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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
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Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice

Richard S Garcia1, Sapphire Coronejo1, Jonathan Concepcion1

  • 1School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA.

International Journal of Molecular Sciences
|February 15, 2022
PubMed
Summary
This summary is machine-generated.

Weedy rice PSRR-1 exhibits day-neutral flowering due to unique gene variants. OsMADS56 is identified as a key regulator, impacting flowering time and adaptation in this adaptable weed.

Keywords:
Oryza sativaRNA-Sequencingdays to headinggenetic interactionphotosensitivityred rice

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Area of Science:

  • Plant genetics and genomics
  • Agronomy and crop science
  • Weed biology and management

Background:

  • Flowering time is a critical agronomic trait affecting crop adaptation and productivity.
  • Weedy rice accession PSRR-1 shows a unique photoinsensitive flowering response despite possessing a photosensitive allele of the Hd1 gene.

Purpose of the Study:

  • To investigate the genetic basis of the day-neutral flowering response in weedy rice PSRR-1.
  • To identify specific genes and variants contributing to flowering time regulation in PSRR-1.

Main Methods:

  • Whole-genome and RNA sequencing of cultivated and weedy rice.
  • De novo assembly of unaligned sequences to identify PSRR-1 specific genes.
  • Variant comparison with the 3K Rice Genome dataset and analysis of differentially expressed genes (DEGs) under short-day (SD) and long-day (LD) conditions.

Main Results:

  • Identified 45 genes specific to PSRR-1, including two flowering-associated genes.
  • Discovered unique variants within heading date quantitative trait loci (QTLs) in PSRR-1.
  • Found that DEGs, including Hd1, OsMADS56, Hd3a, and RFT1, possess unique variants in PSRR-1; OsMADS56 showed differential expression and alternative splicing (AS) and was notably absent in Cypress under both LD and SD conditions.

Conclusions:

  • The unique day-neutral flowering response in PSRR-1 is attributed to high-impact variants in flowering genes.
  • OsMADS56 is proposed as a key regulator responsible for the day-neutral flowering phenotype in weedy rice PSRR-1.