470
17.4.3 Transcriptome Sequencing of Cedrela balansae
Cedrela balansae C. DC. is an endangered and economically important native species that inhabit the subtropical rainforests in Northwestern Argentina. Its wood has
a great value in the market, and consequently it has been intensively exploited. This
context has generated severe fragmentation processes with an impact on its levels of
genetic diversity (Kageyama and Gandara 1998). Molecular research was scarce
until recently because of the limited genomic information available. In order to
complement strategies of conservation and breeding in this species with great
potential for forest plantations, C. balansae transcriptome was developed through
RNA-Seq using 454 GS FLX (Torales et al. 2018). The assembling and annotation
process (Fig. 17.2) generated 92.3 Mb of sequence data and an important number of
unigenes, SSRs and SNPs (Table 17.1).
A subset of 70 SSRs allocated in sequences of important “stress tolerance” genes
[transcription factors (Zinc fingers, Myb), peroxidases, among other categories]
were selected for PCR-validation in eight genotypes from eight populations of the
species. The validated and polymorphic SSRs showed putative biological functions
corresponding to response to cold (64%) and other stress stimulus (36%).
Furthermore, the transferability of functional markers to other Cedrela species
(C. fissilis, C. saltensis and C. angustifolia) inhabiting in northwest and northeast of
Argentina was performed. As expected in congeneric species, high levels of crossamplification were obtained, reaching values between 77% (C. angustifolia) and
93% (C. fissilis). Finally, the 70 SSRs analysed resulted in about 46% (32) polymorphic markers for all the studied species.
In general, RNA-Seq has speeded up the investigation of the complexity of gene
transcription patterns, functional analyses and gene regulation networks. Cedrela
balansae is a cold-sensitive species; therefore, low temperatures and freezing conditions are factors that limit their cultivation. The knowledge of the molecular
mechanisms of response to abiotic stress is relevant to identify genes linked to cold
in the seedling development stages. The C. balansae transcriptome database
obtained will be useful for discovering genes of interest related to abiotic and biotic
stresses, to assist breeding programmes and develop genetic markers, to investigate
functional diversity in remnant natural populations and to identify key populations
for its preservation.
17.5 Ongoing HTS Projects
17.5.1 Transcriptome Sequencing of Austrocedrus chilensis,
Handroanthus impetiginosus and Cordia trichotoma
Austrocedrus chilensis (D. Don) Pic. Serm. et Bizzarri (Patagonian cypress) is a
native conifer of the Andean-Patagonian Forests, with high adaptive potential to
water stress conditions. Its range covers a wide gradient of precipitation in the
S. L. Torales et al.
17.4.3 Transcriptome Sequencing of Cedrela balansae
Cedrela balansae C. DC. is an endangered and economically important native species that inhabit the subtropical rainforests in Northwestern Argentina. Its wood has
a great value in the market, and consequently it has been intensively exploited. This
context has generated severe fragmentation processes with an impact on its levels of
genetic diversity (Kageyama and Gandara 1998). Molecular research was scarce
until recently because of the limited genomic information available. In order to
complement strategies of conservation and breeding in this species with great
potential for forest plantations, C. balansae transcriptome was developed through
RNA-Seq using 454 GS FLX (Torales et al. 2018). The assembling and annotation
process (Fig. 17.2) generated 92.3 Mb of sequence data and an important number of
unigenes, SSRs and SNPs (Table 17.1).
A subset of 70 SSRs allocated in sequences of important “stress tolerance” genes
[transcription factors (Zinc fingers, Myb), peroxidases, among other categories]
were selected for PCR-validation in eight genotypes from eight populations of the
species. The validated and polymorphic SSRs showed putative biological functions
corresponding to response to cold (64%) and other stress stimulus (36%).
Furthermore, the transferability of functional markers to other Cedrela species
(C. fissilis, C. saltensis and C. angustifolia) inhabiting in northwest and northeast of
Argentina was performed. As expected in congeneric species, high levels of crossamplification were obtained, reaching values between 77% (C. angustifolia) and
93% (C. fissilis). Finally, the 70 SSRs analysed resulted in about 46% (32) polymorphic markers for all the studied species.
In general, RNA-Seq has speeded up the investigation of the complexity of gene
transcription patterns, functional analyses and gene regulation networks. Cedrela
balansae is a cold-sensitive species; therefore, low temperatures and freezing conditions are factors that limit their cultivation. The knowledge of the molecular
mechanisms of response to abiotic stress is relevant to identify genes linked to cold
in the seedling development stages. The C. balansae transcriptome database
obtained will be useful for discovering genes of interest related to abiotic and biotic
stresses, to assist breeding programmes and develop genetic markers, to investigate
functional diversity in remnant natural populations and to identify key populations
for its preservation.
17.5 Ongoing HTS Projects
17.5.1 Transcriptome Sequencing of Austrocedrus chilensis,
Handroanthus impetiginosus and Cordia trichotoma
Austrocedrus chilensis (D. Don) Pic. Serm. et Bizzarri (Patagonian cypress) is a
native conifer of the Andean-Patagonian Forests, with high adaptive potential to
water stress conditions. Its range covers a wide gradient of precipitation in the
S. L. Torales et al.