandana Pahi' 'Anoop Gurjar' 'Challa Venkateshwarlu' 'Sanjay Kalia' 'Arvind Kumar' 'Shalabh Dixit' 'Ajay Kohli' 'Uma Maheshwer Singh' 'Vikas Kumar Singh' 'Pallavi Sinha'] Using extreme bulk pooling and allele frequency assessment, the graphical user interface (GUI)-enabled association technique successfully revealed relationships between genetic variations and grain yield under drought stress condition.

A figure from Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome Et-GWAS for rare variants — fig. from the paper

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Et-GWAS, a GUI-enabled extreme bulk pooling GWAS, identified dozens of drought-yield MTAs and candidate genes in 3,000 rice genomes.

What’s new

i.Developed a user-friendly GUI Et-GWAS pipeline for extreme bulk pooling GWAS.
ii.Identified 54 MTAs (including 17 genic) and 141 candidate genes associated with grain yield under drought.
iii.Validated MTAs against known QTLs and discovered 30 novel signals beyond traditional MLM GWAS.
iv.Performed haplotype analysis to pinpoint top‑performing haplotypes in the rice diversity panel.

How they did it

The study applied extreme bulk pooling of phenotypic extremes and allele frequency assessment across a 30K SNP dataset using a Shiny GUI that guides users through bulk size, trait name, and phenotype input. Association analysis was performed with a GLM‑based Et‑GWAS pipeline and results were compared to MLM GWAS for validation.

What they found

54 MTAs detected; 17 located in genic regions.
PVE of key SNPs ~3.9%–4% (e.g., OsGL1-2).
16 overlapping MTAs between 2019 and 2020 seasons.
24 MTAs fell within the qDTY2.2 QTL (PVE 3.6%–4.6%).
30 additional signals identified beyond MLM, 15 of which are genic.

Caveats

✕The hosted Et‑GWAS server can handle a maximum of 30K markers.
✕Validation was performed only on two drought seasons (2019‑2020) in rice.

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