Unraveling the Genetic Architecture of Photoperiod Sensitivity in Myanmar Rice Landraces Through Integrated GWAS and Transcriptome Analysis

TL;DR

This study identifies genetic factors controlling flowering time in Myanmar rice landraces using genome and gene expression data.

Contribution

The study discovers novel genetic loci and candidate genes specific to Myanmar rice landraces affecting photoperiod sensitivity.

Findings

Thirteen major QTLs for heading date were identified, including known genes and novel loci specific to Myanmar rice.

Two high-confidence candidate genes, Os06g0275000 and Os07g0606600, were confirmed to be stage-specifically expressed and linked to photoperiod sensitivity.

Transcriptional reprogramming under short-day conditions showed higher plasticity in photoperiod-sensitive rice genotypes.

Abstract

Photoperiod sensitivity (PS) is the major determinant of flowering time in rice and has played a critical role in adaptation across diverse ecotypes. To dissect the genetic and molecular architecture of PS in MYR landraces, we combined GWAS with transcriptomic profiling on 236 diverse accessions. Thirteen major QTL underlying heading date were mapped on chromosomes 1, 2, 3, 6, 7, and 8, consisting of the previously reported flowering genes (OsHd1, OsFTIP9) and a number of novel loci specific to Myanmar germplasm. Comparative RNA-seq analysis, using a photoperiod-sensitive (V10) and a photoperiod-insensitive (V3) indica genotype to the japonica cultivar ‘H479B’ as reference, showed distinct transcriptional reprogramming in response to short-day conditions, with higher-expression plasticity occurring in V10. By integrating GWAS signals with differential expressions, we narrowed our candidate gene set of two high-confidence regulators: Os06g0275000, encoding a zinc finger transcription factor, and Os07g0606600 (NF-YB10). Both genes were highly expressed in a stage-specific manner and further confirmed by qRT-PCR. Our results suggest a complex genetic regulatory network attracting conserved photoperiod pathways with unique novel allelic variant populations in Myanmar landraces. These candidate genes will be potential targets for precision breeding to optimize flowering time and enhance adaptation both in response to climate change and photoperiodic changes.

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