Identification and expression pattern of two novel alternative splicing variants of EEF1D gene of dairy cattle.
Our recent genome-wide association study (GWAS) has identified 105 genome-wide significant SNPs for milk production traits. Of these, one SNP (rs109661298) for milk fat percentage is located within the first intron of the bovine EEF1D gene on BTA14, thus that the EEF1D gene was considered as a novel candidate in dairy cattle. Until now, however, its genomic organization remains undetermined yet and no studies of EEF1D in relation to milk production traits have been reported. To layout the groundwork for the validation of gene function in dairy cattle, we herein investigated its expression pattern in lactating dairy cows. With rapid amplification of 5' cDNA end (5' RACE), two novel alternatively spliced transcript variants of 1202bp and 2195bp were isolated in bovine mammary in lactation, named EEF1Da and EEF1Db (GenBank: KC190039 and KC190038KC190039KC190038). Such two variants contain the different first exon from each other (exon1a vs exon1b: 294bp vs 1287bp) with no overlap and the same remaining 7 exons. Coding sequence similarity between EEF1Da and EEF1Db and three of human EEF1D transcript variants were 85-88%. With semi-quantitative and quantitative real-time RT-PCR, we found that the mRNA level of EEF1Da was similar to the overall EEF1D mRNA and much higher than EEF1Db in the mammary of lactating cows, indicating EEF1Da functions as the dominant transcript variant to encode the EEF1D protein. Tissue expression pattern showed that the mRNA expression of EEF1D and EEF1Da in mammary gland was significantly higher compared with other 7 tissues (P<0.05, P<0.01) with the exception of EEF1D between mammary and lung. Together, our findings present the first report on the alternative splicing of the bovine EEF1D gene and provided basis for further investigation on function validation of EEF1D in dairy cattle.
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Yan
Y
Xie
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Shaohua
S
Yang
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Xiaogang
X
Cui
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Li
L
Jiang
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Shengli
S
Zhang
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Qin
Q
Zhang
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China.
Yuan
Y
Zhang
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing 100193, China. Electronic address: sundx@cau.edu.cn.
Dongxiao
D
Sun
D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D002417:Cattle / Q000235:genetics* / Q000378:metabolism; D005091:Exons; D005260:Female; D015870:Gene Expression; D055106:Genome-Wide Association Study / Q000379:methods; D056914:Genomic Structural Variation; D006801:Humans; D007774:Lactation / Q000235:genetics; D008168:Lung / Q000378:metabolism; D008321:Mammary Glands, Animal / Q000378:metabolism; D008892:Milk; D008969:Molecular Sequence Data; D020648:Peptide Elongation Factor 1 / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment
D020648:Peptide Elongation Factor 1
5′ RACE; ABCG2; ATP binding cassette transporter subfamily G; Alternative splice variant; CDK1; CK2; DGAT1; EEF1D; ESE; ESS; Expression pattern; G-protein; GAPDH; GEF; GTP-bindendes protein; GWAS; Holstein cow; IGF-I; ISE; ISS; KH domains; NCBI; NOVA; PKC; S6K; SCD1; SIAH-1; SNP; SR; aa-tRNA; aminoacyl tRNAs; casein kinase II; cyclin-dependent kinase; diacylglycerol o-acyltransferase 1; eEF1; eEF1A; eEF1B; eEF1Bα; eEF1Bγ; eEF1Bδ; eukaryotic elongation factor 1; eukaryotic elongation factor 1A; eukaryotic elongation factor 1B; eukaryotic elongation factor 1Bδ; eukaryotic elongation factor 1α; eukaryotic elongation factor 1γ; eukaryotic translation elongation factor 1 delta; exon splicing enhancer; exon splicing silencer; genome-wide association study; glyceraldehyde-3-phosphate dehydrogenase; guanine nucleotide exchange factor; heterogeneous nuclear ribonucleoprotein; hnRNP; hnRNP K Homology (KH) domain; insulin-like growth factor-I; intron splicing enhancer; intron splicing silencer; multipotential S6 kinase; neuro-oncologica ventral antigen; protein kinase C; rapid amplification of 5′ cDNA end; serine-arginine (SR) protein; seven in absentia homolog E3 ubiquitin protein ligase 1; single nucleotide polymorphism; stearoyl-CoA desaturase 1; the National Center for Biotechnology Information