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Plant Science Today (PST)

Research Articles

Early Access

Haplotype-phenotype association in key grain size-controlling genes in rice (Oryza sativa L.)

DOI
https://doi.org/10.14719/pst.13842
Submitted
26 January 2026
Published
02-07-2026
Versions

Abstract

Grain size is the key determinant of yield potential and consumer preference in rice, making it a primary target for genetic improvement. However, the allelic architecture underlying the traits needs to be resolved for precision breeding. Here, we conducted a haplotype-based dissection of four major grain size regulating candidate genes (OsGS3.1, OsGW2, OsGW7 and OsGW8) using high-quality single nucleotide polymorphism (SNP) data from 197 indica accessions of the 3K rice genome panel. Neutrality and diversity analyses revealed heterogeneous evolutionary histories. OsGS3.1 exhibited reduced haplotype diversity consistent with directional selection, whereas OsGW7 and OsGW8 showed strong negative Tajimas’ D (< -1.2) and Fus’ Fs (< -2.5), indicating an excess of rare alleles under purifying or expansion-driven selection. The LD block structure varied markedly across loci, suggesting selective retention of favourable alleles in OsGW2. Marker-trait associations identified exonic SNPs within OsGW2 (chr02_8115620) and OsGW7 (chr07_24666398), explaining up to 5.3 % of the phenotypic variance. Significant haplotype effects were observed in OsGS3.1, OsGW2, OsGW7 and OsGW8, with specific allelic combinations jointly modulating grain length (GL) and grain breadth (GB). These results establish a validated haplotype map and causal SNPs suitable for haplotype-based breeding, marker-assisted selection and genomic prediction models targeting grain size ideotype development in rice.

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