Development of polymorphic markers in quail by next generation sequencing

Mireille Morisson (1) , Florence Vignoles (1) , Katia Feve (1) , Sophie Leroux (1) , David Gourichon (2) , Christine Leterrier (3) , Cécile Arnould (3) , Olivier Bouchez (1) , Christophe C. Klopp (4) , Christian Diot (5) , Catherine Beaumont (6) , Francis Minvielle (7) , Alain Vignal (1) , Frederique Pitel (1)

1 LGC - Laboratoire de Génétique Cellulaire
2 UE PEAT - Pôle d'Expérimentation Avicole de Tours
3 PRC - Physiologie de la reproduction et des comportements [Nouzilly]
4 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
5 GARen - Génétique Animale
6 URA - Unité de Recherches Avicoles
7 GABI - Génétique Animale et Biologie Intégrative

Molecular genetic analyses in quail will benefi t greatly from a higher density of genetic markers. We chose therefore to obtain high numbers of SNP (Single Nucleotide Polymorphism) by high-throughput sequencing (Titanium 454 GS-FLX, Roche) of two main types of reduced representations of the genome: restriction digested fractions of genomic DNA and EST (Expressed Sequence Tag), representing the expressed genes. The genomic fractions were generated as AFLP (Amplifi ed Fragment Length Polymorphism) fragments and the expressed ones by preparing cDNA libraries from two tissues: embryo and brain. To optimize the information content of the SNP detected for subsequent analyses, libraries were prepared from individuals selected in the two lines involved in a QTL cross and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA, and 1,107,451 from genomic fragments, covering over 433 Mb of sequence in total and allowing the detection of 17,400 putative SNP. Further analyses using the tags information will allow the estimation of heterozygozity in the F1 males. Besides the interest of the production of a large number of new SNP, this technology should allow to sequence GC rich regions corresponding to the smallest microchromosomes for which there is no or few sequence in chicken. The comparison of the quail sequences with the chicken genome assembly will allow a virtual mapping of the SNP obtained, based on the high synteny conservation between these two avian species.

Domaines: Sciences du Vivant [q-bio]

Mireille Morisson, Florence Vignoles, Katia Feve, Sophie Leroux, David Gourichon, et al.. Development of polymorphic markers in quail by next generation sequencing. 32nd Conference of the International Society of Animal Genetics (ISAG), Jul 2010, Edinburgh, United Kingdom. 2010, Proceedings of the 32nd International Conference on Animal Genetics. ⟨hal-01193847⟩