Abstract
We previously used the RNA sequencing technique to detect the hepatic transcriptome of Chinese Holstein cows among the dry period, early lactation, and peak of lactation, and implied that the nucleobindin 2 (NUCB2) gene might be associated with milk production traits due to its expression being significantly increased in early lactation or peak of lactation as compared to dry period (q value < 0.05). Hence, in this study, we detected the single nucleotide polymorphisms (SNPs) of NUCB2 and analyzed their genetic associations with milk yield, fat yield, fat percentage, protein yield, and protein percentage. We re-sequenced the entire coding and 2000 bp of 5′ and 3′ flanking regions of NUCB2 by pooled sequencing, and identified ten SNPs, including one in 5′ flanking region, two in 3′ untranslated region (UTR), and seven in 3′ flanking region. The single-SNP association analysis results showed that the ten SNPs were significantly associated with milk yield, fat yield, fat percentage, protein yield, or protein percentage in the first or second lactation (p values <= 1 × 10−4 and 0.05). In addition, we estimated the linkage disequilibrium (LD) of the ten SNPs by Haploview 4.2, and found that the SNPs were highly linked in one haplotype block (D′ = 0.98–1.00), and the block was also significantly associated with at least one milk traits in the two lactations (p values: 0.0002–0.047). Further, we predicted the changes of transcription factor binding sites (TFBSs) that are caused by the SNPs in the 5′ flanking region of NUCB2, and considered that g.35735477C>T might affect the expression of NUCB2 by changing the TFBSs for ETS transcription factor 3 (ELF3), caudal type homeobox 2 (CDX2), mammalian C-type LTR TATA box (VTATA), nuclear factor of activated T-cells (NFAT), and v-ets erythroblastosis virus E26 oncogene homolog (ERG) (matrix similarity threshold, MST > 0.85). However, the further study should be performed to verify the regulatory mechanisms of NUCB2 and its polymorphisms on milk traits. Our findings first revealed the genetic effects of NUCB2 on the milk traits in dairy cows, and suggested that the significant SNPs could be used in genomic selection to improve the accuracy of selection for dairy cattle breeding.
Highlights
Milk provides rich nutrients, protein, fatty acids, and vitamins, etc., for human [1], so the milk production traits are considered as the most important economic traits in the dairy industry, including milk yield, fat yield, fat percentage, protein yield, and protein percentage [2]
The RNA sequencing has been widely applied to study the specific gene expression patterns at different developmental stages or in different tissues [3]. We previously used this technique to obtain hepatic transcriptome of Chinese Holstein cows among dry period, early lactation, and peak of lactation, and found that the expression of the nucleobindin 2 (NUCB2) gene was significantly increased in early lactation (q value = 0.00811) and the peak of lactation (q value = 0.049246) as compared to dry period, respectively [4], so we considered that the NUCB2 might be associated with milk production traits
In this study, we detected the polymorphisms of the NUCB2 gene and estimated the haplotype block that was formed by the identified single nucleotide polymorphisms (SNPs), and analyzed their associations with five milk traits, including milk yield, fat yield, fat percentage, protein yield, and protein percentage
Summary
Protein, fatty acids, and vitamins, etc., for human [1], so the milk production traits are considered as the most important economic traits in the dairy industry, including milk yield, fat yield, fat percentage, protein yield, and protein percentage [2]. The RNA sequencing has been widely applied to study the specific gene expression patterns at different developmental stages or in different tissues [3] We previously used this technique to obtain hepatic transcriptome of Chinese Holstein cows among dry period, early lactation, and peak of lactation, and found that the expression of the nucleobindin 2 (NUCB2) gene was significantly increased in early lactation (q value = 0.00811) and the peak of lactation (q value = 0.049246) as compared to dry period, respectively [4], so we considered that the NUCB2 might be associated with milk production traits. In this study, we detected the polymorphisms of the NUCB2 gene and estimated the haplotype block that was formed by the identified SNPs, and analyzed their associations with five milk traits, including milk yield, fat yield, fat percentage, protein yield, and protein percentage
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