QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study

Abstract

Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.

Impact of riceGENERAL REGULATORY FACTOR14h(GF14h) on low-temperature seed germination and its application to breeding

“…Although the regulation of seed germination by GF14h was recently documented, its activity under low-temperature conditions remained unclear (Sun et al ., 2022; Yoshida et al ., 2022). While many genomic regions associated with LTG have been detected through QTL mapping and GWAS, only a few studies have identified the causal genes (Miura et al ., 2001; Fujino et al ., 2004; Han et al ., 2006; Jiang et al ., 2006; Fujino et al ., 2008; Nguyen et al ., 2012; Li et al ., 2013; Fujino et al ., 2015; Pan et al ., 2015; Satoh et al ., 2015; Jiang et al ., 2017; Shakiba et al ., 2017; Wang et al ., 2018; Jiang et al ., 2020; Shim et al ., 2020; Yang et al ., 2020; Pan et al ., 2021; Mao et al ., 2022). Indeed, LTG is a quantitative trait involving the cumulative effects of multiple genes and their epistatic relationships, making it difficult to assess the specific effect of a single genomic region on LTG.…”

“…LTG is a quantitative trait regulated by complex molecular mechanisms. Linkage mapping and genome-wide association studies (GWAS) have identified over 30 LTG-related quantitative trait loci (QTLs) or genomic regions associated with this trait, located on all 12 rice chromosomes (Miura et al ., 2001; Fujino et al ., 2004; Han et al ., 2006; Jiang et al ., 2006; Fujino et al ., 2008; Nguyen et al ., 2012; Li et al ., 2013; Fujino et al ., 2015; Pan et al ., 2015; Satoh et al ., 2015; Jiang et al ., 2017; Shakiba et al ., 2017; Wang et al ., 2018; Jiang et al ., 2020; Shim et al ., 2020; Yang et al ., 2020; Pan et al ., 2021; Mao et al ., 2022). However, only a few genes involved in LTG have been described, such as qLTG3-1 (Fujino et al ., 2008) and STRESS-ASSOCIATED PROTEIN16 ( OsSAP16 ) (Wang et al ., 2018).…”

Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice

“…Refs. [57][58][59][60][61][62][63][64][65][66][67][68][69][70] are cited in the Supplementary Materials.…”

Identification of QTLs and candidate genes for rice seed germinability under low temperature using high‐density genetic mapping and RNA‐seq

“…Genome‐wide association studies (GWAS) are useful for identifying genes associated with complex traits (Huang et al, 2010) and have been applied successfully to the identification of LTG‐related loci (Fujino et al, 2015; Mao et al, 2022; Schläppi et al, 2017; Thapa et al, 2020; Wang, Lee, et al, 2018; Wang, Zou, et al, 2018; Yang, Yang, et al, 2020; Yang, Zhou, et al, 2020). Fujino et al (2015) identified 17 LTG‐related QTLs in a GWAS with 63 accessions and 117 markers, while Thapa et al (2020) used a GWAS with 257 accessions and an array of 7000 SNP markers to identify a large number of QTLs.…”

“…Fujino et al (2015) identified 17 LTG‐related QTLs in a GWAS with 63 accessions and 117 markers, while Thapa et al (2020) used a GWAS with 257 accessions and an array of 7000 SNP markers to identify a large number of QTLs. Further GWAS studies that identified LTG‐associated QTLs are those of Yang, Yang, et al (2020), Yang, Zhou, et al (2020) and Mao et al (2022).…”