Sequencing & Pangenomes

Huaxi cattle reference genome: Integrating structural variation to enhance association mapping and genomic prediction for economic trait

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Abstract

Constructing a high-quality genome for Huaxi cattle is a critical foundation for exploring the relationships between genetic variation and phenotypic traits. In this study, we de novo assembled a chromosome-level genome of Huaxi cattle using 41à— PacBio HiFi reads combined with 100x coverage of Hi-C data. The genome size is 3.06 Gb, with a Contig N50 of 99.52 Mb, and 24 chromosomes were fully assembled. Using the de novo assembly as a reference, we constructed a reference panel based on whole-genome resequencing (WGS) of 218 Huaxi cattle. This panel was used to perform genotype imputation for 5,193 Huaxi cattle genotyped with Illumina BovineHD BeadChips, achieving an average imputation accuracy of 0.96. We further integrated 20à— PacBio HiFi sequencing data from eight individuals to characterize the structural variation (SV) landscape, identifying a total of 119,243 insertions and deletions. The linkage disequilibrium (LD) between SVs and SNPs was relatively low (average r2=0.28), indicating that most SNPs do not fully capture SV information. We then performed a genome-wide association study (GWAS) using a Mixed Linear Model (MLM) for 46 economically important traits to identify putative functional variants and candidate genes. The phenotypic correlations ranged from −0.323 (lung with trachea and spleen weight) to 0.986 (lean meat and carcass weight). The GWAS revealed 1,258 significant SNPs and 846 SVs at the Bonferroni-corrected threshold, with most overlapping known QTLs for live weight, carcass weight, and average daily gain. Notably, a 1,347 bp deletion in the NCAPG gene on chromosome 6 was significantly associated with thigh thickness and hind-leg circumference. Furthermore, a 496 bp insertion in the intergenic region between CHCHD7 and SDR16C5 was significantly associated with knuckle weight, providing valuable targets for future functional investigation. Additionally, we performed genomic best linear unbiased prediction (GBLUP) to evaluate genomic estimated breeding values (GEBVs) using four different loci sets: Illumina BovineHD BeadChip, WGS, SVs, and SNPs from the newly assembled Huaxi cattle genome. The heritability of the traits ranged from 0.06 (Stomach weight) to 0.84 (Carcass chest depth). Results from a 5-fold cross-validation showed that incorporating Huaxi cattle-specific loci into the Illumina BovineHD BeadChip increased GBLUP prediction accuracy by 5.4% - 10.4% compared with using the chip alone. Furthermore, using SVs for GBLUP prediction improved accuracy for traits such as shin weight and striploin weight by approximately 4%. In summary, this study enabled the exploration of SVs for fine-mapping functional variants and to enhance genomic prediction. These findings support precision breeding in Huaxi cattle and contribute to the "Global Cattle Pan-Genome Project." The identified SVs offer promising targets for future validation and practical breeding applications.

Keywords: 2026

How to Cite:

Ge, F., Li, J. & Rosa, G., (2026) “Huaxi cattle reference genome: Integrating structural variation to enhance association mapping and genomic prediction for economic trait”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284091. doi: https://doi.org/10.31274/wcgalp.23548

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