Detection of a polymorphism associated with shank length and body weight in Japanese quail (Coturnix japonica)by AFLP

Abstract

In this stuy, we attemptedto use amplifiedfragment length polymorphism (AFLP) in combination with selective genotyping to detect loci that affectedshank length andbody weight at 10 weeks of age in Japanese quail (Coturnix japonica). A total of 88 primer pairs were usedin AFLP analyses of 10 and13 males with the longest and shortest shank lengths, respectively, from an F2 intercross population derived from lines differentiated by large and small body size (LL and SS, respectively). Ten AFLP bands differed strikingly in frequency between the two groups (P<0.005). Genotyping of the 10 bands in 10 females with the longest shank lengths and 10 with the shortest revealedthat one banddifferedsignificantly in frequency between the two groups for both males andfemales (P< 0.05). This fragment shared86.4% identity with a 361-bp sequence of chicken chromosome 1 locatedfrom position 51,672,791 to 51,673,152, as determinedby chicken BLAT search. Polymerase chain reaction andsequence analysis revealed that a 190-bp insertion/deletion was the causal polymorphism. Genotypes of this indel marker were associatedsignificantly with shank length andbody weight in the F 2 intercross population (P<0.005). The insertion allele hada positive effect on both traits. To confirm the association of this marker with the two traits, we conducted association analysis in a population derived from heterozygous quails of another line. In this analysis, the indel genotypes showedno significant association with shank length or male boy weight (P>0.05), but did show a significant association with female body weight (P<0.05). © 2012, Japan Poultry Science Association.