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. 2014 Nov 4;66(1):293–306. doi: 10.1093/jxb/eru419

Fig. 6.

Fig. 6.

Sequence analysis of RING (LOC_Os05g29710) as a candidate gene underlying the peak for t-LBS on chromosome 5. (A) The polymorphic sites of the RING gene. The genomic sequences of the RING gene from 50 accessions are shown together with two adjacent SNP markers and those among the top 50 SNP markers for LBS, which were located within the LD block (shown with asterisks). In the observed polymorphic sites, the number after RING shows the position from the transcription initiation site. The sites with black frames (RING469, RING475, RING635, and RING652) cause amino acid substitution/insertion. The matrix shows the r 2 values of each pair-wise comparison of markers and polymorphic sites. Higher values are shown in a darker colour. The number in the square shows the 100-fold value of r 2, which ranged from 0 to 100. The sequence aa 29–50 is a transmembrane domain (TM), and aa 133–175 is a zinc-finger motif (RING). (B) Allele frequency of each subpopulation at id5006874. ‘0’ stands for missing data in the original genotyping. Accessions containing A at this position are termed ‘type 1’ and those containing G are termed ‘type 2’. (C) t-LBS in the tropical japonica subpopulation. The asterisks indicate that the allele G at id5006874 is associated with a significantly higher t-LBS by Student’s t-test (P<0.01). (D) Amino acid sequence comparison of the 42 aa RING motif between the rice RING protein and other previously reported cell death or defence reaction-related proteins: Arabidopsis ATL9 (Berrocal-Lobo et al., 2010), Arabidopsis RING1 (Lin et al., 2008), rice EL5 (Takai et al., 2001), potato StRFP1 (Ni et al., 2010), and pepper RING1 (Lee et al., 2011). Completely conserved amino acids are shown against a black background. Strong groups (as defined by a Pam250 score of >0.5) are shown against a dark grey background and weak groups (as defined by a Pam250 sore of ≤0.5) are shown against a light grey background (Gonnet et al., 1992). An amino acid substitution between type 1 and type 2 (R→S) is shown in bold in the arrowed position.