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Integrating Meta-QTL mapping and RNA-seq analysis identifies candidate genes for cold tolerance at rice seedling
Xiu-Jie Li1, Pedro García-Caparros2, Ye-Dong Sun1
1Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.
BMC Plant Biology
|January 30, 2026
Summary
This study identifies key genes for cold tolerance in rice using advanced genetic mapping and gene expression analysis. These findings offer precise targets for breeding climate-resilient rice varieties.
Area of Science:
- Plant Science
- Genetics
- Agronomy
Background:
- Cold stress significantly hinders rice (Oryza sativa) growth and agricultural yield.
- Conventional quantitative trait loci (QTL) mapping has limitations in pinpointing specific genes.
Purpose of the Study:
- To systematically identify genes conferring cold tolerance in rice seedlings.
- To overcome limitations of traditional QTL mapping through an integrated approach.
Main Methods:
- Meta-analysis of 553 QTLs from 28 studies (2005-2023) to identify robust meta-QTLs.
- RNA sequencing (RNA-seq) to analyze gene expression in rice seedlings under cold stress, identifying differentially expressed genes (DEGs).
- Integration of meta-QTL and RNA-seq data to pinpoint candidate cold tolerance genes.
Main Results:
- Identified 41 robust meta-QTLs across 12 rice chromosomes with an average confidence interval of 2.08 Mb.
- Detected 14,692 DEGs in rice seedlings subjected to cold stress.
- Pinpointed 34 high-confidence candidate genes within meta-QTL intervals, including 13 known stress-responsive genes and 21 novel loci.
- Validated dynamic gene expression of candidates using qRT-PCR.
Conclusions:
- Provides precise genetic targets for breeding cold-tolerant rice.
- Establishes a validated framework for identifying genes related to cold adaptation.
- Enhances understanding of the genetic architecture governing rice cold tolerance.
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