Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice

Overview

Journal Plants (Basel)

Date 2022 Sep 23

PMID 36145730

Authors

Dianwen Wang

Yulong Xiao

Hongping Chen

Cheng Huang

Ping Chen

Dazhou Chen

Wei Deng

Jilin Wang

Affiliations

Soon will be listed here.

Abstract

Rice, a cold-sensitive crop, is a staple food for more than 50% of the world's population. Low temperature severely compromises the growth of rice and challenges China's food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0-6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, was putatively identified as a candidate gene for the major effect locus . These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.

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