Pipeline for Haplotype Frequencies Estimation from Pooled Targeted Sequencing in Maize

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Raphaël, Minguella | Canaguier, Aurélie | Madur, Delphine | Bérard, Aurélie | Le Clainche, Isabelle | Galaretto, Agustin O. | Hinsinger, Damien | Nicolas, Stephane | Faivre Rampant, Patricia

Edité par CCSD -

International audience. Haplotypes are useful markers in population genetics due to a tighter link to populations history than SNP and are therefore considered more informative for populations structuration analyses However, capturing populations diversity can be challenging because it requires to genotype many individuals which can be very expensive An usual solution is to genotype populations in pool meaning that several individuals of a same population are mixed and their DNA extraction is done in pool Unfortunately, information about haplotypes is lost during the process because the DNA is fragmented and mixed Several approaches have been proposed to rebuild haplotypes with reads overlap Here implemented one of these algorithm in a pipeline to estimates short haplotypes frequencies from targeted genotyping by sequencing tGBS technology, which reduces costs by sequencing only desired genomic regions

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