This study was conducted to detect polymorphisms in intron 1 of porcine POU1F1 (POU domain, class 1, transcription factor 1, Pit 1, renamed as POU1F1) by comparative sequencing. Within the intron, 23 sites of variation were identified, including 16 single-nucleotide substitutions, 4 single-nucleotide indels, 2 short (3-bp and 17-bp), and one long (313-bp) indels. Several important regulatory motifs were found within the 313-bp indel by in silico analysis. The 313-bp indel was next genotyped in 11 Chinese native pig breeds and 4 western meat-type pig breeds. The appearance of genotypes varied between breeds: among Chinese native breeds, no AA and AB genotypes were found in Tibetan, Lingao, Min, Rongchang, and Songliao Black pigs, no AA genotype was found in Fenjing and Leping Spotted pigs, whereas in Pietrain and Landrace there were no BB genotypes, and all 19 Duroc pigs were A A homozygotes. The western meat-type pigs had high A allele frequencies and the Chinese pigs had more B alleles, except Jianquhai pigs. A positive association of the AA genotype with birth weight was observed in a commercial pig line. This paper demonstrated that the genetic variation in intron 1 of the pig POU1F1 gene was high and these polymorphisms may provide useful makers for QTL analysis.
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