Novel genotyping assay for a 212-kb deletion from the <i>BBS9</i> 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 (<i>BBS9</i>) gene has been linked to a reduction in the number of piglets born alive per litter. The <i>BBS9</i> mutant gene carrier-by-carrier mating scheme could result in mummification of piglets carrying 2 copies of the <i>BBS9</i> 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 <i>BBS9</i> 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 <i>BBS9</i> genomic sequence. We genotyped 420 animals from Yorkshire, Duroc, and Landrace purebred populations in Vietnam. We found that while the <i>BBS9</i> mutant allele was not identified in Duroc pigs, the frequency of <i>BBS9</i> 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 <i>BBS9</i> screening test in pig breeding programs.