473
For the first step of this sequencing project, leaves from plants of the drier provenances of both species, which are expected to be more severely affected by climate
change in the near future, were harvested for RNA-Seq. In total, ten samples were
sequenced on an Illumina HiSeq4000 after RNA extraction and library preparation
in Novogene (Davis, California, USA). These samples were control group and
stressed group at the beginning and end of the experiment, two biological replicates
(eight samples) for N. alpina and stressed group at the beginning and end of the
experiment, one biological replicate (two samples) for N. obliqua. The sequencing
emphasized N. alpina because it was shown to be less tolerant to drought stress
(Varela et al. 2010) and potentially more affected by climate change in its natural
range (Marchelli et al. 2017). Around 22 million paired-end 150 bp reads were
obtained for each sample, which are currently being analysed in a similar fashion to
the N. pumilio transcriptomes related to high-temperature stress (López Laphitz,
Bellora et al. unpublished data). Apart from further enlarge the -omic resources for
Nothofagus, this study will give insight into these species’ response to drought
stress, which was never until now studied in a genome-wide approach.
17.6 Current and Future Genetic Studies on Native Forest
Tree Species and Implications for Breeding
Breeding programmes have to deal with complex problems, such as diversity evaluation and selection of individuals adapted to stressing conditions or expressing better phenotypes, identification of clones, kinship information, genetic diversity and/
or genetic contamination in seed orchards, among others. Genetic diversity information of natural populations of the focus species is crucial for any breeding programme. Moreover, genetic breeding programmes require versatile and low-cost
tools that allow a better selection of the material to be reproduced in less time. For
South American native tree species, breeding programmes are, with some variations, in their initial stages. This section highlights how genomic resources and
molecular markers recently developed by HTS technologies in these species can
contribute to deal with inherent problems and, therefore, to assist and accelerate
breeding programmes.
Selection assisted by molecular markers in combination with progeny tests could
allow faster and more accurate results in the selection of complex characters such as
growth rate and quality of the wood. In Prosopis alba, Klein et al. (2019) identified
progenies that showed better behaviour and genetic stability in 19 families from the
Province of Chaco. They performed morphological (stem straightness, stem height,
stem bifurcation height and diameter) and genetic (17 SSRs) characterization on
progenies of a 5-year-old plantation from selected parent trees with desired phenotypic characteristics. Genetic characterization revealed (1) low probability of
inbreeding, suggesting a low level of kinship between progenies, (2) higher genetic
differentiation within families than between families and (3) good differentiation
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…
For the first step of this sequencing project, leaves from plants of the drier provenances of both species, which are expected to be more severely affected by climate
change in the near future, were harvested for RNA-Seq. In total, ten samples were
sequenced on an Illumina HiSeq4000 after RNA extraction and library preparation
in Novogene (Davis, California, USA). These samples were control group and
stressed group at the beginning and end of the experiment, two biological replicates
(eight samples) for N. alpina and stressed group at the beginning and end of the
experiment, one biological replicate (two samples) for N. obliqua. The sequencing
emphasized N. alpina because it was shown to be less tolerant to drought stress
(Varela et al. 2010) and potentially more affected by climate change in its natural
range (Marchelli et al. 2017). Around 22 million paired-end 150 bp reads were
obtained for each sample, which are currently being analysed in a similar fashion to
the N. pumilio transcriptomes related to high-temperature stress (López Laphitz,
Bellora et al. unpublished data). Apart from further enlarge the -omic resources for
Nothofagus, this study will give insight into these species’ response to drought
stress, which was never until now studied in a genome-wide approach.
17.6 Current and Future Genetic Studies on Native Forest
Tree Species and Implications for Breeding
Breeding programmes have to deal with complex problems, such as diversity evaluation and selection of individuals adapted to stressing conditions or expressing better phenotypes, identification of clones, kinship information, genetic diversity and/
or genetic contamination in seed orchards, among others. Genetic diversity information of natural populations of the focus species is crucial for any breeding programme. Moreover, genetic breeding programmes require versatile and low-cost
tools that allow a better selection of the material to be reproduced in less time. For
South American native tree species, breeding programmes are, with some variations, in their initial stages. This section highlights how genomic resources and
molecular markers recently developed by HTS technologies in these species can
contribute to deal with inherent problems and, therefore, to assist and accelerate
breeding programmes.
Selection assisted by molecular markers in combination with progeny tests could
allow faster and more accurate results in the selection of complex characters such as
growth rate and quality of the wood. In Prosopis alba, Klein et al. (2019) identified
progenies that showed better behaviour and genetic stability in 19 families from the
Province of Chaco. They performed morphological (stem straightness, stem height,
stem bifurcation height and diameter) and genetic (17 SSRs) characterization on
progenies of a 5-year-old plantation from selected parent trees with desired phenotypic characteristics. Genetic characterization revealed (1) low probability of
inbreeding, suggesting a low level of kinship between progenies, (2) higher genetic
differentiation within families than between families and (3) good differentiation
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…