Novel genotyping assay for a 212-kb deletion from the BBS9 gene, and frequency of the allele in pig populations in Vietnam

Piglet lethality is one of the major concerns in pig breeding programs. Deletion of a 212-kb region within the Bardet-Biedl syndrome 9 (BBS9) gene has been linked to a reduction in the number of piglets born alive per litter. The BBS9 mutant gene carrier-by-carrier mating scheme could result in mummification of piglets carrying 2 copies of the BBS9 mutant allele, which ultimately affects the reproductive performance of the sow. Our aim was to develop a simple, rapid, and cost-efficient method that could be applied in a BBS9 mutant gene carrier screening program in low- and middle-income countries within basic laboratory settings. Here, we report an optimized multiplex PCR assay that we have established successfully for detection of a 212-kb deletion within the BBS9 genomic sequence. We genotyped 420 animals from Yorkshire, Duroc, and Landrace purebred populations in Vietnam. We found that while the BBS9 mutant allele was not identified in Duroc pigs, the frequency of BBS9 carriers was 10% in both Yorkshire and Landrace populations. We subsequently validated our results using Sanger sequencing. Our multiplex PCR method could be utilized as a BBS9 screening test in pig breeding programs.