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Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus.

Lu G, Harper AL, Trick M, Morgan C, Fraser F, O'Neill C, Bancroft I - DNA Res. (2014)

Bottom Line: A weighted gene co-expression network analysis provided additional 40 candidate genes.Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b.These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.

View Article: PubMed Central - PubMed

Affiliation: Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK Oil Crops Research Institute, CAAS, Wuhan 430062, Hubei, China.

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Associations and genomic locations of two candidate genes for the seed glucosinolate content. Top, marker association scans are illustrated, for both SNP (black dot) and GEM (red dot) markers, with significance of association (as −log10P values) plotted against positions within a specific chromosome pseudomolecule. Bottom, a representation of the pairwise r2 (a measure of LD) among the mapped SNPs surrounding the peak, where the colour of each box corresponds to the r2 value according to the legend. The positions of the candidate genes are indicated by arrows. (a) A locus identified on A2, and (b) A locus identified on C9.
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DSU024F3: Associations and genomic locations of two candidate genes for the seed glucosinolate content. Top, marker association scans are illustrated, for both SNP (black dot) and GEM (red dot) markers, with significance of association (as −log10P values) plotted against positions within a specific chromosome pseudomolecule. Bottom, a representation of the pairwise r2 (a measure of LD) among the mapped SNPs surrounding the peak, where the colour of each box corresponds to the r2 value according to the legend. The positions of the candidate genes are indicated by arrows. (a) A locus identified on A2, and (b) A locus identified on C9.

Mentions: The first unigene of interest is JCVI_13343 (BnaA.GTR2a); the Arabidopsis ortholog encodes proteins for transporting GS compounds from leaf to seed.33BnaA.GTR2a is located in a genomic region within the peak on A2 (Fig. 3a), and its expression was positively correlated with the accumulation of GS in seeds (r = 0.43, P < 10−4), accounting for 18.8% of trait variation (Supplementary Fig. S10a). Although there were nine known SNPs (at positions 469, 625, 655, 667, 688, 775, 860, 861, and 952) within this unigene, none of them was strongly associated with GS. To detect the potential new sequence variation (i.e. insertion or deletion, InDel) within this locus, specific primers were designed and used to amplify the complete unigene (ca. 600 bp) from 42 lines. By sequences alignment, all nine known SNPs were re-identified although some of them were not polymorphic (as only a subset of lines were analysed), and six were previously unidentified SNPs (at positions 538, 565, 571, 640, 727, and 748) (Supplementary Table S4). These results confirmed the robustness and efficiency of SNP development via mRNA-Seq in B. napus. However, none of the 10 polymorphic SNPs (at positions 469, 538, 565, 571, 640, 655, 727, 748, 860, and 861) were correlated with the GS content (r < 0.11, P > 0.500) and thus were not likely to be causative for trait variation.Figure 3.


Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus.

Lu G, Harper AL, Trick M, Morgan C, Fraser F, O'Neill C, Bancroft I - DNA Res. (2014)

Associations and genomic locations of two candidate genes for the seed glucosinolate content. Top, marker association scans are illustrated, for both SNP (black dot) and GEM (red dot) markers, with significance of association (as −log10P values) plotted against positions within a specific chromosome pseudomolecule. Bottom, a representation of the pairwise r2 (a measure of LD) among the mapped SNPs surrounding the peak, where the colour of each box corresponds to the r2 value according to the legend. The positions of the candidate genes are indicated by arrows. (a) A locus identified on A2, and (b) A locus identified on C9.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263295&req=5

DSU024F3: Associations and genomic locations of two candidate genes for the seed glucosinolate content. Top, marker association scans are illustrated, for both SNP (black dot) and GEM (red dot) markers, with significance of association (as −log10P values) plotted against positions within a specific chromosome pseudomolecule. Bottom, a representation of the pairwise r2 (a measure of LD) among the mapped SNPs surrounding the peak, where the colour of each box corresponds to the r2 value according to the legend. The positions of the candidate genes are indicated by arrows. (a) A locus identified on A2, and (b) A locus identified on C9.
Mentions: The first unigene of interest is JCVI_13343 (BnaA.GTR2a); the Arabidopsis ortholog encodes proteins for transporting GS compounds from leaf to seed.33BnaA.GTR2a is located in a genomic region within the peak on A2 (Fig. 3a), and its expression was positively correlated with the accumulation of GS in seeds (r = 0.43, P < 10−4), accounting for 18.8% of trait variation (Supplementary Fig. S10a). Although there were nine known SNPs (at positions 469, 625, 655, 667, 688, 775, 860, 861, and 952) within this unigene, none of them was strongly associated with GS. To detect the potential new sequence variation (i.e. insertion or deletion, InDel) within this locus, specific primers were designed and used to amplify the complete unigene (ca. 600 bp) from 42 lines. By sequences alignment, all nine known SNPs were re-identified although some of them were not polymorphic (as only a subset of lines were analysed), and six were previously unidentified SNPs (at positions 538, 565, 571, 640, 727, and 748) (Supplementary Table S4). These results confirmed the robustness and efficiency of SNP development via mRNA-Seq in B. napus. However, none of the 10 polymorphic SNPs (at positions 469, 538, 565, 571, 640, 655, 727, 748, 860, and 861) were correlated with the GS content (r < 0.11, P > 0.500) and thus were not likely to be causative for trait variation.Figure 3.

Bottom Line: A weighted gene co-expression network analysis provided additional 40 candidate genes.Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b.These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.

View Article: PubMed Central - PubMed

Affiliation: Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK Oil Crops Research Institute, CAAS, Wuhan 430062, Hubei, China.

Show MeSH