Evaluation of eight microsatellite loci polymorphism in four Japanese quail (Coturnix japonica) strain in Iran

Allele frequencies of eight microsatellite loci as GUJ0001, GUJ0021, GUJ0034, GUJ0041, GUJ0049, GUJ0059, GUJ0070 and GUJ0097 was estimated for four strain of Japanese quail in Iran. Whole blood samples were collected from 200 individuals belonging to four strain (Pharach, Panda, Tuxedo and Golden).Total Genomic DNA was extracted by the GUSN-Silica Gel kit. The extracted DNA was amplified through Polymerase Chain Reaction (PCR). Of the eight microsatellite loci used in this study, two loci ( GUJ0001 and GUJ0041 ) were monomorphic in Panda and Texedo, respectively. The highest and the lowest PIC values belonged to GUJ0059 in Golden (0.815) and GUJ0041 in Panda strain (0.427), respectively. The expected heterozygosity varied between 0.708 and 0.849. All locus-strain combinations deviated from Hardy-Weinberg equilibrium except GUJ0041 in Pharach strain, GUJ0021, GUJ0034, GUJ0041 and GUJ0097 in Panda strain and GUJ0034, GUJ0049 and GUJ0070 in Golden strain (p < 0.001). Results suggest the effectiveness of this set of loci for testing genetic relatedness.

Integrated maps in quail (Coturnix japonica) confirm the high degree of synteny conservation with chicken (Gallus gallus) despite 35 million years of divergence

BACKGROUND

By comparing the quail genome with that of chicken, chromosome rearrangements that have occurred in these two galliform species over 35 million years of evolution can be detected. From a more practical point of view, the definition of conserved syntenies helps to predict the position of genes in quail, based on information taken from the chicken sequence, thus enhancing the utility of this species in biological studies through a better knowledge of its genome structure. A microsatellite and an Amplified Fragment Length Polymorphism (AFLP) genetic map were previously published for quail, as well as comparative cytogenetic data with chicken for macrochromosomes. Quail genomics will benefit from the extension and the integration of these maps.

RESULTS

The integrated linkage map presented here is based on segregation analysis of both anonymous markers and functional gene loci in 1,050 quail from three independent F2 populations. Ninety-two loci are resolved into 14 autosomal linkage groups and a Z chromosome-specific linkage group, aligned with the quail AFLP map. The size of linkage groups ranges from 7.8 cM to 274.8 cM. The total map distance covers 904.3 cM with an average spacing of 9.7 cM between loci. The coverage is not complete, as macrochromosome CJA08, the gonosome CJAW and 23 microchromosomes have no marker assigned yet. Significant sequence identities of quail markers with chicken enabled the alignment of the quail linkage groups on the chicken genome sequence assembly. This, together with interspecific Fluorescence In Situ Hybridization (FISH), revealed very high similarities in marker order between the two species for the eight macrochromosomes and the 14 microchromosomes studied.

CONCLUSION

Integrating the two microsatellite and the AFLP quail genetic maps greatly enhances the quality of the resulting information and will thus facilitate the identification of Quantitative Trait Loci (QTL). The alignment with the chicken chromosomes confirms the high conservation of gene order that was expected between the two species for macrochromosomes. By extending the comparative study to the microchromosomes, we suggest that a wealth of information can be mined in chicken, to be used for genome analyses in quail.