Genome-wide association study reveals candidate genes related to low temperature tolerance in rice (Oryza sativa) during germination
In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.
KeywordsOryza sativa L. Low temperature germination Re-sequencing GWAS Haplotype
This work was supported by National Research Foundation of Korea (NRF) grant funded by the Korean government (NRF-2015R1C1A1A01054699).
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Conflict of interest
All the authors declare that they have on conflict of interest in the publication.
- Chen L, Lou QJ, Sun ZX, Xing YZ, Yu XQ, Luo LJ (2006) QTL mapping of low temperature on germination rate of rice. Rice Sci 13(2):93–98Google Scholar
- Ellis RH, Roberts EH (1981) The quantification of ageing and survival in orthodox seeds. Seed Sci Technol (Neth)Google Scholar
- Fujino K (2004) A major gene for low temperature germinability in rice (Oryza sativa L.). Euphytica 136(1):63–68. https://doi.org/10.1023/B:EUPH.0000019519.43951.67 CrossRefGoogle Scholar
- Ji SL, Jiang L, Wang YH, Liu SJ, Liu X, Zhai HQ, Yoshimura A, Wan JM (2008) QTL and epistasis for low temperature germinability in rice. Acta Agron Sin 34(4):551–556Google Scholar
- Mao D, Yu L, Chen D, Li L, Zhu Y, Xiao Y et al (2015) Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theor Appl Genet 128(7):1359–1371. https://doi.org/10.1007/s00122-015-2511-3 CrossRefPubMedGoogle Scholar
- Sasaki T, Kinoshita T, Takahashi ME (1974) Estimation of the number of genes in the germination ability at low temperature in rice: genetical studies in rice plant, LVII. J Fac Agric Hokkaido Univ 57(3):301–312Google Scholar
- Shakiba E, Edwards JD, Jodari F, Duke SE, Baldo AM, Korniliev P et al (2017) Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PloS One 12(3):e0172133. https://doi.org/10.1371/journal.pone.0172133 CrossRefPubMedPubMedCentralGoogle Scholar
- Yang Z, Huang D, Tang W, Zheng Y, Liang K, Cutler AJ et al (2013) Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes. Plos One 8(7):e68433. https://doi.org/10.1371/journal.pone.0068433 CrossRefPubMedPubMedCentralGoogle Scholar