Identification of quantitative trait locus and positional candidate loci influencing chicken egg quality under tropical conditions.

Egg quality is a vital factor in the poultry industry. High-quality eggs not only meet consumer expectations for appearance, taste, and nutritional value but also have high marketability, profitability, and consumer satisfaction. Accordingly, we executed our research with the purpose of determining chromosomal regions and genetic markers associated with egg quality in an F2 cross-bred chicken population under tropical conditions; we determined these through a genome-wide association study and quantitative trait locus (QTL) mapping. This population was created by cross-breeding the L2 line of Taiwan Country chickens, which is adapted to local conditions in Taiwan, with an experimental line (R-line) of Rhode Island Red layer chickens, which was developed by the French National Research Institute for Agriculture, Food and the Environment. A 60 K single nucleotide polymorphism (SNP) genotyping array for chickens was employed to execute the analysis. Our analysis revealed 40 QTLs associated with egg quality under tropical conditions, namely 20 QTLs with genome-wide statistical significance and 20 QTLs with chromosome-wide statistical significance. Furthermore, we identified 93 SNPs exerting discernible effects on egg quality, with 10 of these effects exhibiting genome-wide significance and 83 exhibiting potential significance. The majority of the detected QTL regions and SNPs agreed with those identified as having an association with egg quality or production traits in previous studies, thus supporting the interrelationships determined between the studied characteristics. The findings of this study enhance the understanding regarding the genetic regulation governing chicken egg quality, thereby serving as a valuable reference for future functional investigations.