Development of polymorphic markers in quail by next generation sequencing
Résumé
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]
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