Abstract
Understanding the genetic mechanism of cold tolerance in rice is important to mine elite genes from rice landraces and breed excellent cultivars for this trait. In this study, a genome-wide association study (GWAS) was performed using high-density single nucleotide polymorphisms (SNPs) obtained using specific-locus amplified fragment sequencing (SLAF-seq) technology from a core collection of landraces of rice. A total of 67,511 SNPs obtained from 116,643 SLAF tags were used for genotyping the 150 accessions of rice landraces in the Ting’s rice core collection. A compressed mixed liner model was used to perform GWAS by using the high-density SNPs for cold tolerance in rice landraces at the seedling stage. A total of 26 SNPs were found to be significantly (P < 1.48 × 10-7) associated with cold tolerance, which could explained phenotypic variations ranging from 26 to 33%. Among them, two quantitative trait loci (QTLs) were mapped closely to the previously cloned/mapped genes or QTLs for cold tolerance. A newly identified QTL for cold tolerance in rice was further characterized by sequencing, real time-polymerase chain reaction, and bioinformatics analyses. One candidate gene, i.e., Os01g0620100, showed different gene expression levels between the cold tolerant and sensitive landraces under cold stress. We found the difference of coding amino acid in Os01g0620100 between cold tolerant and sensitive landraces caused by polymorphism within the coding domain sequence. In addition, the prediction of Os01g0620100 protein revealed a WD40 domain that was frequently found in cold tolerant landraces. Therefore, we speculated that Os01g0620100 was highly important for the response to cold stress in rice. These results indicated that rice landraces are important sources for investigating rice cold tolerance, and the mapping results might provide important information to breed cold-tolerant rice cultivars by using marker-assisted selection.
Highlights
Low temperature affects seed germination and male sterility of rice, and decreases yield (Koseki et al, 2010; Saito et al, 2010; Suh et al, 2010)
This study aimed to (1) use the SLAF-seq technology to develop genome-wide distributed markers from the rice core collection; (2) perform genome-wide association study (GWAS) for rice cold tolerance to reveal the genetic basis for this complex trait; and (3) identify novel functional candidate genes associated with the mapped QTLs by using multiple molecular biological and bioinformatics approaches
To identify candidate genes and analyze their biological function and determine whether they are associated with cold tolerance, we investigated the expression levels of candidate genes by using RT-polymerase chain reaction (PCR)
Summary
Low temperature affects seed germination and male sterility of rice, and decreases yield (Koseki et al, 2010; Saito et al, 2010; Suh et al, 2010). With the rapid development of molecular biology, increasing number of studies have been focusing on the identification of quantitative trait loci (QTLs) responsible for cold tolerance in rice. Fujino et al generated recombinant inbred lines (RILs) by crossing temperate japonica varieties Italica Livorno with Hayamasari and cloned a major gene, qLTG3 on chromosome 3 (Fujino et al, 2004); this is the first cloned gene known to be associated with low-temperature germination in rice that encodes the unknown protein (Fujino and Matsuda, 2010; Fujino and Sekiguchi, 2011). Zhang et al (2017) revealed that CTB4a was responsible for cold tolerance at the booting stage and cloned this gene, which encoded a conserved leucine-rich repeat receptor-like kinase. The Ctb locus only contained two candidate genes (F-box and protein serine/threonine kinase); molecular characterization showed that the F-box protein was the candidate gene of Ctb and was highly expressed in young panicles (Saito et al, 2004)
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