Molecular Marker-Assisted Selection of ABCG2, CD44, SPP1 Genes Contribute to Milk Production Traits of Chinese Holstein

Abstract

Based on our results of genome-wide association analysis, we performed gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis; three candidate genes (ABCG2, CD44, SPP1) were screened in this study for SNPs association analysis with production traits in 999 Holstein cattle. In this research, flight mass spectrometry genotyping was used to detect the polymorphism of SNP seats. It was shown that four, four, and two single nucleotide polymorphisms (SNP) loci were detected for the ABCG2, CD44, and SPP1 genes, respectively, and the different genotypes of these 10 SNPs significantly affected the milk production performance of Chinese Holstein cattle in terms of milk yield, milk fat percentage, milk protein percentage, somatic cell score, and urea nitrogen content. Among them, ABCG2-G.80952G > T locus, ABCG2-G.120017G > A locus and CD44-G.2294G > C locus had significant effects on somatic cell score (p < 0.01). Cows with GG genotypes at ABCG2-G.80952G > T locus, AA and GG genotypes at ABCG2-G.120017G > A locus, and GG genotypes at CD44-G.2294G > C locus had lower somatic cell scores. The present study elucidated that ABCG2, CD44, and SPP1 could be selected for marker-assisted selection and will benefit for future precise molecular breeding.

Keywords: ABCG2; CD44; Chinese Holstein cattle; SNP loci; SPP1; association analysis; production performance.

Figure 1

GO annotation and KEGG pathway enrichment of ABCG2, CD44 and SPP1 genes. (A) GO annotation results of three genes in BP, CC and MF. (B) Distribution of enriched KEGG pathway.

Figure 2

Sequencing peak map of four SNPs in ABCG2 gene sequence. The sequence map at ABCG2-g.57261A > G site for AG, AA and GG (A), The sequence map at ABCG2-g.80952G > T site for GT, GG and TT (B), The sequence map at ABCG2-g.94683A > G site for AG, AA and GG (C), The sequence map at ABCG2-g.120017G > A site for AG, GG and AA (D). The arrow indicates the location of the mutation sites.

Figure 3

Sequencing peak map of four SNPs in CD44 gene sequence. The sequence map at CD44-g.2263A > G site for AG, AA and GG (A), The sequence map at CD44-g.2294G > C site for CG, GG and CC (B), The sequence map at CD44-g.86895A > G site for AG, AA and GG (C), The sequence map at CD44-g.86978G > A site for AG, AA and GG (D). The arrow indicates the location of the mutation sites.

Figure 4

Sequencing peak map of two SNPs in SPP1 gene sequence. The sequence map at SPP1-g.50265G > A site for GA, GG and AA (A), The sequence map at SPP1-g.50315C > T site for CT, TT and CC (B). The arrow indicates the location of the mutation sites.

Figure 5

The linkage map of SNPs loci of ABCG2, CD44, SPP1 genes. LD value D′ > 0.7, r² > 1/3 indicates relatively high linkage strength. (A) The LD map of 4 SNPs loci of ABCG2 gene. (B) The LD map of 4 SNPs loci of CD44 gene. (C) The LD map of 2 SNPs loci of SPP1 gene.

Figure 6

Effect of different genotypes in ABCG2 four SNP loci on production traits in Chinese Holstein cattle. (A) The milk fat percentage of GG-type cows in the ABCG2-g.57261A > G locus was significantly higher than that of AA-type and AG-type cows. (B) ABCG2-g.94683A > G locus had significantly higher urea nitrogen content in the milk of AA type cows than AG and GG types. In ABCG2-g.80952G > T locus, the tested day milk yield (C) of TT type cows was significantly lower than that of GG and GT type cows; somatic cell score (D), milk protein percentage (E), and urea nitrogen (F) of TT type cows were significantly higher than GG and GT types. In ABCG2-g.120017G > A locus, AA type cows tested day milk yield (G) was significantly higher than that of AG and GG type cows, and the milk protein percentage (H), milk fat percentage (I), somatic cell score (J) and urea nitrogen (K) of AG type cows were significantly higher than those of AA and GG type cows. Data in the same column with different lowercase letters on the shoulder indicate significant differences (p < 0.05).

Figure 7

Effect of different genotypes in CD44 four SNP loci on production traits in Chinese Holstein cattle. In CD44-g.2263A > G locus, AA type urea nitrogen content of was significantly higher than that of AG and GG genotypes (A). In CD44-g.2294G > C locus, milk fat percentage (B) and milk urea nitrogen content of CG-type (D) cows were significantly higher than CC and CG types. Higher SCS for CC- and CG-type cows (C). In CD44-g.86978G > A locus, Type AA cows have the highest milk fat percentage (E). In CD44-g.86895A > G locus, tested day milk yield (F), milk fat rate (G), and milk urea nitrogen content (I) of GG-type cows were significantly higher than those of AA, AG types; AA and AG cows had the highest protein rates (H). Data in the same column with different lowercase letters on the shoulder indicate significant differences (p < 0.05).

Figure 8

SPP1-g.50265G > A and SPP1-g.50315C > T loci on the productive performance of different genotypes. tested day milk yield (A) and milk urea nitrogen content (C) were significantly higher in AG and GG types of cows than in AA-type; CT and TT types of cows were significantly higher than the CC-type, milk fat rate (B) of CT and TT types were significantly higher than that of CC-type. Data in the same column with different lowercase letters on the shoulder indicate significant differences (p < 0.05).