Genome-wide Association Study For Porcine Ear Morphology And Research Of The Important Candidate MSRB3

Ear morphology is an important characteristic of some pig breeds, which plays an indispensable role in the identification of pig varieties. However,only a few researches about gene mapping for porcine ear morphology were carried out. In this study, in order to mapping the ear-morphology QTL, Genome-wide association study(GWAS) was performed with an Illumina Porcine SNP 60 K DNA chip in a Large White × Minzhu F2 resource population. Furthermore, fine mapping was carried out to refine the QTL interval. In addition, MSRB3, a very important candidate for ear morphology, was further studied by rapid-amplification of c DNA ends(RACE), bioinformatics analyses, quantitative real time PCR(q PCR) and single nucleotide polymorphisms(SNPs) detection. Major contents in this research are as follows.The genome-wide rapid association using the mixed model and regression-genomic control(GRAMMAR-GC) method was used to perform a GWAS on ear morphology in 552 pigs from F2 population. As a result, a total of 23 SNPs were identified to be significantly associated with ear morphology in a 5.8Mb interval on SSC5 and the most significant SNP(ASGA0025237) was located within WIF1. Further, a reduced region of 639 kb, which only contains 3 annotated genes, WIF1, LEMD3 and MSRB3, was obtained by using marker-assisted segregation analysis(MASS), identical by descent(IBD) analysis and haplotype analysis.A full length c DNA sequence of porcine MSRB3 was cloned by RACE. The c DNA is composed of 3765 bp which has got the accession number of Gen Bank database,KP772260. The sequence contains a 5′ untranslated regions(UTR) of 189 bp, an open reading frame(ORF) of 552 bp which encodes a protein of 183 amino acids, and a 3′- UTR of 3017 bp. Porcine MSRB3 c DNA sequence and amino acid sequence shared 70%-87% and 67-91% identities with those of human, orangutan, mouse, chicken and zebrafish respectively. Sel R domain, containing a site binding zinc which is indispensable for MSRBs catalysis and structure, was predicted by SMART. Porcine MSRB3 was moderately expressed in ear. Relative m RNA abundance was highest in muscle while that was lowest in lymph. A total of 8 single nucleotide polymorphisms(SNPs) were identified, one in the 3′-UTR, one in the ORF which was a synonymous mutation and others in the promotor sequence. c.-1750A>T was located in a predicted promoter. This research make a solid foundation for the further study of MSRB3.In present study, MSRB3 was identified as an outstanding candidate for porcine ear morphology by GWAS and fine mapping. This is beneficial to explore the major ear-morphology gene and provide an assistant method to identify swine breeds.