Genome-wide Detection Of Quantitative Trait Loci(QTL) For The Length Of Small Intestine In Pigs

The small intestine is a vital organ in animal gastrointestinal system, in which a large variety of nutrients are absorbed. To identify quantitative trait loci (QTL) for the length of porcine small intestine, phenotypic values were measured in1034individuals at240days from a White-Duroc×Chinese Erhualian intercross F2population. The length of small intestine showed strong correlation with growth traits and carcass length in this population. A whole-genome scan was performed based on183microsatellites covering the pig genome in the F2population. A total of10QTL for this trait were identified on8pig chromosomes (SSC), including four1%genome-wide significant QTL on SSC2,4,7and8, one5%genome-wide significant QTL on SSC12, and five5%chromosome-wide significant QTL on SSC5,7,13and14. The Erhualian alleles were generally associated with shorter length of the small intestine except the alleles on SSC7and13. The QTL on SSC4overlapped with the previously reported QTL for the length of small intestine. Several significant QTL on SSC2,8and12were consistent with previous reports. The significant QTL detected on SSC7was reported for the first time. All QTL identified in this study coincided to the known QTL regions significantly affected the growth traits, supporting the important role of the length of small intestine in pig growth.To refine the location of the above-mentioned QTL, we further genotyped929F2animals from the White Duroc×Erhualian resource population using porcine60K SNP chips. A genome-wide association analysis (GWAS) was performed and a total of18significant regions around18most significant SNP (P<2.68e-7) were evidenced on12chromosomes, namely, SSC1,2,3,4,5,7,8,9,10,11,13and15. Most of the QTL detected by microsatellite markers based linkage analysis were replicated in GWAS, while the significant regions on SSC3,9,10,11and15were detected for the first time. The18significant SNP jointly explained31.5%of the phenotypic variance. We found some interesting candidate genes in the significant regions, e.g., the PLAG1near INRA0014995at78.63Mb on SSC4and HMGA1near MARC0058766at34.55Mb on SSC7are strong candidate genes that are worthwhile for further investigation, given that the two genes reside in the same molecular networks that are enriched for genes related to anatomical structure morphogenesis. Based on the genotypes of the18significant SNPs, we inferred the causal relationship between small intestine length and growth related traits like carcass weight and average daily gain using a likelihood ratio test which compared the likelihood of two reciprocal causal models. The resulting statistics supported that the change of small intestine length can be one of the causatives to variation in growth traits. These findings reflect the complex genetic architecture of porcine small intestine length, and provide a more detailed landscape of genomic regions and candidate genes underlying variation in pig intestine length compared with previous reports.