Identification of long noncoding RNA LOC416755 and its polymorphisms associated with carcass traits in chicken.

Long non-coding RNAs (lncRNAs) are known to regulate skeletal muscle development in mammals, but their roles and potential as genetic markers in chickens remain largely unknown. Carcass traits such as breast muscle weight and body weight are economically important in poultry production. Based on our previous RNA-seq data (accession number PRJNA751251), LOC416755 is differentially expressed between the Soleus (SOL) and Pectoralis major (PEM) in Xinghua (XH) chickens. In this study, we further revealed that LOC416755 was highly expressed in the PEM, localized in the nucleus of chicken primary myoblasts, and progressively upregulated during myoblast differentiation. Nine SNPs were identified within LOC416755. Association analysis revealed that SNP1, SNP2, SNP4, SNP5, and SNP7 were significantly associated with shank length, full-bore weight, breast muscle weight, body weight, and abdominal fat weight (P < 0.05). Linkage disequilibrium analysis defined two haplotype blocks, and haplotype variation within block 2 showed a significant association with shank length. The heterozygous genotype consistently exhibited superior phenotypic values for most associated traits. Collectively, these results suggest a potential role for LOC416755 in skeletal muscle development and highlight its potential as a molecular marker for marker-assisted selection to accelerate breed improvement in chickens.