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High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources.

Perdereau AC, Douglas GC, Hodkinson TR, Kelleher CT - Biotechnol Biofuels (2013)

Bottom Line: However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions.The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus.This study characterises the variation in several lignocellulose gene markers for such purposes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland. perderea@tcd.ie.

ABSTRACT

Background: Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation.

Results: Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix.

Conclusions: The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.

No MeSH data available.


Related in: MedlinePlus

Regression analysis of the putative ploidy level against the number of SNPs/kbp. The trendline and R2 are shown.
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Figure 3: Regression analysis of the putative ploidy level against the number of SNPs/kbp. The trendline and R2 are shown.

Mentions: Regression analysis was used to explore the relationship between DNA ploidy and number of SNPs/kbp on 20 Salix genotypes. It showed that there was a positive correlation between ploidy and the number of scored fragments (F20=8.94, P<0.005, R2=0.34) (FigureĀ 3).


High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources.

Perdereau AC, Douglas GC, Hodkinson TR, Kelleher CT - Biotechnol Biofuels (2013)

Regression analysis of the putative ploidy level against the number of SNPs/kbp. The trendline and R2 are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750764&req=5

Figure 3: Regression analysis of the putative ploidy level against the number of SNPs/kbp. The trendline and R2 are shown.
Mentions: Regression analysis was used to explore the relationship between DNA ploidy and number of SNPs/kbp on 20 Salix genotypes. It showed that there was a positive correlation between ploidy and the number of scored fragments (F20=8.94, P<0.005, R2=0.34) (FigureĀ 3).

Bottom Line: However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions.The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus.This study characterises the variation in several lignocellulose gene markers for such purposes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland. perderea@tcd.ie.

ABSTRACT

Background: Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation.

Results: Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix.

Conclusions: The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.

No MeSH data available.


Related in: MedlinePlus