Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep

Abstract

Adaptation to high-altitude hypoxia is essential for domestic animals, such as yak, Tibetan chicken, and Tibetan sheep, living on high plateaus, as it ensures efficient oxygen absorption and utilization. Red blood cells are the primary medium for transporting oxygen in the blood. However, little is known about the genetic mechanism of erythrocyte traits. Genome-wide association studies (GWASs) based on single markers or haplotypes have identified potential mechanisms for genetic variation and quantitative traits. To identify loci associated with erythrocyte traits, we performed a GWAS based on the method of the single marker and haplotype in 498 Alpine Merino sheep for six erythrocyte traits: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV). Forty-two significant single-nucleotide polymorphisms (SNPs) associated with the six erythrocyte traits were detected by means of a single-marker GWAS, and 34 significant haplotypes associated with five erythrocyte traits were detected by means of haplotype analysis. We identified six genes (DHCR24, SPATA9, FLI1, PLCB1, EFNB2, and SH2B3) as potential genes of interest via gene function annotations, location, and expression variation. In particular, FLI1 and PLCB1 were associated with hematopoiesis and erythropoiesis, respectively. These results provide a theoretical basis for analyzing erythrocyte traits and high-altitude hypoxia adaptation in Alpine Merino sheep and will be a useful reference for future studies of plateau-dwelling livestock.

Keywords: alpine merino sheep; erythrocyte traits; genome-wide association study; haplotype; high-altitude hypoxia adaptation; single-nucleotide polymorphism.

FIGURE 1

Quantile-quantile (Q–Q) plots of genome-wide association studies (GWASs) for six erythrocyte traits for: (A) single-marker analysis and (B) haplotype analysis. The six traits were: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV).

FIGURE 2

Manhattan plots of single-marker analysis for six erythrocyte traits. Chromosomes 1 to 26 are shown in different colors; the horizontal dotted green line and solid line indicate the suggestive and genome-wide significance level, respectively. Single-nucleotide polymorphisms (SNPs) surpassing the genome-wide threshold are highlighted in red, and SNPs reaching the suggestive threshold are highlighted in green. The strips below each chromosome indicate the density of the markers. The six traits were: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV).

FIGURE 3

Manhattan plots of haplotype-based analysis for six erythrocyte traits. Chromosomes 1 to 26 are shown in different colors; the horizontal dotted green line and solid line indicate the suggestive and genome-wide significance level, respectively. Haplotypes surpassing the genome-wide threshold are highlighted in red, and haplotypes reaching the suggestive threshold are highlighted in green. The strips below each chromosome indicate the density of the markers. The six traits were: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV).