The Japanese quail (Coturnix japonica) is a notably valuable egg and meat producer but has also been used as a laboratory animal. In the present study, we constructed a Japanese quail linkage map with 1735 polymorphic amplified fragment length polymorphisms markers, and nine chicken microsatellite (MS) markers, as well as sex and phenotypes of two genetic diseases; a muscular disorder (LWC) and neurofilament-deficient mutant (Quv). Linkage analysis revealed 578 independent loci. The resulting linkage map contained 44 multipoint linkage groups covering 2597.8 cM and an additional 218.2 cM was contained in 21 two-point linkage groups. The total map was 2816 cM in length with an average marker interval of 5.5 cM. The Quv locus was located on linkage group 5, but linkage was not found between the LWC locus and any of the markers. Comparative mapping with chicken using orthologous markers revealed chromosomal assignments of the quail linkage group 1 to chicken chromosome 2 (GGA2), 5 to GGA22, 2 to GGA5, 8 to GGA7, 27 to GGA11, 29 to GGA1 and 45 to GGA4.

The objective of this work was to develop polymorphic microsatellite markers derived from Japanese quail embryonic and cardiac cDNA libraries and to locate these markers on Kobe-NIBS Japanese quail (KNQ) linkage map constructed mainly by AFLP markers in previous study. Of the 20 positive clones, /+ clones were unique and identified as genes or ESTs by BLAST searches, and ,/ from /+ clones were possible to design the PCR primers after partial sequencing. Only six markers were polymorphic and used by linkage analysis in KNQ resource family. These markers were mapped on four linkage groups, JQG +, JQG 3, JQG +3 and JQG 00, and then these linkage groups were assigned to chromosome of Japanese quail, CJA ,, CJA +., CJA +1 and CJA ,-, respectively. These markers derived from cDNA are useful and powerful tool, and contribute to the comparative map between Japanese quail and the other species.

In our previous study, a Kobe-NIBS Japanese quail (KNQ) linkage map was constructed mainly using amplified fragment length polymorphism (AFLP) markers. In order to compare chicken and quail chromosomes, we developed expressed sequence tag (EST) markers derived from cDNA-AFLP fragments and localized these markers on the linkage map. Using a total of 128 AFLP primer combinations, 24 polymorphic bands were obtained between a neurofilament-deficient mutant quail line male and a muscular disorder quail line female, which were the parents of the KNQ resource family. Nine of the 24 markers were mapped by linkage analysis. These markers were mapped to seven linkage groups, namely 1, 2, 3, 6, 8, 15 and 42. A subsequent homology search using chicken genome sequences strongly suggests that these linkage groups correspond with chicken chromosomes 1, 2, 3, 5, 15, 23 and 26.