Identification of Genetic Associations of <i>IDH2</i>, <i>LDHA</i>, and <i>LDHB</i> Genes with Milk Yield and Compositions in Dairy Cows
Yu Song,
Zhe Wang,
Lingna Xu,
Bo Han,
Dongxiao Sun
Affiliations
Yu Song
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, Agricultural University, Beijing 100193, China
Zhe Wang
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, Agricultural University, Beijing 100193, China
Lingna Xu
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, Agricultural University, Beijing 100193, China
Bo Han
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, Agricultural University, Beijing 100193, China
Dongxiao Sun
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, Agricultural University, Beijing 100193, China
Previous study revealed that isocitrate dehydrogenase (NADP (+)) 2, mitochondrial (IDH2), lactate dehydrogenase A (LDHA), and lactate dehydrogenase B (LDHB) genes were significantly differentially expressed in liver tissues of Holstein cows among different lactation periods and associated with lipid and protein metabolism; hence, they were considered as candidates for milk production traits. Herein, the genetic effects of the three genes on milk yield, fat, and protein traits were studied by association analysis using 926 Chinese Holstein cows from 45 sire families. As a result, five single nucleotide polymorphisms (SNPs) in IDH2, one in LDHA, and three in LDHB were identified by re-sequencing, and subsequently, they were genotyped in 926 Chinese Holstein cows by genotyping by target sequencing (GBTS). With the animal model, single-locus association analysis revealed that four SNPs in IDH2 and one SNP in LDHA were significantly associated with milk, fat, and protein yields (p ≤ 0.0491), and three SNPs in LDHB were associated with milk yield, milk fat yield, and fat percentage (p ≤ 0.0285). Further, four IDH2 SNPs were found to form a haplotype block significantly associated with milk yield, fat yield, protein yield, and protein percentage (p ≤ 0.0249). In addition, functional predictions indicated that one SNP in LDHA, g.26304153G>A, may affect transcription factor binding and two SNPs, g.88544541A>G and g.88556310T>C could alter LDHB mRNA secondary structure. In summary, this study profiled the significant genetic effects of IDH2, LDHA, and LDHB on milk yield and composition traits and provided referable genetic markers for genomic selection programs in dairy cattle.
