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Novel genetic variants of GA-insensitive Rht-1 genes in hexaploid wheat and their potential agronomic value.

Tan MK, Koval J, Ghalayini A - PLoS ONE (2013)

Bottom Line: In addition, novel mutants which differ from reported alleles of Rht-B1b, Rht-B1e and Rht-D1b have been found in Quarrion, Carnamah and Whistler.Mutations in the conserved C-terminal GRAS domain of Rht-A1 alleles with possible effects on expression have been found in WW1842, Quarrion and Drysdale.Genetic variants with putative spliceosomal introns in the GRAS domain have been found in all accessions except Spica.

View Article: PubMed Central - PubMed

Affiliation: Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, New South Wales, Australia. mui-keng.tan@dpi.nsw.gov.au

ABSTRACT
This study has found numerous novel genetic variants of GA-insensitive dwarfing genes with potential agricultural value for crop improvement. The cultivar, Spica is a tall genotype and possesses the wild-type genes of Rht-A1a, Rht-B1a and Rht-D1a. The cultivar Quarrion possesses a mutant in the DELLA motif in each of the 3 genomes. This is a first report of a mutant of Rht-A1. In addition, novel mutants which differ from reported alleles of Rht-B1b, Rht-B1e and Rht-D1b have been found in Quarrion, Carnamah and Whistler. The accession, Aus1408 has an allele of Rht-B1 with a mutation in the conserved 'TVHYNP' N-terminal signal binding domain with possible implications on its sensitivity to GA. Mutations in the conserved C-terminal GRAS domain of Rht-A1 alleles with possible effects on expression have been found in WW1842, Quarrion and Drysdale. Genetic variants with putative spliceosomal introns in the GRAS domain have been found in all accessions except Spica. Genome-specific cis-sequences about 124 bp upstream of the start codon of the Rht-1 gene have been identified for each of the three genomes.

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Mutations in the C-terminal GRAS domain of Rht-A1 alleles.Sequences are translated from DNA sequences of representative amplicons from primer pair, Dell_RhtF6/Dell_RhtR6 (RP 3604−3935 of FN649763 or RP 1571−1902 in Table S2) and aligned. The reference amino acid sequences for Rht-A1a/Rht-B1a and Rht-D1a are Genbank JF930277 (3065−3396) and Q9ST59 (491−601) respectively. Amplicons with sequences similar to Rht-A1a/Rht-B1a include WH-70%, SP-72%, WW-70%, DR-68%, AU-60%, CA-74% and QU-75% (JX255403−JX255409 respectively). Amplicons with sequences similar to Rht-D1a include WH-27%, SP-28%, WW-25%, AU-29%, DR-28%, CA-22% and QU-23% (JX255410−JX255416 respectively). Amplicons with sequences similar to Rht-A1 include DR-4% (JX255417), WW-5% (JX255418) and QU-3% (JX255419). Please refer to nt sequences in GenBank accession numbers for SNPs that do not result in amino acid substitutions sequences (Table S2).
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pone-0069690-g003: Mutations in the C-terminal GRAS domain of Rht-A1 alleles.Sequences are translated from DNA sequences of representative amplicons from primer pair, Dell_RhtF6/Dell_RhtR6 (RP 3604−3935 of FN649763 or RP 1571−1902 in Table S2) and aligned. The reference amino acid sequences for Rht-A1a/Rht-B1a and Rht-D1a are Genbank JF930277 (3065−3396) and Q9ST59 (491−601) respectively. Amplicons with sequences similar to Rht-A1a/Rht-B1a include WH-70%, SP-72%, WW-70%, DR-68%, AU-60%, CA-74% and QU-75% (JX255403−JX255409 respectively). Amplicons with sequences similar to Rht-D1a include WH-27%, SP-28%, WW-25%, AU-29%, DR-28%, CA-22% and QU-23% (JX255410−JX255416 respectively). Amplicons with sequences similar to Rht-A1 include DR-4% (JX255417), WW-5% (JX255418) and QU-3% (JX255419). Please refer to nt sequences in GenBank accession numbers for SNPs that do not result in amino acid substitutions sequences (Table S2).

Mentions: The region bounded by Dell_RhtF6/Dell_RhtR6 (RP 3604−3935 of FN649763 or RP 1571−1902 in Table S2) is part of the GRAS family transcription factor [30], and is conserved across the published Rht-A1 and Rht-B1 sequences and differ from Rht-D1 only by a glycine insertion (Fig. 3). These 2 groups of conserved amplicons were amplified in the expected ratio of 2∶1 for the 7 accessions (Fig. 3).


Novel genetic variants of GA-insensitive Rht-1 genes in hexaploid wheat and their potential agronomic value.

Tan MK, Koval J, Ghalayini A - PLoS ONE (2013)

Mutations in the C-terminal GRAS domain of Rht-A1 alleles.Sequences are translated from DNA sequences of representative amplicons from primer pair, Dell_RhtF6/Dell_RhtR6 (RP 3604−3935 of FN649763 or RP 1571−1902 in Table S2) and aligned. The reference amino acid sequences for Rht-A1a/Rht-B1a and Rht-D1a are Genbank JF930277 (3065−3396) and Q9ST59 (491−601) respectively. Amplicons with sequences similar to Rht-A1a/Rht-B1a include WH-70%, SP-72%, WW-70%, DR-68%, AU-60%, CA-74% and QU-75% (JX255403−JX255409 respectively). Amplicons with sequences similar to Rht-D1a include WH-27%, SP-28%, WW-25%, AU-29%, DR-28%, CA-22% and QU-23% (JX255410−JX255416 respectively). Amplicons with sequences similar to Rht-A1 include DR-4% (JX255417), WW-5% (JX255418) and QU-3% (JX255419). Please refer to nt sequences in GenBank accession numbers for SNPs that do not result in amino acid substitutions sequences (Table S2).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3716649&req=5

pone-0069690-g003: Mutations in the C-terminal GRAS domain of Rht-A1 alleles.Sequences are translated from DNA sequences of representative amplicons from primer pair, Dell_RhtF6/Dell_RhtR6 (RP 3604−3935 of FN649763 or RP 1571−1902 in Table S2) and aligned. The reference amino acid sequences for Rht-A1a/Rht-B1a and Rht-D1a are Genbank JF930277 (3065−3396) and Q9ST59 (491−601) respectively. Amplicons with sequences similar to Rht-A1a/Rht-B1a include WH-70%, SP-72%, WW-70%, DR-68%, AU-60%, CA-74% and QU-75% (JX255403−JX255409 respectively). Amplicons with sequences similar to Rht-D1a include WH-27%, SP-28%, WW-25%, AU-29%, DR-28%, CA-22% and QU-23% (JX255410−JX255416 respectively). Amplicons with sequences similar to Rht-A1 include DR-4% (JX255417), WW-5% (JX255418) and QU-3% (JX255419). Please refer to nt sequences in GenBank accession numbers for SNPs that do not result in amino acid substitutions sequences (Table S2).
Mentions: The region bounded by Dell_RhtF6/Dell_RhtR6 (RP 3604−3935 of FN649763 or RP 1571−1902 in Table S2) is part of the GRAS family transcription factor [30], and is conserved across the published Rht-A1 and Rht-B1 sequences and differ from Rht-D1 only by a glycine insertion (Fig. 3). These 2 groups of conserved amplicons were amplified in the expected ratio of 2∶1 for the 7 accessions (Fig. 3).

Bottom Line: In addition, novel mutants which differ from reported alleles of Rht-B1b, Rht-B1e and Rht-D1b have been found in Quarrion, Carnamah and Whistler.Mutations in the conserved C-terminal GRAS domain of Rht-A1 alleles with possible effects on expression have been found in WW1842, Quarrion and Drysdale.Genetic variants with putative spliceosomal introns in the GRAS domain have been found in all accessions except Spica.

View Article: PubMed Central - PubMed

Affiliation: Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, New South Wales, Australia. mui-keng.tan@dpi.nsw.gov.au

ABSTRACT
This study has found numerous novel genetic variants of GA-insensitive dwarfing genes with potential agricultural value for crop improvement. The cultivar, Spica is a tall genotype and possesses the wild-type genes of Rht-A1a, Rht-B1a and Rht-D1a. The cultivar Quarrion possesses a mutant in the DELLA motif in each of the 3 genomes. This is a first report of a mutant of Rht-A1. In addition, novel mutants which differ from reported alleles of Rht-B1b, Rht-B1e and Rht-D1b have been found in Quarrion, Carnamah and Whistler. The accession, Aus1408 has an allele of Rht-B1 with a mutation in the conserved 'TVHYNP' N-terminal signal binding domain with possible implications on its sensitivity to GA. Mutations in the conserved C-terminal GRAS domain of Rht-A1 alleles with possible effects on expression have been found in WW1842, Quarrion and Drysdale. Genetic variants with putative spliceosomal introns in the GRAS domain have been found in all accessions except Spica. Genome-specific cis-sequences about 124 bp upstream of the start codon of the Rht-1 gene have been identified for each of the three genomes.

Show MeSH
Related in: MedlinePlus