SNP (single nucleotide polymorphism) chips were applied to screen the candidate genes linked with anorectal malformation,and the Fibronectin1 (FN1) gene on porcine chromosome 15 was captured as a candidate gene.By direct sequencing using the cDNA pools,we obtained the porcine FN1 mRNA sequence with a 7 437 bp ORF,encoding 2 478 aa.And 21 SNPs as well as three regions subject to alternative splicing were also identified.Of these SNPs,two (148 A>G in exon 22,50 G>C in exon 27) were non-synonymous (1 167Ile>Val,1435Glu-Asp).PCR-RFLP analysis of these two SNPs suggested that the allele and genotype frequencies in the AA pigs and unaffected pigs were different (P<0.05).Therefore,FN1 mutations may affect the normal development of anorectal process,but the result need to be further verified.