Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality

Abstract

Background: Mongolian cattle, a unique breed indigenous to China, represent valuable genetic resources and serve as important sources of meat and milk. However, there is a lack of high-quality genomes in cattle, which limits biological research and breeding improvement.

Findings: In this study, we conducted whole-genome sequencing on a Mongolian bull. This effort yielded a 3.1 Gb Mongolian cattle genome sequence, with a BUSCO integrity assessment of 95.9%. The assembly achieved both contig N50 and scaffold N50 values of 110.9 Mb, with only 3 gaps identified across the entire genome. Additionally, we successfully assembled the Y chromosome among the 31 chromosomes. Notably, 3 chromosomes were identified as having telomeres at both ends. The annotation data include 54.31% repetitive sequences and 29,794 coding genes. Furthermore, a population genetic variation analysis was conducted on 332 individuals from 56 breeds, through which we identified variant loci and potentially discovered genes associated with the formation of marbling patterns in beef, predominantly located on chromosome 12.

Conclusions: This study produced a genome with high continuity, completeness, and accuracy, marking the first assembly and annotation of a near telomere-to-telomere genome in cattle. Based on this, we generated a variant database comprising 332 individuals. The assembly of the genome and the analysis of population variants provide significant insights into cattle evolution and enhance our understanding of breeding selection.

Keywords: Mongolian cattle; beef quality; near telomere-to-telomere genome; population genetic variation.

Figure 1:

(A) Morphological photograph of Mongolian cattle. (B) Hi-C chromatin interaction map of the Mongolian cattle assembly, with chromosomes presented from top to bottom and from left to right, representing Chr1 to Chr29, ChrX.

Figure 2:

(A) The pairwise genome alignments of the Mongolian genome and the Hereford cattle genome are displayed. (B) Bar chart illustrating the BUSCO assessment of the Mongolian cattle genome. (C) The circos plot of the Mongolian cattle genome assembly. The rings from outside to inside indicate (a) chromosomes of the Mongolian genome, (b) GC density, (c) gene density, and (d) repeat density; b–d were drawn in 100-kb sliding windows.

Figure 3:

(A) Bar chart depicting the number and proportion of various variations in cattle. Among them, nSNPs account for 101,612,545 (88%), nInsertions for 4,899,369 (4.2%), nDeletions for 5,408,006 (4.7%), nComplex for 1,532,156 (1.3%), and nMixed for 1,980,238 (1.7%), with the remainder being zero. (B) Distribution of SNPs on chromosomes.

Figure 4:

(A) Manhattan plot of the variant sites from the comparative analysis between Mongolian cattle and Wagyu. (B) Manhattan plot of the variant sites the comparative analysis between Wagyu and other beef cattle. (C) GWAS analysis of beef cattle populations using GLM and MLM models.