Novel genetic variants at 5′ end of Rht-1 genes.

Alignment of the amino acid sequences translated from DNA sequence amplicons from primer pair, Dell_RhtF2/Dell_RhtR2 (RP 2293−2565 of FN649763 or RP 260−532 in Table S2) of accessions Aus1408 (AU), Whistler (WH), WW1842 (WW), Carnamah (CA), Drysdale (DR), Spica (SP) and Quarrion (QU) with homologous regions of published (A) Rht-A1a, Rht-B1and Rht-D1 sequences and (B) New Variants. Percentage denotes the relative frequency of the amplicon. * denotes a stop codon or an amber mutation. GenBank accession numbers for the sequences are as denoted. Refer to GenBank nt sequences for SNPs that do not result in amino acid substitutions. Amplicon sequences with Rht-A1a sequence are AU-37%, WH-23%, WW-42%, DR-33%, CA-42% and SP-40% (GenBank JX255420−JX255425 respectively). Sequences in Rht-A1 Group 1 include QU-60% (JX255426) and WW-0.5% (JX255427). Sequences in Rht-A1 Group 2 include WH-18% JX255428) and SP-4% (JX244429). Sequences with Rht-B1a include WH-30%, DR-48% and SP-33% (JX255430−JX255432 respectively). Sequences with Rht-B1b include WW-34%, QU-26% and CA-7% (JX255434−JX255436 respectively). Sequences in Rht-B1 Group 1 include QU-2% (JX255440) and CA-0.5% (JX255439). Sequences with Rht-D1a include SP-4%, WH-9%, DR-8% and WW-7% (JX255448−JX255451 respectively). Sequences in Rht-D1 Group 1 include CA-7% (JX255446) and QU-4% (JX255447). Sequences in Rht-D1 Group 2 include WW-2% (JX255452) and QU-2% (JX255453). Sequences in Rht Group 1 include CA-18%, WW-14%, SP-6% and WH-7% (JX255455−JX255458 respectively). Sequences in Rht Group 2 include WH-0.1% and SP-1% (JX255459). Sequences in Rht Group 3 include AU-17% (JX255464) and DR-2% (JX255468). Sequences in Rht Group 4 include CA-4% (JX255462) and SP-1% (JX255463).