Pangenomes

Identification and characterization of structural variants using long reads sequencing in the Windsnyer and Kolbroek indigenous pigs

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Abstract

Pigs are an important source of animal protein and play a significant role in supporting food security and local farming systems in South Africa. However, the indigenous Kolbroek and Windsnyer breeds remain insufficiently studied, limiting genetic improvement efforts and increasing the exposure to genetic erosion, particularly due to indiscriminate crossbreeding and the widespread use of commercial breeds. These indigenous pigs are well adapted to hardy and harsh conditions of South Africa, and this unique adaption underscores the need to better understand their genetic differences for effective conservation strategies. This study applied PacBio HiFi long-read sequencing complemented by Illumina Novaseq 6000 Omni-C data, to generate chromosomal level assemblies for identifying structural variants (SVs) in Kolbroek and Windsnyer genomes and comparing them with publicly available Duroc, Large White and Landrace genomes. Genome coverage and average read length were 30X and 10 kb for Windsnyer and 31X and 12 kb for Kolbroek, while the Sus scrofa 11.1 reference genome and the Duroc, Large White and Landrace were generated at 65X, 110X, 25X and 44X coverage, respectively. Assemblies were aligned to the Sus scrofa 11.1 reference genome using Minimap2 and structural variants were identified using svim-asm. Structural variant data were filtered, standardised to autosomal and X chromosomes, and integrated across breeds to generate a unified presence-absence matrix for comparative analyses. The assembled genomes showed high quality and completeness (2.5-2.6 Gb) with BUSCO completeness of 98.9-99.4%. Insertions (53.3-59.2%) and deletions (40.3-46.2%) were the dominant SV classes. Fisher's exact testing confirmed significant enrichment of deletions in genic regions (p < 2.2 x 10-16; OR = 3.18). Windsnyer and Kolbroek had the highest SV densities (18.02 and 17.69 SVs/Mb), while Duroc showed the lowest. Landrace and Large White clustered closely, whereas Windsnyer and Duroc were the most structurally divergent breeds. Most SVs were shared across breeds (41.7%), with Windsnyer showing highest proportion of private variants. Small variants (< 1 kb) accounted for 89-96% of all SVs, highlighting short indels as the dominant source of structural diversity. Kolbroek shared 3,937 SVs with Windsnyer, supporting intermediate ancestral connectivity. Structural variant gene intersection analysis identified 293 SVs overlapping 1,962 genes associated with reproduction (TEX14, RBFOX1), growth (PRDM16, PIK3R4), carcass traits (NAV2, LAMB4) and immunity (ITK, CUBN). In summary, the current results indicates that indigenous breeds exhibited distinct structural variation profiles compared to commercial pigs, reflecting their unique evolutionary history and adaptation to local environments. These findings highlight the importance of indigenous pig genetic resources for conservation and their potential contribution to breeding strategies aimed at improving resilience and productivity under low-input production systems.

Keywords: Indigenous pigs, long read sequencing, genomic variation, comparative genomics, genetic improvement

How to Cite:

Hlongwane, N., Smith, R., Mdyogolo, S., Nesengani, L., Molotsi, A., Tshilate, T., Hadebe, S., Masebe, T. & Mapholi, N., (2026) “Identification and characterization of structural variants using long reads sequencing in the Windsnyer and Kolbroek indigenous pigs”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1). doi: https://doi.org/10.31274/wcgalp.25477