Analysis of Genetic Effects of FBP2 Gene on Milk Production Traits in Chinese Holstein (Bos taurus)
LI Qian1, 2, LI Yan3, SHI Li-Jun4, GAO Yan-Xia1, LI Qiu-Feng1, SUN Dong-Xiao4, *, LI Jian-Guo1, *
1 College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China;
2 Hebei Animal Husbandry and Veterinary Institute, Baoding 071000, China;
3 College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China;
4 College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Abstract：Identification of functional genes and mutations that have large genetic effects on milk production traits can provide molecular information for marker-assisted selection in order to increase selection accuracy and accelerate genetic gain in dairy cattle (Bos Taurus). Nowadays RNA-seq is one of strategies for identification of key genes affecting complex traits in human (Homo sapiens), domestic animals and plants. In previous RNA-seq study on the transcriptomes of liver tissues from Chinese Holstein at different lactation stages (50 d before parturition , 15 d after parturition, 60 d after parturition), 40 candidate genes for milk production traits were identified. Of them, the fructose-bisphosphatase 2 gene (FBP2) was significantly differentially expressed among different periods. It encoded a gluconeogenesis regulatory enzyme which participated in glycogen synthesis from carbohydrate precursors and played an important role in gluconeogenesis. Thus, the purpose of this study was to further validate whether the FBP2 gene showed significant genetic effects on milk production traits in dairy cattle. By re-sequencing the entire exons, and 2 000 bp of 5' and 3' flanking regions of FBP2 gene using pooled DNA, 11 single nucleotide polymorphisms (SNPs) were detected, including 7 in 5' flanking region and 4 in 3' flanking region. These identified SNPs were genotyped with matrix-assisted laser adsorption time of flight mass spectrometry (MALDI-TOF-MS) technology and tested for association with 5 milk production traits in 1 099 Chinese Holstein from Beijing region. All 11 SNPs were found to be statistically significant for protein yield (P=0.0495~<0.0001). Also, 6 of them were significantly associated with protein percentage (P=0.0434~0.0004), 5 of them were significantly associated with milk yield (P=0.018~0.007) and 1 SNP was significantly associated with fat yield (P=0.0143). The additive and allele substitution effects of the most SNPs reached significance (P<0.05, P<0.01). On the other hand, with linkage disequilibrium (LD) analysis, the 11 SNPs were found to be highly linked (r2=0.48~0.99), and 2 blocks were inferred. Haplotype-based association analysis showed that the 6 haplotype combinations in block 1 were significantly associated with the 5 milk traits (P=0.0413~<0.0001), and the haplotype combinations in block 2 were significantly associated with milk yield, fat yield, protein percentage and protein yield (P=0.0413~<0.0001). H2 and H3 in block1 and H2 in block2 were advantegous haplotypes for higher milk yield and composition. This study first indicated that the FBP2 gene had significant genetic effects on milk yield and milk composition traits in dairy cattle, especially affecting milk protein, and could be useful to provide valuable gene information for molecular breeding programs of Chinese Holstein.
李茜, 李妍, 石丽君, 高艳霞, 李秋凤, 孙东晓, 李建国. 中国荷斯坦牛FBP2基因对产奶性状的遗传效应分析[J]. 农业生物技术学报, 2019, 27(9): 1582-1595.
LI Qian, LI Yan, SHI Li-Jun, GAO Yan-Xia, LI Qiu-Feng, SUN Dong-Xiao, LI Jian-Guo. Analysis of Genetic Effects of FBP2 Gene on Milk Production Traits in Chinese Holstein (Bos taurus). 农业生物技术学报, 2019, 27(9): 1582-1595.
1 丁向东, 张沅, 张勤. 2014. 中国荷斯坦牛基因组选择进展[C]//. 第六届全国动植物数量遗传学术研讨会论文集,中国遗传学会, 北京, pp.21.
(Ding X D, Zhang Y, Zhang Q.2014. Process in genomic selection of Chinese holstein[C]//. Proceedings of the sixth national symposium on quantitative genetics of plants and animals, Chinese Society of Genetics, Beijing, pp.21.)
2 李茜. 2017. 基于RNA-seq技术鉴定奶牛产奶性状功能基因及遗传效应验证[D]. 博士学位论文, 河北农业大学, 导师: 李建国, pp. 78-114.
(Li Q.2017. Functional gene identification by RNA-seq and their genetic effects on milk production traits in dairy cows[D].Thesis for Ph. D., Hebei Agricultural University, Supervisor: Li J G,pp. 78-114.)
3 王梦琦, 倪炜, 唐程, 等. 2018. 中国荷斯坦牛乳铁蛋白启动子区-131C>T和-28A>C位点SNP与泌乳性状、乳房炎和生产寿命的关联分析[J]. 农业生物技术学报, 26(5): 811-818.
(Wang M Q, Ni W, Tang C, et al.2018. Association analysis on the SNP of LF -131C>T and LF -28A>C with milk performance, clinical mastitis and lifetime for Chinese Holstein[J]. Journal of Agricultural Biotechnology, 26(5): 811-818.)
4 杨少华. 2015. 中国荷斯坦牛TRIB3和SAA家族基因对产奶性状的遗传效应分析及功能验证[D]. 博士学位论文, 中国农业大学, 导师: 孙东晓, pp. 24-25.
(Yang S H.2015. Genetic effects analysis and functional verification of TRIB3 and SAA associated with milk production traits in Chinese Holstein[D]. Thesis for Ph. D., China Agricultural University, Supervisor: SUN D X, pp. 24-25.)
5 Agius L.2016. Hormonal and metabolite regulation of hepatic glucokinase[J]. Annual Review of Nutrition, 36: 389-415.
6 Barrett J C, Fry B, Maller J, et al.2005. Haploview: Analysis and visualization of LD and haplotype maps[J]. Bioinformatics, 21(2): 263-265.
7 Ben C H, Boutinaud M, Bemier-Dodier P, et al.2010. Disruption of cell junctions induces apoptosis and reduces synthetic activity in lactating goat mammary gland[J]. Journal of Dairy Science, 93(7): 2938-2951.
8 Cole J B, Wiggans G R, Ma L, et al.2011. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows[J]. BMC Genomics, 12: 408.
9 Dzugaj A.2006. Localization and regulation of muscle fructose-1,6-bisphosphatase, the key enzyme of glyconeogenesis[J]. Advances in Enzyme Regulation, 46: 51-71.
10 Gabriel S B, Schaffner S F, Nguyen H, et al.2002. The structure of haplotype blocks in the human genome[J]. Science, 296(5576): 2225-2229.
11 Hagenblad J, Tang C, Molitor J, et al.2004. Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci[J]. Genetics, 168(3): 1627-1638.
12 Ibeagha-Awemu E M, Li R, Ammah A A, et al.2016. Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways[J]. BMC Genomics, 17: 104.
13 Li H, Wang J, Xu H, et al.2013. Decreased fructose-1,6-bisphosphatase-2 expression promotes glycolysis and growth in gastric cancer cells[J]. Molecular Cancer, 12(1): 110.
14 Liang R, Han B, Li Q, et al.2017. Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver[J]. Scientific Reports, 7(1): 6396.
15 Nothnagel M, Rohde K.2005. The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates[J]. American Journal of Human Genetics, 77(6): 988-998.
16 Rukkwamsuk T, Wensing T, Geelen M J.1999. Effect of fatty liver on hepatic gluconeogenesis in periparturient dairy cows[J]. Journal of Dairy Science, 82(3): 500-505.
17 Smith J L, Lear S R, Forte T M, et al.1998. Effect of pregnancy and lactation on lipoprotein and cholesterol metabolism in the rat[J]. Journal of Lipid Research, 39(11): 2237-2249.
18 Song S, Andrikopoulos S, Filippis C, et al.2001. Mechanism of fat-induced hepatic gluconeogenesis: Effect of metformin[J]. American Journal of Physiology Endocrinology and Metabolism, 281(2): E275-E282.
19 Wu C, Khan S A, Peng L J, et al.2006. Roles for fructose-2,6-bisphosphate in the control of fuel metabolism: Beyond its allosteric effects on glycolytic and gluconeogenic enzymes[J]. Advances in Enzyme Regulation, 46: 72-88.
20 Zhang Z, Ober U, Erbe M, et al.2014. Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies[J]. PLOS ONE, 9(3): e93017.
21 Zhao L F, Iwasaki Y, Nishiyama M, et al.2012. Liver X receptor alpha is involved in the transcriptional regulation of the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene[J]. Diabetes, 61(5): 1062-1071.
