Identification Of QTL For Pig Small Intestine Length Using A Genome-wide Association Study

Small intestine is an important digestive organ. The length of pig small intestine wassignificantly correlated with traits related to growth, fat deposition and feed conversionrate that are of economic importance. In previous study, we analyzed the small intestinallength and60K genotyping data from the White Duroc×Erhualian F2resourcepopulation (N=1034) and sutai population(N=276), and identified genetic loci onchromosome4and7chromosomes that are significantly associated with intestine length.In order to further investigate genetic architecture of small intestine length, we measuredsmall intestine length of157sutai pigs. and1259pigs from3other experimentalpopulations including Duroc-Landrance-Large white hybrid pigs, Laiwu and Erhualianpurebred pigs. We compared average small intestine length among experimentalpopulations under study, we found that Chinese indigenous pigs generally have intestinelength3.6-5.9meters shorter than those of Western pigs. Under the same feeding andbutchering stage, the intestine length of Laiwu pigs was significantly longer than that ofErhualian pigs. We also found that small intestine length was significantly and positivelycorrelated with growth traits such as daily weight gain and fat deposition, this result agreewith previous studies. The large difference of small intestine length among populationscould be results of different nature and artificial selection on these pig populations. Wecalculated the heritability of small intestine length for the5populations based on60K SNPdata ranged from0.3to0.64.We performed genome-wide association analysis (GWAS) ineach experimental population. For sutai pigs, the sample size increased from276to433,we found the GWAS signals on chromosome5became more significant. InDuroc-Landrance-Large white hybrid pigs, Laiwu and Erhualian purebred pigs, we found3suggestive significance in chromosome4, and X. Among these, the region aroundMARC0006524on chromosome4, ASGA0103288on chromosome X achieved genomewide significance. We next conducted a GWAS meta analysis on the five experimentalpopulations,the results shown that association signatures on chromosome4,5and7became more significant. This indicated that two or more populations could share the same functional variants for the small intestine length. We searched for candidate genes near thesignificant loci in public database, and found that the PLAG1on chromosome4and GLI1on chromosome5have potential role in regulating small intestine length.This study illustrated the intestine length is significantly different among differentpopulations. Intestine length associated with many growth traits. GWAS in differentpopulations evidence that there are several genetic loci to influence small intestine lengthand these loci has population specific. This work provided further insight into the geneticbasis underlying variation of intestine length of pigs, and identified potential candidategenes for following up studies.