Gene function & annotation

Investigation of the Swine Leukocyte Antigen Complex in PCV2 susceptibility

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Abstract

Our previous research using in vivo and in vitro infection models demonstrated that host-genetics plays an important role in the susceptibility to Porcine Circovirus type 2 (PCV2). Our piglet infection model included maternal hybrids (Large White x Landrace) originated from 14 lines and 7 genetic programs. A major Quantitative Trait Locus (QTL) affecting PCV2 viremia was mapped on chromosome (chr.) 7 in the Swine Leukocyte Antigen Complex (SLA). This region is rich in genes involved in immunity, high genetic diversity, and linkage disequilibrium. Currently, no sources of the differences in PCV2 susceptibility attributed to SLA have been identified. Some reasons for the limited progress include reliance on a single individual-based reference genome, inaccurate assembly of a complex region that harbors substantial genetic diversity and structural variation. These issues could be addressed by long-read sequencing to capture structural variation and highly polymorphic genes, de novo assembly and functional annotation using germplasm tailored to measures of PCV2. Genomic DNA of a maternal hybrid sow was sequenced using Oxford Nanopore Technology (ONT) PromethION P2 Solo. We obtained 10.1 million reads, with the N50 statistic of 28.43 kb, and a coverage of 36.59-fold. De novo assembly was carried out with hifiasm, a haplotype-resolved assembler that employs a fast error correction algorithm to overcome the higher error rate of ONT reads. Following the assembly, there were 526 and 421 contigs generated for the chromosomal haplotypes (maternal/paternal) and 182 contigs for the primary assembly. Each of the SLA class regions (I, II, III) were completely assembled with a centromeric gap of 66.5 kb. Alignment of the assembled haplotypes to the reference genome uncovered 45,541 SNPs, 286 small indels, and 22 structural variations (56 to 36,361 bp). The quality of the ONT data is exemplified by the clearly defined parental SLA's DQB1 gene haplotypes (DQB1*06/DQB1*07). Alignment of SowPro91 SNPs, a genotyping array enriched in SLA variants, to chr. 7 assembled contigs, uncovered 27 SNPs (out of 8,977 SNPs), subjected to rearrangements, an issue that could impact QTL mapping. A genome-based association based on adjusted robust SNP mapping was conducted using BayesIM haplotype model (lambda=7kb; MAF >0.15) and SowPro91 genotypes of the pigs that represent the tails (n=391) of the distribution for PCV2b viral load. The largest effect was observed at the proximal end of SLA on chr. 7 (model freq. >0.05) close to genes involved in immune response. However, the exclusive use of genotyping arrays will limit the discovery effort, missing structural variation and genome rearrangements observed in this preliminary study. As a result, we expected that expanding long-read sequencing and de novo genome assembly tailored to pigs with extreme response to PCV2 will provide critical information on the role of this region in viral disease susceptibility.

Keywords: 2026

How to Cite:

Ciobanu, D., Kachman, S. & Wijesena, H., (2026) “Investigation of the Swine Leukocyte Antigen Complex in PCV2 susceptibility”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283593. doi: https://doi.org/10.31274/wcgalp.23505

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