Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes

Abstract

Meat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line B) and slow-growing, yellow-feathered chickens (Jingxing Yellow), which have significant differences in meat color. The differentially expressed genes (DEGs) between Line B and Jingxing Yellow were identified in beast muscle. The fixation index (FST) method was used to detect signatures of positive selection between the two breeds. Screening of 1109 genes by the FST and 1317 candidate DEGs identified by RNA-seq. After gene ontology analysis along with the Kyoto Encyclopedia of Genes and Genomes, 16 genes associated with glycolysis, fatty acid metabolism, protein metabolism, and heme content were identified as candidate genes that regulate the color of chicken breast meat, especially TBXAS1 (redness), GDPD5 (yellowness), SLC2A6 (lightness), and MMP27 (lightness). These findings should be helpful for further elucidating the molecular mechanisms and developing molecular markers to facilitate the selection of chicken meat color.