Identification of Heat-Tolerant Genes in Non-Reference Sequences in Rice by Integrating Pan-Genome, Transcriptomics,...

Area of Science:

• Genomics
• Plant Science
• Agricultural Science

Background:

• Large-scale genomic data facilitates mining genes for agricultural traits in rice.
• Pan-genomes reveal genome diversity and aid crop improvement.
• Comprehensive variation studies require pan-genomes for heat-resistant and susceptible rice.

Purpose of the Study:

• To construct a rice pan-genome using heat-tolerant and -sensitive varieties.
• To identify heat-tolerance-related genetic variations and genes.
• To map these genes to heat stress-resistant quantitative trait loci (QTLs).

Main Methods:

• Constructed a rice pan-genome from 45 heat-tolerant and 15 heat-sensitive varieties.
• Identified 38,998 pan-genome genes, including 1141 in non-reference contigs.
• Analyzed 76,435 single nucleotide polymorphisms (SNPs) and RNA-sequencing data.

Main Results:

• Detected 76,435 heat-tolerance-related SNPs in heat-resistant rice cultivars.
• Identified 3214 upregulated and 2212 downregulated genes with heat stress tolerance-related SNPs.
• Mapped 1677 differentially expressed genes (DEGs) to 46 heat stress-resistant QTL regions, including 2 non-reference genes.

Conclusions:

• The constructed pan-genome is a valuable resource for improving rice heat stress resistance.
• Findings offer insights into non-reference gene functions, particularly two genes in heat stress-resistant QTLs.
• This work supports efficient genetic improvement of rice productivity under environmental stress.