The Identification of a Novel Transcript Variant of Chicken Lmbr1 and the Sequence Variation Analysis

Abstract

Lmbr1 has been reported to be associated with chicken polydactyly and carcass traits. Based on the hypothesis that chicken Lmbr1 should have multiple alternative splices as human and mouse Lmbr1/C7orf2, we successfully identified one novel chicken Lmbr1 transcript variant (designated as Lmbr1-2) by bioinformatics analysis and RT-PCR confirmation. Chicken Lmbr1-2 transcript was predicted to encode a 30 amino acid protein. Lmbr1-2 transcript was ubiquitously expressed in a range of chicken tissues. A SNP (rs14135851: G>T, also named as 288G>T reference to 603234777F1) was found to be located at the 5′ boundary (first base) of alternatively spliced exon (IN2) of chicken Lmbr1-2. Eight variants/10 haplotypes were detected from 4 breeds in a 300-bp genomic fragment surrounding 288G>T. The 288T>G and 331G>A changes were predicted resulting to the formation/loss of SRSF5 and SRSF6 motifs. The genotype/allele distribution for a G/A variant (331G>A, reference to 603234777F1) and haplotype types in polydactylous Silkie presented distinct difference with that in other four-toed breed chickens. Association analysis showed that chicken 331G>A variation had significant effect on meat quality traits including breast muscle water loss rate, leg muscle water loss rate and leg muscle fiber density, and carcass traits including evisceration weight, pancreas weight in Gushi chicken F₂ resource population. These data demonstrated that chicken Lmbr1 was alternatively spliced to produce multiple splice forms as was the case in mammals, and it suggested that chicken Lmbr1-2 variation might have important effect on the carcass and meat quality traits in chicken.