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Previous issue date: 2017-07-11 === In the last twenty-five years, we have witnessed the wide adoption of DNA markers for
the study of genetic variation in many organisms. A DNA marker must have two or more
identifiable allelic DNA sequences to be useful. It usually does not have a biological effect, but
instead functions as a traceable landmark in the genome, found in a specific location, and
transmitted by the standard laws of inheritance from one generation to the next. Its application
goes beyond genetic mapping and includes the analysis of genetic diversity, marker-trait
association studies, marker assisted selection and, more recently, with the advent of wholegenome
sequencing, whole-genome association and genomic selection.
Among the several types of DNA sequence polymorphisms that can be used as DNA
marker, Single Nucleotide Polymorphisms (SNPs) are the most powerful for large-scale variation
analysis. There are vast numbers of SNPs in every genome and they can be typed by methods
that have been proven easy to automate. Detection of alternative alleles is rapid and effortless
because it is based on well-known polymerase chain reaction and DNA oligomer hybridization
assays. Various strategies have been devised to discriminate alleles at a SNP, including fixed
DNA arrays technologies, solution hybridization techniques and many sequencing-based
genotyping.
In our study, we have developed high-throughput DNA marker systems for non-model,
highly heterozygous, diploid tree species. We took advantage of the combined power of Next
Generation Sequencing (NGS) technologies, well-established highly automated methods of SNP
typing and bioinformatics algorithms to perform genome-wide DNA variation analysis.
We used whole genome resequencing of pooled individuals to develop a high-density
60K SNP chip for Eucalyptus species (EucHIP60k) providing a 96% genome-wide coverage with
1 SNP/12???20 kbp, and 47,069 SNPs at ??? 10 kb from 30,444 of the 33,917 genes in the
Eucalyptus genome. We then used high-density SNP data and whole-genome pooled
resequencing to examine the landscape of population recombination (??) and theta (??), assess the
extent of linkage disequilibrium (r2) and build the highest density linkage maps for Eucalyptus to
date. Chromosome-wide ancestral recombination graphs allowed us to date the split of
Eucalytpus grandis (1.7???4.8 million yr. ago) and identify a scenario for the recent demographic
history of the species.
In a final set of studies, we built the first genome assembly for a Neotropical forest tree,
the Pink Ip?? (Handroanthus impetiginosus), a highly-valued keystone timber species. Genome
sequence was screened for the development of a targeted-capture sequencing system for SNP
genotyping consisting of nearly 24,000 probe sequences. This genotyping system showed
flexibility as it allowed the identification of SNPs across different populations of the species in
moderate sample sizes. The good genome coverage, consistent Ts/Tv ratio estimated across
samples and fair technical reproducibility between replicates, in terms of recall and precision of
the SNP calling and accuracy on genotypes, indicate that this genotyping platform can be
confidently used to estimate population genetics parameters and carry out population genomics
investigations at the genome-wide scale === ***
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