Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States

Abstract

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise F_ST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.

Keywords: genetic diversity; lowline cattle; population structure.

Figure 1

Sample sizes for the genotyped population grouped by purebred, admixed, and primary breed types (PBT) sub-populations after filtering. Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Purebred cattle were sourced from Web-Interfaced next generation database dedicated to genetic Diversity Exploration (WIDDE) [23] and North Dakota State University Dickinson Research Extension Center (DREC) herd. Admixed cattle, sourced from DREC, included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B, F₁ B × C, and F₁ C × C, where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM.

Figure 2

Attributes of genetic markers retained across populations of cattle by chromosome. Attributes include proportion of markers (P_markers) out of total (n = 11,195) and proportion by chromosome for markers of pairwise genotypic correlation (r²; a measure of linkage disequilibrium) greater than 10% (1) within and (2) across chromosomes.

Figure 3

Median and 95% confidence interval estimates of all primary breed types (PBT) with the pruned marker set (n = 4843) for (A) proportion of polymorphic loci and (B) allelic richness (A_R; bi-allelic markers, rarefraction = 6). Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B, F₁ B × C, and F₁ C × C, where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. The PBT are colored based on breed origin, where origin 1 (Australia) are dark red, origin 2 (United Kingdom) are green, origin 3 (Continental Europe) are dark yellow, and origin 4 (mixed origins) are black.

Figure 4

Median and 95% confidence interval estimates of all primary breed types (PBT) with the pruned marker set (n = 4843) for (A) observed heterozygosity (H_O) and (B) within PBT gene diversity (H_S). Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B, F₁ B × C, and F₁ C × C, where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. The PBT are colored based on breed origin, where origin 1 (Australia) are dark red, origin 2 (United Kingdom) are green, origin 3 (Continental Europe) are dark yellow, and origin 4 (mixed origins) are black.

Figure 5

Median and 95% confidence interval estimates of all primary breed types (PBT) with the pruned marker set (n = 4843) for (A) inbreeding coefficients (F_IS) and (B) fixation indexes (F_ST). Expected levels of heterozygosity (F_IS = 0.00) are shown with a red line in (A). Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B, F₁ B × C, and F₁ C × C, where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. The PBT are colored based on breed origin, where origin 1 (Australia) are dark red, origin 2 (United Kingdom) are green, origin 3 (Continental Europe) are dark yellow, and origin 4 (mixed origins) are black.

Figure 6

Phylogenetic trees with purebred primary breed types (PBT) only (A) or all PBT (C) and their fit (B and D, respectively) using unrooted neighbor-joining estimation methods based on Latter’s F_ST estimates. Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B (F1BB), F₁ B × C (F1BC), and F₁ C × C (F1CC), where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. The PBT are colored based on breed origin, where origin 1 (Australia) are dark red, origin 2 (United Kingdom) are green, origin 3 (Continental Europe) are dark yellow, and origin 4 (mixed origins) are black.

Figure 7

Analysis of molecular variance considering (A) purebred only (n = 8) and (B) all (n = 18) primary breed types (PBT). Corresponding colors between (A,B) are the same level of population strata. Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B, F₁ B × C, and F₁ C × C, where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. Purebred types (PT) stratum (n = 8 or 11 for (A) or (B), respectively) reduced influenced individuals into their respective purebred PBT except for F₁ crosses. Origin stratum grouped PT by country of origin such that AD was labeled as origin 1 (Australia); AN, AR, HH, SH, and F₁ B × B individuals as origin 2 (United Kingdom); GV, LM, SM, and F₁ C × C individuals as origin 3 (Continental Europe); and F₁ B × C as origin 4 (mixed origin). Significance of the observed variance is indicated as * (p < 0.05) and ** (p < 0.005) above the observed variance marker (black segmented diamond).

Figure 8

Three-dimensional visualization of the first four linear discriminant axes (LDA) from discriminant analysis of principal components for purebred only (A,B) and all (C,D) primary breed types (PBT). Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B (F1BB), F₁ B × C (F1BC), and F₁ C × C (F1CC), where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. The PBT are colored based on breed origin, where origin 1 (Australia) are dark red, origin 2 (United Kingdom) are green, origin 3 (Continental Europe) are dark yellow, and origin 4 (mixed origins) are black. The 95% confidence ellipses are shaded regions around a given PBT.

Figure 9

Loading plot of variable contribution per SNP marker by chromosome across four discriminant analyses of principal component axes (LDA; part (A)) and allele frequency by purebred primary breed types (PBT) for nine markers with variable contribution over 0.0025 (B). Markers in the top 2% per LDA are colored by axes with the average threshold across axes as a solid red line (A). Markers above the 0.0025 threshold (blue line) in (A) are presented as proportion of allele 1 (colored) and allele 2 (grey) by population in (B). Colors reflect breed country of origin. Purebred PBT included American Aberdeen (AD, dark red), Angus (AN, green), Red Angus (AR, green), Gelbvieh (GV, yellow), Hereford (HH, green), Limousin (LM, yellow), Shorthorn (SH, green), and Simmental (SM, yellow). The nine SNP markers include: 653 (ARS-BFGL-NGS-1038: BTA 3 104.37 Mb), 1402 (ARS-BFGL-NGS-12557: BTA 7 45.67 Mb), 2695(ARS-BFGL-NGS-110427: BTA 14 22.67 Mb), 3080 (ARS-BFGL-NGS-56: BTA 16 76.44 Mb), 3235 (ARS-BFGL-NGS-118636: BTA 17 58.11 Mb), 3588 (ARS-BFGL-NGS-34277: BTA 20 2.06 Mb), 3617 (Hapmap-42340-BTA-84327: BTA 20 15.75 Mb), 3834 (ARS-BFGL-NGS-42945: BTA 21 44.60 Mb), and 4821 (US-IF-ASA-1370: BTA 29 44.42 Mb).

Figure 10

Loading plot of variable contribution per SNP marker by chromosome across four discriminant analyses of principal component axes (LDA; part (A)) and allele frequency by primary breed types (PBT) for four markers with variable contribution over 0.0025 on LDA-1 and LDA-3 (B). Markers in the top 2% per LDA are colored by axes with the average threshold across axes as a solid red line (A). Specified markers above the 0.0025 threshold (blue line) in (A) are presented as proportion of allele 1 (colored) and allele 2 (grey) by PBT in (B). Purebred cattle (PBT = 1) included American Aberdeen (AD), Angus (AN), Red Angus (AR), Gelbvieh (GV), Hereford (HH), Limousin (LM), Shorthorn (SH), and Simmental (SM). Admixed cattle included influenced (breed designation + I) and true first crosses (F₁). Influenced cattle were individuals with PBT at least 0.50 but less than 1 and at least 5% more than the next largest (secondary) breed fraction. True F₁ groups in the genotyped population included: F₁ B × B (F1BB), F₁ B × C (F1BC), and F₁ C × C (F1CC), where B refers to breeds AN, AR, HH, or SH and C refers to breeds GV or SM. The PBT are colored based on breed origin, where origin 1 (Australia) are dark red, origin 2 (United Kingdom) are green, origin 3 (Continental Europe) are dark yellow, and origin 4 (mixed origins) are black. The four SNP markers include: 653 (ARS-BFGL-NGS-1038: BTA 3 104.37 Mb), 1882 (Hapmap-38533-BTA-84943: BTA 9 96.18 Mb), 3893 (ARS-BFGL-NGS-103597: BTA 22 51.40 Mb), and 4665 (ARS-BFGL-NGS-111706: 28 33.87 Mb).