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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.


Differences in the levels of SNPs in predicted exons within the genes found in Salix and Populus. The data are ranked based on the levels of variation in Salix. The number of Salix genotypes or Populus species studied is indicated above each column.
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Figure 5: Differences in the levels of SNPs in predicted exons within the genes found in Salix and Populus. The data are ranked based on the levels of variation in Salix. The number of Salix genotypes or Populus species studied is indicated above each column.

Mentions: When levels of variation are compared between Salix and Populus in predicted exons, half of the genes show a trend towards larger diversity in Salix compared to Populus (Pal1, Knat7, Kor1, Mybr2r3, CesA2, C4H) (FigureĀ 5) and the remaining half show the opposite - Populus more variable than Salix. For example, the CAD gene is the most variable region in Salix but is one of the least variable in both the species of Populus studied. This could potentially be due to copy-number variation or differential regulation of wood formation in the 2 different genera, but further study is necessary to establish any patterns. Variation was found to be much lower in intraspecific studies of natural populations of P. tremula[38,39], where 17 SNPs/kbp were detected within five nuclear genes[38], 19 SNPs/kbp with 77 gene fragments[39] and 18 SNPs/kbp in P. tremuloides[17]. However, as the previous studies[17,38,39] are based on intraspecific variation it is understandable that the levels from the current study are much higher - 53 SNPs/kbp in Salix and 30 in Populus in the current study.


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

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

Differences in the levels of SNPs in predicted exons within the genes found in Salix and Populus. The data are ranked based on the levels of variation in Salix. The number of Salix genotypes or Populus species studied is indicated above each column.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Differences in the levels of SNPs in predicted exons within the genes found in Salix and Populus. The data are ranked based on the levels of variation in Salix. The number of Salix genotypes or Populus species studied is indicated above each column.
Mentions: When levels of variation are compared between Salix and Populus in predicted exons, half of the genes show a trend towards larger diversity in Salix compared to Populus (Pal1, Knat7, Kor1, Mybr2r3, CesA2, C4H) (FigureĀ 5) and the remaining half show the opposite - Populus more variable than Salix. For example, the CAD gene is the most variable region in Salix but is one of the least variable in both the species of Populus studied. This could potentially be due to copy-number variation or differential regulation of wood formation in the 2 different genera, but further study is necessary to establish any patterns. Variation was found to be much lower in intraspecific studies of natural populations of P. tremula[38,39], where 17 SNPs/kbp were detected within five nuclear genes[38], 19 SNPs/kbp with 77 gene fragments[39] and 18 SNPs/kbp in P. tremuloides[17]. However, as the previous studies[17,38,39] are based on intraspecific variation it is understandable that the levels from the current study are much higher - 53 SNPs/kbp in Salix and 30 in Populus in the current study.

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.