Whole-Genome Insights into the Genetic Basis of Conformation Traits in German Black Pied (DSN) Cattle

Abstract

Background: The German Black Pied Dairy (DSN) cattle is an endangered dual-purpose breed considered an ancestor of the modern Holstein population. DSN is known for its high milk yield, favorable milk composition, and good meat quality. Maintaining a functional body structure is essential for ensuring sustained performance across multiple lactations in dual-purpose breeds like DSN. This study aims to identify candidate genes and genetic regions associated with conformation traits in DSN cattle through genome-wide association studies (GWAS).

Methods: The analysis utilized imputed whole-genome sequencing data of 1852 DSN cows with conformation data for 19 linear traits and four composite scores derived from these traits. GWAS was performed using linear mixed models.

Results: In total, we identified 118 sequence variants distributed across 24 quantitative trait locus (QTL) regions comprising 74 positional candidate genes. Among the most significant findings were variants associated with "Rump width" on chromosome 21 and "Teat length" on chromosome 22, with AGBL1 and SRGAP3 identified as the most likely candidate genes. Additionally, a QTL region on chromosome 15 linked to "Central ligament" contained 39 olfactory receptor genes, and a QTL region on chromosome 23 associated with "Hock quality" included eight immune-related genes, notably, BOLA and TRIM family members.

Conclusions: Selective breeding for favorable alleles of the investigated conformation traits may contribute to DSN's longevity, robustness, and overall resilience. Hence, continuous focus on healthy udders, feet, and legs in herd management contributes to preserving DSN's positive traits while improving conformation.

Keywords: conservation; dual-purpose cattle; endangered cattle breed; genome-wide association study (GWAS); whole-genome sequencing (WGS).

Figure 1

Genome-wide association results for LIN_{DAIRY_CHARACTER} on chromosome 20 in DSN cattle. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant rs381893684 at position 21,627,470 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.

Figure 2

Genome-wide association results for LIN_{RUMP_WIDTH} on chromosome 21. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant rs210390204 at 17,993,077 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.

Figure 3

Genome-wide association results for LIN_{RUMP_ANGLE} on chromosome 26. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant rs110956215 at 21,470,978 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.

Figure 4

Genome-wide association results for LIN_{REAR_LEG_SIDE} on chromosome 20. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant at 29,327,008 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.

Figure 5

Genome-wide association results for LIN_{HOCK_QUALITY} on chromosome 23. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant rs800639948 at 28,684,391 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.

Figure 6

Genome-wide association results for LIN_{CENTRAL_LIGAMENT} on chromosome 15. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant at 50,014,862 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.

Figure 7

Genome-wide association results for LIN_{TEAT_LENGTH} on chromosome 22. (A) Manhattan plot displaying the genomic positions versus the significance of genetic variants. The horizontal lines represent Bonferroni-corrected thresholds for genome-wide significance (red, p < 0.05) and suggestive association (blue, p < 0.1). (B) Regional association plot highlighting a detailed region around the significant locus, showing positional candidate genes. (C) Variant effect plot illustrating genotype-specific phenotypic effects for the top variant rs378674848 at 17,411,573 bp. Additionally, p-values between genotype groups and the number of animals in each genotype group are provided.