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Development of polymorphic markers in quail by next generation sequencing
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Session : Exploiting Genomics to Dissect the Genetic Control of Complex Traits
Session : Exploiting Genomics to Dissect the Genetic Control of Complex Traits.
Molecular genetic analyses in quail will benefi t greatly from a higher density ofgenetic markers. We chose therefore to obtain high numbers of SNP (Single NucleotidePolymorphism) by high-throughput sequencing (Titanium 454 GS-FLX, Roche) of twomain types of reduced representations of the genome: restriction digested fractionsof genomic DNA and EST (Expressed Sequence Tag), representing the expressedgenes. The genomic fractions were generated as AFLP (Amplifi ed Fragment LengthPolymorphism) fragments and the expressed ones by preparing cDNA libraries fromtwo tissues: embryo and brain. To optimize the information content of the SNPdetected for subsequent analyses, libraries were prepared from individuals selectedin the two lines involved in a QTL cross and each individual in the AFLP librarywas tagged. Sequencing runs produced 399,189 sequence reads from cDNA, and1,107,451 from genomic fragments, covering over 433 Mb of sequence in totaland allowing the detection of 17,400 putative SNP. Further analyses using the tagsinformation will allow the estimation of heterozygozity in the F1 males.Besides the interest of the production of a large number of new SNP, thistechnology should allow to sequence GC rich regions corresponding to the smallestmicrochromosomes for which there is no or few sequence in chicken. The comparisonof the quail sequences with the chicken genome assembly will allow a virtualmapping of the SNP obtained, based on the high synteny conservation betweenthese two avian species.
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