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Traditional single-trait genetic analyses, such as quantitative trait locus (QTL) and genome-wide association studies (GWAS), have been used to understand genotype–phenotype relationships for egg traits in chickens. Even though these techniques can detect potential genes of major effect, they cannot reveal cryptic causal relationships among QTLs and phenotypes. Thus, to better understand the relationships involving multiple genes and phenotypes of interest, other data analysis techniques must be used. Here, we utilized a QTL-directed dependency graph (QDG) mapping approach for a joint analysis of chicken egg traits, so that functional relationships and potential causal effects between them could be investigated. The QDG mapping identified a total of 17 QTLs affecting 24 egg traits that formed three independent networks of phenotypic trait groups (eggshell color, egg production, and size and weight of egg components), clearly distinguishing direct and indirect effects of QTLs towards correlated traits. For example, the network of size and weight of egg components contained 13 QTLs and 18 traits that are densely connected to each other. This indicates complex relationships between genotype and phenotype involving both direct and indirect effects of QTLs on the studied traits. Most of the QTLs were commonly identified by both the traditional (single-trait) mapping and the QDG approach. The network analysis, however, offers additional insight regarding the source and characterization of pleiotropy affecting egg traits. As such, the QDG analysis provides a substantial step forward, revealing cryptic relationships among QTLs and phenotypes, especially regarding direct and indirect QTL effects as well as potential causal relationships between traits, which can be used, for example, to optimize management practices and breeding strategies for the improvement of the traits. [ABSTRACT FROM AUTHOR]

Since the growth traits of chickens are largely related to the production of meat and eggs, it is definitely important to understand genetic basis of growth traits. Although many quantitative trait loci (QTLs) that affect growth traits have recently been reported in chickens, little is known about genetic architecture of growth traits across all growth stages. Therefore, we conducted a longitudinal QTL study of growth traits measured from 0 to 64 weeks of age using 134 microsatellite DNA markers on 26 autosomes from 406 F2 females, which resulted from an intercross of Oh-Shamo and White Leghorn chicken breeds. We found 27 and 21 independent main-effect QTLs for body weight and shank length, respectively. Moreover, 15 and 4 pairs of epistatic QTLs were found for body weight and shank length, respectively. Taken together, the present study revealed 48 QTLs for growth traits on 21 different autosomes, and these loci clearly have age-specific effects on phenotypes throughout stages that are important for meat and egg productions. Approximately 60% of Oh-Shamo-derived alleles increased the phenotypic values, corresponding to the fact that Oh-Shamo traits were higher than those of White Leghorn. On the other hand, remaining Oh-Shamo alleles decreased the phenotypic values. Our results clearly indicated that the growth traits of chickens are regulated by several main and epistatic QTLs that are widely distributed in the chicken genome, and that the QTLs have age-dependent manners of controlling the traits. This study implies importance of not only cross-sectional but also longitudinal growth data for further understanding of the complex genetic architecture in animal. [ABSTRACT FROM AUTHOR]

Background: Japanese indigenous chicken breeds are often used to improve meat quality rather than broilers in the Jidori industry. There are sometimes severe crowding accidents caused by many birds frightened by environmental stimuli. To prevent the economic loss, the chickens need to be more gentle, tame, and imperturbable. Methods: In this study, a new handling test for tameness in adult chickens in individual cages was performed with 100 birds from each sex of Shamo, Rhode Island Red, Nagoya, Australorp, and Ukokkei, as well as 10 hens of F1 hybrid between Shamo and Rhode Island Red, to measure both active and passive tameness. We counted the number heading toward human hands (heading) and retreating in other directions (avoiding) in both active and passive tameness phases, as well as the number of steps taken (step) during the handling test. Results: Male chickens exhibited higher avoidance behavior than females. Nagoya females displayed the lowest level of avoidance behavior, which implies passive tameness. In terms of active tameness, a variety of phenotypes can be obtained in different combinations of breed and sex. These results suggested the handling test will be good method for rapid screening of individual differences in tameness. In addition, there were heterosis effects on avoidance and locomotive behaviors. Since F1 is often used in the Jidori industry, the breeders should be tested not only for meat production but also for tameness. Conclusions: In the future, combining both the behavioral screening and the population genomics will establish typical evidence about mechanisms of tameness and domestication in animals. [ABSTRACT FROM AUTHOR]