畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (11): 4980-4991.doi: 10.11843/j.issn.0366-6964.2024.11.017
王欢1(), 陈韬羽1, 吴慧2, 蒙勇1, 李世元1, 钱和洁1, 牛世华1, 满初日嘎1, 陈巧玲1, 高宏岩1, 杜丽1, 王凤阳1, 陈思1,*(
)
收稿日期:
2024-05-14
出版日期:
2024-11-23
发布日期:
2024-11-30
通讯作者:
陈思
E-mail:772101737@qq.com;chensi.ruth@hotmail.com
作者简介:
王欢(1997-), 女, 河南南阳人, 硕士生, 主要从事动物遗传育种与繁殖研究, E-mail: 772101737@qq.com
基金资助:
Huan WANG1(), Taoyu CHEN1, Hui WU2, Yong MENG1, Shiyuan LI1, Hejie QIAN1, Shihua NIU1, Churiga MAN1, Qiaoling CHEN1, Hongyan GAO1, Li DU1, Fengyang WANG1, Si CHEN1,*(
)
Received:
2024-05-14
Online:
2024-11-23
Published:
2024-11-30
Contact:
Si CHEN
E-mail:772101737@qq.com;chensi.ruth@hotmail.com
摘要:
旨在研究海南黑山羊ATG16L2基因启动子区的结构特征及其遗传分布情况,为进一步探索该基因的表达调控机制及功能提供理论依据。本研究以200头海南黑山羊为研究对象,构建DNA混池,采用Sanger法测序对海南黑山羊ATG16L2基因启动子区的多态性进行初筛,应用PCR-RFLP技术对200头海南黑山羊个体进行基因型鉴定。对筛选到的SNP位点进行连锁不平衡分析,构建单倍型。利用生物信息学方法分析SNP位点对海南黑山羊ATG16L2基因表达的影响。在海南黑山羊ATG16L2基因启动子区共检测到3个SNPs位点,分别为SNP1(g.30667970T>C)、SNP2(g.30668540T>C)和SNP3(g.30668664C>T),且彼此连锁。SNP1和SNP2位点均表现为中度多态性,SNP3位点表现为低度多态性,且符合Hardy-Weinberg平衡(P>0.05)。单倍型分析结果显示,H1、H2、H3和H4单倍型频率分别为0.321、0.304、0.271和0.097,且H1(CGC)为优势单倍型。生物信息学分析显示,山羊ATG16L2基因共预测到3个启动子和4个CpG岛区域;存在2个重复元件LINE2(—1 989~—1 826 bp、—562~—426 bp)、hAT-Charlie (—1 804~—1 511 bp)以及5个CCAAT-Box、13个CAAT-Box、10个CGCG-Box、11个GATA-Box和2个TATA-Box。综合多种在线软件预测发现,上述SNPs可能通过影响ATG16L2基因的启动子区的顺式作用元件,从而影响海南黑山羊ATG16L2基因的转录表达。本研究在海南黑山羊ATG16L2基因启动子序列中发现3个SNPs位点,其中SNP1和SNP2表现为中度多态性,SNP3表现为低度多态性,并预测这些SNPs可能影响转录因子结合,从而调控基因表达,为进一步探究ATG16L2基因功能及其调控机制提供了理论依据。
中图分类号:
王欢, 陈韬羽, 吴慧, 蒙勇, 李世元, 钱和洁, 牛世华, 满初日嘎, 陈巧玲, 高宏岩, 杜丽, 王凤阳, 陈思. 海南黑山羊ATG16L2基因启动子区多态性研究[J]. 畜牧兽医学报, 2024, 55(11): 4980-4991.
Huan WANG, Taoyu CHEN, Hui WU, Yong MENG, Shiyuan LI, Hejie QIAN, Shihua NIU, Churiga MAN, Qiaoling CHEN, Hongyan GAO, Li DU, Fengyang WANG, Si CHEN. Polymorphism Analysis of the ATG16L2 Gene Promoter Region in Hainan Black Goat[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(11): 4980-4991.
表 1
海南黑山羊ATG16L2基因引物信息"
名称Name | 上游引物(5′→3′) Forward primer | 下游引物(5′→3′) Reverse primer | 产物长度/bp Length | 退火温度/℃ Annealing temperature |
P1 | TGGGCAGGAGCCAGACTAAGC | AAGGGGATGGTACGCATGGAG | 668 | 63.2 |
P2 | CGGCTAGCGGAAATCCTGACCCCAATATGAC | CAGCTGATTTCATCGAGCAAACCCC | 847 | 62.0 |
P3 | GGCTAGCGCTCCACTGAATCACTCCTT | TCTGGACCAGGCGGTGCACTAAACT | 658 | 62.0 |
P4 | GGCTAGCGCTGCCTGGTATCCGTTTC | CCTCGAGATAGGGCCTTTTGCGTTCGATCC | 729 | 62.0 |
P5 | CAGCAGCATACACGCTCCTGCG | GCTGAGCCGGCCAGCAGCT | 294 | 66.6 |
P6 | ATCCTGACCCCAATATGACTC | ATGGTACGCATGGAGGATC | 198 | 55.3 |
P7 | ATTGGTCATCACTTCATGGCTTTCT | CATATTGTCAAGGCTTTGCCTTCAT | 317 | 60.0 |
表 2
生物信息学分析ATG16L2启动子区所用的软件"
软件分析Software analysis | 网站Website |
启动子序列的特征分析Characteristic analysis of promoter sequences | |
重复元件分析Repeat element analysis | |
顺式作用元件分析Analysis of cis-acting elements | |
CpG岛位点分析CpG island site analysis | |
转录因子结合预测Transcription factor binding prediction | |
转录因子结合预测Transcription factor binding prediction |
表 3
海南黑山羊与不同物种ATG16L2基因的相似性"
物种Species | 相似性/% Similarity | 物种Species | 相似性/% Similarity | |
羚羊Budorcas taxicolor | 99.03 | 绵羊Ovis aries | 98.64 | |
普通牛Bos taurus | 96.81 | 瘤牛Bos indicus | 91.61 | |
猪Sus scrofa | 86.87 | 马Equus caballus | 86.51 | |
雪貂Mustela putorius furo | 82.71 | 老虎Panthera tigris | 80.35 | |
骆驼Camelus dromedarius | 76.47 | 双峰驼Camelus bactrianus | 74.47 | |
蓝鲸Balaenoptera musculus | 71.44 | 人Homo sapiens | 68.23 | |
狗Canis lupus familiaris | 64.19 | 羊驼Vicugna pacos | 62.73 | |
鸭嘴兽Ornithorhynchus anatinus | 62.44 | 大熊猫Ailuropoda melanoleuca | 61.76 | |
家鼠Mus musculus | 53.87 | 鸡Gallus gallus | 42.02 | |
斑马鱼Danio rerio | 38.34 |
表 4
海南黑山羊ATG16L2基因启动子区SNPs位点的群体遗传学分析"
SNP位点SNP site | 基因型频率(样本数) Genotype frequency (sample number) | 等位基因频率Allele frequency | Ho | He | Ne | PIC | χ2 (HWE) |
SNP1 (g.30667970T>C) | TT:0.365(73) | T:0.575 | 0.511 | 0.489 | 1.956 | 0.369 | 3.957 (P>0.05) |
TC:0.420(84) | C:0.425 | ||||||
CC:0.215(43) | |||||||
SNP2 (g.30668540T>C) | GG:0.505(101) | G:0.723 | 0.599 | 0.401 | 1.669 | 0.321 | 1.439 (P>0.05) |
TG:0.435(87) | T:0.278 | ||||||
TT:0.060(12) | |||||||
SNP3 (g.30668664C>T) | CC:0.800(160) | C:0.900 | 0.820 | 0.180 | 1.220 | 0.164 | 2.469 (P>0.05) |
CT:0.200(40) | T:0.100 | ||||||
TT:0.000(0) |
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