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Updated: Feb 28, 2026

Quantification of Circulating Pig-Specific DNA in the Blood of a Xenotransplantation Model
Published on: September 22, 2020
De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of
Jiaolong Wen1,2, Haiqi Qiu1, Shaoxiong Deng1
1National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Abstract:
The Duroc × (Landrace × Yorkshire) (DLY) pig is a cornerstone of three-way crossbreeding system. Nevertheless, advances in commercial crossbred performance have been constrained by the dearth of high-resolution genomic resources for this key population. Here, we report the sequencing and assembly of 16 haplotype-resolved, chromosome-level genome assemblies derived from eight DLY pigs. These assemblies exhibited high continuity (contig N50: 18.17-29.54 Mb) and completeness (BUSCO: 99.3-99.4%), with sequences successfully localized to the 19 chromosomes. Genome annotation revealed an average of 21,922 protein-coding genes and 44.66% repetitive sequences per assembly. Comparative genomic analysis against the current reference genome Sscrofa11.1 enabled the construction of a non-redundant SV catalog comprising 130,416 variants, nearly half of which (48.99%) were novel relative to existing pig pan-genome SV panel. These SVs clustered non-randomly into 231 "SV hotspots" that were significantly enriched in protein-coding genes and putative regulatory elements. Functional analyses further linked these SV hotspots to quantitative trait loci (QTLs) associated with economically important traits. A focused analysis of a 3.43 Mb hotspot on chromosome 1, overlapping a known QTL for average daily gain, revealed eight high-frequency SVs in open chromatin regions near candidate genes (NCS1, HMCN2, FUBP3, ABL1, and FIBCD1), suggesting a cis-regulatory mechanism that may influence gene expression. Collectively, this work provides the first haplotype-resolved genomic resource for commercial crossbred pigs, and establishes a foundational framework for deciphering the genomic architecture of hybrid vigor and advancing precision breeding in swine.
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