Li Y, Han B, Liu L, Zhao F, Liang W, Jiang J, Yang Y, Ma Z, Sun D
Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China.
Beijing Dairy Cattle Center, Beijing, 100192, China.
Anim Genet. 2019 Apr;50(2):123-135. doi: 10.1111/age.12750. Epub 2019 Feb 28.
Previously, we identified by RNA sequencing that DDIT3, RPL23A, SESN2 and NR4A1 genes were significantly differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentages; thus, these four genes are considered as promising candidates potentially affecting milk yield and composition traits in dairy cattle. In the present study, we further verified whether these genes have genetic effects on milk traits in a Chinese Holstein population. By re-sequencing part of the non-coding and the entire coding regions of the DDIT3, RPL23A, SESN2 and NR4A1 genes, a total of 35 SNPs and three insertions/deletions were identified, of which three were found in DDIT3, 12 in RPL23A, 16 in SESN2 and seven in NR4A1. Moreover, two of the insertions/deletions-g.125714860_125714872del and g.125714806delinsCCCC in SESN2-were novel and have not been reported previously. Subsequent single SNP analyses revealed multiple significant association with all 35 SNPs and three indels regressed against the dairy production traits (P-value = <0.0001-0.0493). In addition, with a linkage disequilibrium analysis, we found one, one, three, and one haplotype blocks in the DDIT3, RPL23A, SESN2 and NR4A1 genes respectively. Haplotype-based association analyses revealed that some haplotypes were also significantly associated with milk production traits (P-value = <0.0001-0.0461). We also found that 12 SNPs and two indels (two in DDIT3, two in RPL23A, nine in SESN2 and one in NR4A1) altered the specific transcription factor binding sites in the promoter, thereby regulating promoter activity, suggesting that they might be promising potential functional variants for milk traits. In summary, our findings first determined the genetic associations of DDIT3, RPL23A, SESN2 and NR4A1 with milk yield and composition traits in dairy cattle and also suggested potentially causal variants, which require in-depth validation.
此前，我们通过RNA测序发现，DDIT3、RPL23A、SESN2和NR4A1基因在乳蛋白和脂肪百分比极高和极低的泌乳荷斯坦奶牛的乳腺之间存在显著差异表达；因此，这四个基因被认为是可能影响奶牛产奶量和组成性状的有前景的候选基因。在本研究中，我们进一步验证了这些基因在中国荷斯坦牛群体中对产奶性状是否具有遗传效应。通过对DDIT3、RPL23A、SESN2和NR4A1基因的部分非编码区和整个编码区进行重测序，共鉴定出35个单核苷酸多态性（SNP）和三个插入/缺失，其中在DDIT3中发现3个，在RPL23A中发现12个，在SESN2中发现16个，在NR4A1中发现7个。此外，SESN2中的两个插入/缺失——g.125714860_125714872del和g.125714806delinsCCCC——是新发现的，此前未被报道过。随后的单SNP分析显示，所有35个SNP和三个插入/缺失与奶牛生产性状进行回归分析时均存在多个显著关联（P值 = <0.0001 - 0.0493）。此外，通过连锁不平衡分析，我们分别在DDIT3、RPL23A、SESN2和NR4A1基因中发现了1个、1个、3个和1个单倍型块。基于单倍型的关联分析表明，一些单倍型也与产奶性状显著相关（P值 = <0.0001 - 0.0461）。我们还发现，12个SNP和两个插入/缺失（DDIT3中2个，RPL23A中2个，SESN2中9个，NR4A1中1个）改变了启动子中特定转录因子结合位点，从而调节启动子活性，表明它们可能是产奶性状有前景的潜在功能变异。总之，我们的研究结果首次确定了DDIT3、RPL23A、SESN2和NR4A1与奶牛产奶量和组成性状的遗传关联，并提出了潜在的因果变异，这需要深入验证。
