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Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean.

Lestari P, Van K, Lee J, Kang YJ, Lee SH - Front Plant Sci (2013)

Bottom Line: Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage.These tandem duplicates could contribute on the protein/oil QTL of Chr 20.Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National University Seoul, Korea ; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Bogor, Indonesia.

ABSTRACT
Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL) for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr) 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both Chrs. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

No MeSH data available.


Related in: MedlinePlus

Comparison of two soybean chromosomes. (A) Syntenic dot plot of soybean Chr 10 and Chr 20 [adapted from Cannon and Shoemaker (2012)]. Each dot represents homology of the predicted synteny between two chromosomes. A large inversion of synteny in the upper right quadrant is indicated by a line of homology dots that slope down to the right. A positive correlation based on synteny between two chromosomes is denoted by a discontinuous line with a slope moving up to the right. Red square denotes a determined region for alignment algorithm analysis. (B) The conserved blocks in the recently duplicated regions of Chr 10 and Chr 20 are based on the alignment of large genomic regions using LastZ algorithm, which is available at http://genomevolution.org/r/56zj. (C) Conserved genes in the recently duplicated regions of Chr 10 and Chr 20 based on predicted transcripts using Genome Threader algorithm (spliced alignment of peptides) at http://genomevolution.org/r/56zh.
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Figure 2: Comparison of two soybean chromosomes. (A) Syntenic dot plot of soybean Chr 10 and Chr 20 [adapted from Cannon and Shoemaker (2012)]. Each dot represents homology of the predicted synteny between two chromosomes. A large inversion of synteny in the upper right quadrant is indicated by a line of homology dots that slope down to the right. A positive correlation based on synteny between two chromosomes is denoted by a discontinuous line with a slope moving up to the right. Red square denotes a determined region for alignment algorithm analysis. (B) The conserved blocks in the recently duplicated regions of Chr 10 and Chr 20 are based on the alignment of large genomic regions using LastZ algorithm, which is available at http://genomevolution.org/r/56zj. (C) Conserved genes in the recently duplicated regions of Chr 10 and Chr 20 based on predicted transcripts using Genome Threader algorithm (spliced alignment of peptides) at http://genomevolution.org/r/56zh.

Mentions: A large inversion with synteny in the corresponding regions of Chr 20 and Chr 10 was detected by a dot plot comparison between these two Chrs (Figure 2A; Cannon et al., 2004). A positive linear synteny is also observed with a slight interruption (Figure 2A) and leads to survey the conserved blocks along with conserved genes (Figures 2B,C), showing a higher level of synteny with one another. Schmutz et al. (2010) suggested that most of the duplicated regions were conserved but interspersed with insertions/deletions and inversions. All of the syntenic blocks were conserved and some of the syntenic regions between Chr 20 and Chr 10 still obtained a few syntenic genes (Figure 2C), which may reflect the recent genome duplication event regarding gene content (Pagel et al., 2004; Cannon and Shoemaker, 2012).


Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean.

Lestari P, Van K, Lee J, Kang YJ, Lee SH - Front Plant Sci (2013)

Comparison of two soybean chromosomes. (A) Syntenic dot plot of soybean Chr 10 and Chr 20 [adapted from Cannon and Shoemaker (2012)]. Each dot represents homology of the predicted synteny between two chromosomes. A large inversion of synteny in the upper right quadrant is indicated by a line of homology dots that slope down to the right. A positive correlation based on synteny between two chromosomes is denoted by a discontinuous line with a slope moving up to the right. Red square denotes a determined region for alignment algorithm analysis. (B) The conserved blocks in the recently duplicated regions of Chr 10 and Chr 20 are based on the alignment of large genomic regions using LastZ algorithm, which is available at http://genomevolution.org/r/56zj. (C) Conserved genes in the recently duplicated regions of Chr 10 and Chr 20 based on predicted transcripts using Genome Threader algorithm (spliced alignment of peptides) at http://genomevolution.org/r/56zh.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3672674&req=5

Figure 2: Comparison of two soybean chromosomes. (A) Syntenic dot plot of soybean Chr 10 and Chr 20 [adapted from Cannon and Shoemaker (2012)]. Each dot represents homology of the predicted synteny between two chromosomes. A large inversion of synteny in the upper right quadrant is indicated by a line of homology dots that slope down to the right. A positive correlation based on synteny between two chromosomes is denoted by a discontinuous line with a slope moving up to the right. Red square denotes a determined region for alignment algorithm analysis. (B) The conserved blocks in the recently duplicated regions of Chr 10 and Chr 20 are based on the alignment of large genomic regions using LastZ algorithm, which is available at http://genomevolution.org/r/56zj. (C) Conserved genes in the recently duplicated regions of Chr 10 and Chr 20 based on predicted transcripts using Genome Threader algorithm (spliced alignment of peptides) at http://genomevolution.org/r/56zh.
Mentions: A large inversion with synteny in the corresponding regions of Chr 20 and Chr 10 was detected by a dot plot comparison between these two Chrs (Figure 2A; Cannon et al., 2004). A positive linear synteny is also observed with a slight interruption (Figure 2A) and leads to survey the conserved blocks along with conserved genes (Figures 2B,C), showing a higher level of synteny with one another. Schmutz et al. (2010) suggested that most of the duplicated regions were conserved but interspersed with insertions/deletions and inversions. All of the syntenic blocks were conserved and some of the syntenic regions between Chr 20 and Chr 10 still obtained a few syntenic genes (Figure 2C), which may reflect the recent genome duplication event regarding gene content (Pagel et al., 2004; Cannon and Shoemaker, 2012).

Bottom Line: Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage.These tandem duplicates could contribute on the protein/oil QTL of Chr 20.Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National University Seoul, Korea ; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Bogor, Indonesia.

ABSTRACT
Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL) for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr) 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both Chrs. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

No MeSH data available.


Related in: MedlinePlus