Molecular characterization and genome-wide mutations in porcine anal atresia candidate gene GLI2

Molecular characterization and genome-wide mutations in porcine anal atresia candidate gene GLI2 Anal atresia (i.e., anorectal malformations) is a severe disorder that occurs during the development of the distal hindgut in infants, swine, and many other mammals and has an unclear genetic background. Recently, the Shh-responsive transcription factor GLI2 has been shown as essential to the normal development of the hindgut, and QTL studies in pigs revealed that this gene may be an important candidate for anal atresia (AA). We used the pig as the model to study the contribution of GLI2 to AA. We revealed the genomic structure of the porcine GLI2 gene with 14 exons and obtained the porcine GLI2 mRNA sequence with a 4,656-bp ORF coding a 1,551-amino acid protein. We further scanned the genome-wide mutations in this gene by direct sequencing using three genomic DNA pools from the AA pigs, full-sibs of AA pigs, and unaffected pigs, respectively. Finally, 30 single nucleotide polymorphisms (SNPs) and one intronic 9-nucleotide (nt) deletion were identified. Of these SNPs, 23 are intronic, 6 are synonymous, and 1 (446 G>A) in exon 8 is nonsynonymous (365Met >Ile). NCOI-RFLP of the 446 G>A polymorphism suggested that the predominant genotypes were all GG and AG in the three pig groups. In addition, there was no significant difference among the three groups in allele frequencies, which demonstrated that this locus was not associated with AA in pigs. However, the 12 SNPs encompassing exon 4 to exon 8 showed strong linkage disequilibrium in the AA pigs, which indicated that the mutations somewhere in this region may contribute to AA in pigs. Therefore, further investigation in this region is needed to elucidate the underlying mutations involved in the porcine AA. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Mammalian Genome Springer Journals

Molecular characterization and genome-wide mutations in porcine anal atresia candidate gene GLI2

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Publisher
Springer US
Copyright
Copyright © 2013 by Springer Science+Business Media New York
Subject
Life Sciences; Cell Biology; Anatomy; Zoology
ISSN
0938-8990
eISSN
1432-1777
D.O.I.
10.1007/s00335-013-9485-8
Publisher site
See Article on Publisher Site

Abstract

Anal atresia (i.e., anorectal malformations) is a severe disorder that occurs during the development of the distal hindgut in infants, swine, and many other mammals and has an unclear genetic background. Recently, the Shh-responsive transcription factor GLI2 has been shown as essential to the normal development of the hindgut, and QTL studies in pigs revealed that this gene may be an important candidate for anal atresia (AA). We used the pig as the model to study the contribution of GLI2 to AA. We revealed the genomic structure of the porcine GLI2 gene with 14 exons and obtained the porcine GLI2 mRNA sequence with a 4,656-bp ORF coding a 1,551-amino acid protein. We further scanned the genome-wide mutations in this gene by direct sequencing using three genomic DNA pools from the AA pigs, full-sibs of AA pigs, and unaffected pigs, respectively. Finally, 30 single nucleotide polymorphisms (SNPs) and one intronic 9-nucleotide (nt) deletion were identified. Of these SNPs, 23 are intronic, 6 are synonymous, and 1 (446 G>A) in exon 8 is nonsynonymous (365Met >Ile). NCOI-RFLP of the 446 G>A polymorphism suggested that the predominant genotypes were all GG and AG in the three pig groups. In addition, there was no significant difference among the three groups in allele frequencies, which demonstrated that this locus was not associated with AA in pigs. However, the 12 SNPs encompassing exon 4 to exon 8 showed strong linkage disequilibrium in the AA pigs, which indicated that the mutations somewhere in this region may contribute to AA in pigs. Therefore, further investigation in this region is needed to elucidate the underlying mutations involved in the porcine AA.

Journal

Mammalian GenomeSpringer Journals

Published: Nov 10, 2013

References

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