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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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Putative spliceosomal introns in GRAS domain of Rht-1 genes.Alignment of (A) DNA and (B) amino acid (from translation) sequences of representative amplicons from the primer pair, Dell_RhtF4/Dell_RhtR4 (RP 2797−3171 of FN649763 or RP 764−1138 in Table S2). Bases in lower case are putative intron sequences. Amino acid sequences are translated in Frame 1 from (A). Amplicons with the typical Rht-1 sequence include SP-100%; WH-97%, WW-95%, DR-88%, AU-68%, CA-50% and QU-12% (JX255470−JX255476 respectively). Amplicons that have the putative intron sequence like QU-56% (JX255483) include WH-2%, WW-1%, DR-6%, AU-12% and CA-45% ((JX255477−JX255482 respectively). Amplicons that have a second intron like AU-2% (JX255486) include WH-0.4% (JX255484) and WW-1% (JX255485). Please refer to nt sequences in GenBank accession numbers for SNPs as annotated in Table S2.
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pone-0069690-g005: Putative spliceosomal introns in GRAS domain of Rht-1 genes.Alignment of (A) DNA and (B) amino acid (from translation) sequences of representative amplicons from the primer pair, Dell_RhtF4/Dell_RhtR4 (RP 2797−3171 of FN649763 or RP 764−1138 in Table S2). Bases in lower case are putative intron sequences. Amino acid sequences are translated in Frame 1 from (A). Amplicons with the typical Rht-1 sequence include SP-100%; WH-97%, WW-95%, DR-88%, AU-68%, CA-50% and QU-12% (JX255470−JX255476 respectively). Amplicons that have the putative intron sequence like QU-56% (JX255483) include WH-2%, WW-1%, DR-6%, AU-12% and CA-45% ((JX255477−JX255482 respectively). Amplicons that have a second intron like AU-2% (JX255486) include WH-0.4% (JX255484) and WW-1% (JX255485). Please refer to nt sequences in GenBank accession numbers for SNPs as annotated in Table S2.

Mentions: This study found a second group of amplicons from all the accessions except Spica. This second group of amplicons is characterized by a deletion of 42 bases, followed with a nucleotide sequence beginning with ‘GT’ at RP 830 and a base deletion at RP 867 (Fig. 5A; Table S2). A total deletion of 43 bases [(14×3) +1] will shift the reading frame by 2 positions and is indicative of the possible presence of an intron. If the reading frame of the Rht-1 gene is maintained, this putative intron must extend beyond RP899−901 (TAG) which codes for an amber mutation. An insertion sequence with start ‘GT’ and end with ‘AG’ (Fig. 5A) is typical of a canonical spliceosomal intron [31].


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)

Putative spliceosomal introns in GRAS domain of Rht-1 genes.Alignment of (A) DNA and (B) amino acid (from translation) sequences of representative amplicons from the primer pair, Dell_RhtF4/Dell_RhtR4 (RP 2797−3171 of FN649763 or RP 764−1138 in Table S2). Bases in lower case are putative intron sequences. Amino acid sequences are translated in Frame 1 from (A). Amplicons with the typical Rht-1 sequence include SP-100%; WH-97%, WW-95%, DR-88%, AU-68%, CA-50% and QU-12% (JX255470−JX255476 respectively). Amplicons that have the putative intron sequence like QU-56% (JX255483) include WH-2%, WW-1%, DR-6%, AU-12% and CA-45% ((JX255477−JX255482 respectively). Amplicons that have a second intron like AU-2% (JX255486) include WH-0.4% (JX255484) and WW-1% (JX255485). Please refer to nt sequences in GenBank accession numbers for SNPs as annotated in Table S2.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3716649&req=5

pone-0069690-g005: Putative spliceosomal introns in GRAS domain of Rht-1 genes.Alignment of (A) DNA and (B) amino acid (from translation) sequences of representative amplicons from the primer pair, Dell_RhtF4/Dell_RhtR4 (RP 2797−3171 of FN649763 or RP 764−1138 in Table S2). Bases in lower case are putative intron sequences. Amino acid sequences are translated in Frame 1 from (A). Amplicons with the typical Rht-1 sequence include SP-100%; WH-97%, WW-95%, DR-88%, AU-68%, CA-50% and QU-12% (JX255470−JX255476 respectively). Amplicons that have the putative intron sequence like QU-56% (JX255483) include WH-2%, WW-1%, DR-6%, AU-12% and CA-45% ((JX255477−JX255482 respectively). Amplicons that have a second intron like AU-2% (JX255486) include WH-0.4% (JX255484) and WW-1% (JX255485). Please refer to nt sequences in GenBank accession numbers for SNPs as annotated in Table S2.
Mentions: This study found a second group of amplicons from all the accessions except Spica. This second group of amplicons is characterized by a deletion of 42 bases, followed with a nucleotide sequence beginning with ‘GT’ at RP 830 and a base deletion at RP 867 (Fig. 5A; Table S2). A total deletion of 43 bases [(14×3) +1] will shift the reading frame by 2 positions and is indicative of the possible presence of an intron. If the reading frame of the Rht-1 gene is maintained, this putative intron must extend beyond RP899−901 (TAG) which codes for an amber mutation. An insertion sequence with start ‘GT’ and end with ‘AG’ (Fig. 5A) is typical of a canonical spliceosomal intron [31].

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