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. 2020 Jan 24;71(9):2723–2739. doi: 10.1093/jxb/eraa025

Fig. 1.

Fig. 1.

Correlation of LOC_Os04g24110 haplotypes with percent low-temperature seedling survival (LTSS) in different subpopulations of the Rice Mini-Core (RMC) collection. (a) Haplotype analysis based on 37 single-nucleotide polymorphisms (SNPs) of a 2000-bp genomic DNA fragment spanning LOC_Os04g24110 using RiceVarMap data from a population of 4402 accessions. Haplotypes (Roman numerals) are representative for the subpopulations ‘temperate japonica’ (TeJ), ‘tropical japonica’ (TrJ), ‘various indica’ (Ind), ‘aus’ (Aus), ‘indica admixtures’ (Ind_Admix), ‘japonica admixtures’ (Jap_Admix), and various intra-subspecies ‘admixtures’ (Intermediate). (b) Haplotype–LTSS correlation analysis based on five SNPs using all 203 Oryza sativa accessions of the RMC. Accessions with the ACCTC haplotype belong to the 37-SNP-based haplotype I; accessions with GCTGG belong to haplotypes II, III, and IV; accessions with GTTCC belong to haplotype IX; and accessions with GCCGG belong to haplotype V. (c) Haplotype–LTSS correlation analysis based on five SNPs using only the 24 ‘admixture’ accessions of the RMC. RMC accessions at 2 weeks old were exposed to 10 °C for 7 d and allowed to recover at warm temperatures for 1 week (28/25 °C day/night, 12-h photoperiod), after which LTSS was determined. Data are means (±SE), n=5. Significant differences compared to the ACTCC accessions were determined using two-tailed Student’s t-tests: **P<10–4; ***P<10–20.