Wang Wenjia, Huang Ruizhi, Wu Gengwei, Sun Jian, Zhu Ying, Wang Hua
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China.
Plants (Basel). 2023 Feb 15;12(4):871. doi: 10.3390/plants12040871.
Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 ( f. ) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ L. ssp. ). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG.
低温是影响水稻发芽的主要因素之一，而低温发芽（LTG）是一项重要的农艺性状。尽管在水稻低温发芽研究方面已取得显著进展，但低温发芽的分子机制仍了解甚少。为探索更多水稻低温发芽基因资源，我们首先证明了杂草稻WR04-6（f.）在10℃时的低温发芽能力显著高于栽培稻品种七山占（QSZ，L. ssp.）。利用RNA测序技术研究了种子萌发吸胀后10、12和14天（DAI）时，WR04-6和七山占在10℃下的基因表达情况。基因本体论（GO）富集和京都基因与基因组百科全书（KEGG）富集结果表明，WR04-6和七山占之间的差异表达基因（DEGs）主要集中在对淀粉分解代谢过程的响应以及对脱落酸（ABA）的响应上。这与α-淀粉酶活性、ABA和赤霉素（GA）处理结果一致。利用源自WR04-6和七山占杂交的重组自交系（RIL）群体及其高密度SNP遗传图谱，检测低温发芽率的数量性状位点（QTL）。结果表明，两个新的QTL分别位于第3号染色体和第12号染色体上。结合已定位的QTL和RNA测序DEGs，鉴定出16个可能与低温发芽相关的候选基因。通过qRT-PCR对候选基因表达进行验证，结果与RNA测序数据一致。这些结果将使我们能够了解杂草稻低温发芽的遗传基础，并为培育具有改良低温发芽特性的水稻种质提供新的遗传资源。
