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Conference papers

Exploiting next-generation sequencing to obtain a whole-genome SNP collection in black poplar (Populus nigra L.)

Abstract : Poplar trees can be found in both domesticated and wild environments. This situation provides extensive experimental opportunity for the study of the relationship between naturally occurring genotypic and phenotypic variation. Having access to a population with little or no human disturbance means that extant populations are the result of natural evolutionary forces and questions pertaining to adaptation and demography will not be anthropomorphically confounded. The genus Populus is useful as a model tree species, since many genetic and genomic resources are available, including mapping pedigrees, association populations, genetic and QTL maps and the genome reference sequence of the black cottonwood, P. trichocarpa (Torr. & Gray). Taking advantage of these resources and exploiting rapidly-evolving new sequencing technologies, we set out to produce a sequence-marker map made of SNPs and short indels covering the whole genome. Such data will be used as markers for association studies and genomic-based breeding for adaptive traits (e.g. phenology, leaf development, water use efficiency and rust resistance). This work focused on black poplar (P. nigra L.), the native and most wide-spread poplar species in Europe. A combined process was adopted to resequencing various P. nigra genomes. The first step was deep-coverage resequencing (≥ 20X) of three poplar individuals from different latitudinal origins, which provided for efficient SNP detection. Alignment of 75 and 100 bp sequences to the P. trichocarpa genome reference seems to work well even though two different species are being compared. This part of the work provided consensus sequences of P. nigra and a wide-genome SNP collection. This SNP detection was supported and confirmed by P. nigra sequences of candidate genes for the above-mentioned adaptive traits, which were resequenced using the traditional Sanger method. The consensus sequences obtained will be used in the second step of the process to align sequences from 50 additional individuals in order to maximize SNP discovery. These poplar genotypes have already been selected from various European natural populations and their lower coverage (2X) resequencing is in progress. A final discussion on sequence data analysis and marker distribution across the poplar genome is provided.
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https://hal.inrae.fr/hal-02758125
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Submitted on : Thursday, June 4, 2020 - 3:07:57 AM
Last modification on : Friday, May 13, 2022 - 5:32:51 PM

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  • HAL Id : hal-02758125, version 1
  • PRODINRA : 36106

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Giusi Zaina, Stefania Giacomello, Cristian del Fabbro, Simone Scalabrin, Fabio Marroni, et al.. Exploiting next-generation sequencing to obtain a whole-genome SNP collection in black poplar (Populus nigra L.). Forest ecosystem genomics and adaptation, Jun 2010, San Lorenzo de El Escorial, Spain. ⟨hal-02758125⟩

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