Genome-Wide Association Study of Body Size Traits in Luning Chickens Using Whole-Genome Sequencing

Growth traits are crucial for poultry breeding and production. Marker-assisted selection (MAS) and genomic selection (GS) of growth traits require a substantial number of accurate genetic markers. A genome-wide association study (GWAS) for body size traits was performed on 248 Luning chickens to identify significant single-nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) related to the growth and development of chickens. A total of 30 significant SNPs and 13 INDELs were obtained for body size traits. Two notable regions, spanning from 43.072 to 43.219 Mb on chromosome 1 and from 4.751 to 4.800 Mb on chromosome 11, were found to be significantly associated with growth traits in the GWAS of both SNPs and INDELs. Some genes, including <i>PPFIA2</i>, <i>KITLG</i>, <i>DUSP6</i>, <i>TOX3</i>, <i>MTNR1B</i>, <i>FAT3</i>, <i>PTPRR</i>, <i>VEZT</i>, <i>BBS9</i>, and <i>CYLD</i>, were identified as important candidate genes for the growth of chickens. The results provide valuable information for understanding the genetic basis of growth traits which is beneficial for the subsequent selective breeding in Luning chickens.