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Molecular characterization of barley 3H semi-dwarf genes.

Li H, Chen G, Yan W - PLoS ONE (2015)

Bottom Line: Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population.The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2.These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

View Article: PubMed Central - PubMed

Affiliation: Tasmanian Institute of Agricultural Research and School of Agricultural Science, University of Tasmania, Hobart, Australia; CSIRO Agriculture Flagship, Queensland Bioscience Precinct, St Lucia, Queensland, Australia; Bioscience Research Division, Department of Environment and Primary Industries, Horsham, Victoria, Australia.

ABSTRACT
The barley chromosome 3H accommodates many semi-dwarfing genes. To characterize these genes, the two-rowed semi-dwarf Chinese barley landrace 'TX9425' was crossed with the Australian barley variety 'Franklin' to generate a doubled haploid (DH) population, and major QTLs controlling plant height have been identified in our previous study. The major QTL derived from 'TX9425' was targeted to investigate the allelism of the semi-dwarf gene uzu in barley. Twelve sets of near-isogenic lines and a large NILF2 fine mapping population segregating only for the dwarfing gene from 'TX9425' were developed. The semi-dwarfing gene in 'TX9425' was located within a 2.8 cM region close to the centromere on chromosome 3H by fine mapping. Molecular cloning and sequence analyses showed that the 'TX9425'-derived allele contained a single nucleotide substitution from A to G at position 2612 of the HvBRI1 gene. This was apparently the same mutation as that reported in six-rowed uzu barley. Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population. The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2. A third dwarfing gene, expressed only in winter-sown trials, was identified and located on chromosome 3HS. The effects and interactions of these dwarfing genes under different growing conditions are discussed. These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

No MeSH data available.


Related in: MedlinePlus

PCR amplification detecting the SNP difference between semi-dwarf and tall lines in a doubled haploid population segregating for the uzu locus.Lane 1: marker ladder; Lane 2: semi-dwarf (uzu), undigested; Lane 3: semi-dwarf (uzu), digested with HhaI; Lane 4: tall lines, undigested; Lane 5: tall lines, digested with HhaI.
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pone.0120558.g005: PCR amplification detecting the SNP difference between semi-dwarf and tall lines in a doubled haploid population segregating for the uzu locus.Lane 1: marker ladder; Lane 2: semi-dwarf (uzu), undigested; Lane 3: semi-dwarf (uzu), digested with HhaI; Lane 4: tall lines, undigested; Lane 5: tall lines, digested with HhaI.

Mentions: In order to confirm the allelism between the HvBRI1 SNP and the dwarfing gene isolated from ‘TX9425’, 92 DH lines derived from the ‘TX9425’ × ‘Franklin’ cross were used in the SNP analysis. We applied the dCAPS method to detect the SNPs between these two lines, with or without the semi-dwarf locus. In this study, the combination of constructed mismatch primer (dCAPS primer 1) and the second primer (dCAPS primer 2) created a specific recognition site for the restriction enzyme HhaI in the PCR product derived from the semi-dwarf lines (Fig. 5). In the DH population segregating for this semi-dwarfing gene, the SNP co-segregated with dwarfness in a 3:1 ratio, and the SNP was mapped to the same genomic region that harbored the semi-dwarfing QTL derived from ‘TX9425’ (Fig. 6). Therefore, the marker dCAPSuzu is ideal for the MAS of this dwarfing gene.


Molecular characterization of barley 3H semi-dwarf genes.

Li H, Chen G, Yan W - PLoS ONE (2015)

PCR amplification detecting the SNP difference between semi-dwarf and tall lines in a doubled haploid population segregating for the uzu locus.Lane 1: marker ladder; Lane 2: semi-dwarf (uzu), undigested; Lane 3: semi-dwarf (uzu), digested with HhaI; Lane 4: tall lines, undigested; Lane 5: tall lines, digested with HhaI.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4380412&req=5

pone.0120558.g005: PCR amplification detecting the SNP difference between semi-dwarf and tall lines in a doubled haploid population segregating for the uzu locus.Lane 1: marker ladder; Lane 2: semi-dwarf (uzu), undigested; Lane 3: semi-dwarf (uzu), digested with HhaI; Lane 4: tall lines, undigested; Lane 5: tall lines, digested with HhaI.
Mentions: In order to confirm the allelism between the HvBRI1 SNP and the dwarfing gene isolated from ‘TX9425’, 92 DH lines derived from the ‘TX9425’ × ‘Franklin’ cross were used in the SNP analysis. We applied the dCAPS method to detect the SNPs between these two lines, with or without the semi-dwarf locus. In this study, the combination of constructed mismatch primer (dCAPS primer 1) and the second primer (dCAPS primer 2) created a specific recognition site for the restriction enzyme HhaI in the PCR product derived from the semi-dwarf lines (Fig. 5). In the DH population segregating for this semi-dwarfing gene, the SNP co-segregated with dwarfness in a 3:1 ratio, and the SNP was mapped to the same genomic region that harbored the semi-dwarfing QTL derived from ‘TX9425’ (Fig. 6). Therefore, the marker dCAPSuzu is ideal for the MAS of this dwarfing gene.

Bottom Line: Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population.The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2.These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

View Article: PubMed Central - PubMed

Affiliation: Tasmanian Institute of Agricultural Research and School of Agricultural Science, University of Tasmania, Hobart, Australia; CSIRO Agriculture Flagship, Queensland Bioscience Precinct, St Lucia, Queensland, Australia; Bioscience Research Division, Department of Environment and Primary Industries, Horsham, Victoria, Australia.

ABSTRACT
The barley chromosome 3H accommodates many semi-dwarfing genes. To characterize these genes, the two-rowed semi-dwarf Chinese barley landrace 'TX9425' was crossed with the Australian barley variety 'Franklin' to generate a doubled haploid (DH) population, and major QTLs controlling plant height have been identified in our previous study. The major QTL derived from 'TX9425' was targeted to investigate the allelism of the semi-dwarf gene uzu in barley. Twelve sets of near-isogenic lines and a large NILF2 fine mapping population segregating only for the dwarfing gene from 'TX9425' were developed. The semi-dwarfing gene in 'TX9425' was located within a 2.8 cM region close to the centromere on chromosome 3H by fine mapping. Molecular cloning and sequence analyses showed that the 'TX9425'-derived allele contained a single nucleotide substitution from A to G at position 2612 of the HvBRI1 gene. This was apparently the same mutation as that reported in six-rowed uzu barley. Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population. The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2. A third dwarfing gene, expressed only in winter-sown trials, was identified and located on chromosome 3HS. The effects and interactions of these dwarfing genes under different growing conditions are discussed. These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

No MeSH data available.


Related in: MedlinePlus