In order to determine the effect of transposons on the sequence and structural variations of the porcine ktn1 gene and its flanking regions, we obtained 14 ktn1 sequences (including genic region, 5-kb 5′ flank and 3-kb 3′ flanking regions) from the WGS database in NCBI, multiple sequence alignment by ClustalX and transposon annotation by RepeatMasker. Then we analyzed the effect of transposons on ktn1. A SINEA1 insertion polymorphism was detected by PCR, and correlation was analyzed with related traits in the Sujiang pig population. The ktn1 gene and its flanking regions contained at least 77 transposon fragments, the majority (98.70%) of which was SINE insertions. We observed 9 small structural variations and 4 large structural variations caused by transposons, indicating that transposons were an important source of genetic variations. One of the structural variations caused by SINEA1 insertion polymorphism showed rich polymorphism in different breeds, and in Sujiang pigs, the weaned litter weight of non-inserted individuals (SINE-/-) ((64.20±10.6) kg) was lighter than homozygous insertionindividuals (SINE+/+) ((74.14±9.0) kg) and heterozygous insertion individuals (SINE+/-) ((69.71±7.7) kg) (P<0.05). It is feasible to develop molecular marker based on the transposon insertion polymorphism to provide application potential in molecular-assisted breeding.