扬州大学 动物科学与技术学院,江苏 扬州 225002
收稿日期:2020-10-19;接收日期:2021-02-08;网络出版时间:2021-03-11
基金项目:扬州大学大学生科创基金(No. 20200665),国家自然科学基金(Nos. 31872977,32002146),江苏省农业自主创新项目(No. CX(19)2016),江苏高校优势学科建设工程资助项目(PAPO) 资助
摘要:雌激素受体(Estrogen receptor,esr) 介导雌激素影响相关基因表达,从而调控哺乳动物的生长和繁殖机能。为了探讨esr基因的反转录转座子多态性对猪生长性能的影响,文中应用比较基因组学和生物信息学方法,预测猪esr基因的反转录转座子插入位点,采用PCR方法验证不同品种猪中插入多态性,并将该基因型与大白猪性能进行关联分析。结果显示,esr1和esr2基因验证后得到4个反转录转座子多态性位点,分别是位于esr1基因内含子2的esr1-SINE-RIP1、位于内含子5的esr1-LINE-RIP2和esr1-SINE-RIP3,以及位于esr2基因内含子1的esr2-LINE-RIP。其中esr1-SINE-RIP1的287 bp SINE插入对大白猪的活体背膘厚和100 kg体重背膘厚有显著影响(P < 0.05),纯合有插入(SINE+/+) 的活体背膘厚和100 kg体重背膘厚显著高于杂合有插入(SINE+/-) 和无插入(SINE-/-) 型。这表明esr1-SINE-RIP1位点可作为分子标记辅助选育大白猪的背膘厚性状。
关键词:猪雌激素受体反转录转座子反转录转座子插入多态关联分析
Retrotransposon insertion polymorphism of the porcine esr gene and its association with production performances of Large White pigs
Chenglin Chi, Yalong An, Kaiyuan Li, Hao Gu, Saisai Wang, Cai Chen, Bo Gao, Chengyi Song, Xiaoyan Wang
College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, Jiangsu, China
Received: October 19, 2020; Accepted: February 8, 2021; Published: March 11, 2021
Supported by: Science and Technology Innovation Fund for College Students of Yangzhou University, China (No. 20200665), National Natural Science Foundation of China (Nos. 31872977, 32002146), Jiangsu Agriculture Science and Technology Innovation Fund, China (No. CX(19)2016), Priority Academic Program Development of Jiangsu Higher Education Institutions, China
Corresponding author: Xiaoyan Wang. Tel: +86-514-87979034; E-mail: wxyan@yzu.edu.cn.
Abstract: Estrogen receptor (esr) mediates the effects of estrogen on the expression of related genes, thereby regulating the growth and reproduction of mammals. To investigate the effect of retrotransposon insertion polymorphism (RIP) of the porcine esr gene on porcine growth performance, retrotransposon insertion polymorphism of the esr gene were predicted by comparative genomics and bioinformatics, and PCR was used to verify the insertion polymorphisms in different porcine breeds. Finally, the correlation analysis between the genotypes and performance of Large White pigs was conducted. The results showed that four retrotransposon polymorphic sites were identified in the esr1 and esr2 genes, which are esr1-SINE- RIP1 located in intron 2 of the esr1 gene, esr1-LINE-RIP2 and RIP3-esr1- SINE located in intron 5 of the gene, and esr2-LINE-RIP located in intron 1 of the esr2 gene, respectively. Among them, insertion of a 287 bp of SINE into intron 2 of the esr1 gene significantly affected (P < 0.05) the live back fat thickness and 100 kg body weight back fat thickness of Large White pigs. Moreover, the live back fat thickness and back fat thickness at 100 kg body weight of homozygous with insertion (SINE+/+) was significantly greater than that of heterozygous with insertion (SINE+/–) and homozygous without insertion (SINE–/–). Therefore, esr1-SINE-RIP1 could be used as a molecular marker to assist the selection of deposition traits in Large White pigs.
Keywords: pigestrogen receptorretrotransposonretrotransposon insertion polymorphismassociation analysis
随着分子生物学技术的发展,全基因组关联分析(Genome-wide association study,GWAS) 技术可以准确地定位相关性状的候选基因[1],目前猪育种中常用的分子标记研究集中于插入和缺失(Insertions and deletions,Indels)[2]、单核苷酸多态性(Single nucleotide polymorphism,SNP)[3]和拷贝数变异(Copy number variations,CNVs)[4]等,而有关反转录转座子插入多态性(Retrotransposon insertion polymorphism,RIP) 的研究与应用相对较少。
反转录转座子(Retrotransposon) 是以RNA为中介,在转座酶的参与下,以“复制-粘贴”形式从基因组的一个位点整合到另一个位点的转座元件,可以分为长末端重复序列(Long terminal repeats,LTR) 和非长末端重复序列(Non-long terminal repeats,non-LTR)。其中non-LTR包括短散在重复序列(Short interspersed nuclear elements, SINE) 和长散在重复序列(Long interspersed nuclear elements,LINE)[5]。反转录转座子是许多植物基因组的主要组分,其插入多态性已成为研究植物基因组的进化、生物多样性和分子育种的重要工具[6]。植物上已发现大量关于反转录转座子插入导致植物性状改变的研究。例如,LTR反转录转座子介导调控番茄果实形状基因sun发生重组,从而造成sun1642型果实形状发生改变[7]。反转录转座子插入到控制成花的拟南芥leafy基因中,导致第8代中有些个体的花无雄性器官[8]。
动物反转录转座子插入改变性状的研究报道也越来越多。例如,silv基因11号外显子附近的SINE插入造成狗体型和毛色的改变[9];mstn基因1号内含子中SINE插入使马的肌肉纤维比例发生改变,从而影响马的赛跑距离[10];vrtn基因的SINE插入多态性被认为是导致家猪脊椎数变异的潜在结构突变[11];ktn1基因5号内含子中的SINE插入对苏姜猪的仔猪断奶窝重有显著影响[12]。
雌激素受体是配体激活转录因子家族中的一种核受体,具有转录调控靶基因的功能,影响雌激素在脊椎动物中的表达,介导雌激素的生物学作用[13]。基因组有esr1和esr2基因。在20世纪末以前,人们一直认为只有一种形式的esr存在。然而,1996年多个实验室陆续报道在老鼠[14]和人类[15]中存在第二种类型的esr。这一新发现的受体被称为esr2基因,而经典esr被称为esr1基因。
esr基因是用于分子标记辅助选择繁殖性状的主要候选基因,1996年Rothschild等首次在大白猪群体中发现esr基因的Pvu Ⅱ酶切位点多态性,这个多态性位点与母猪产仔数显著相关[16]。该位点已在猪育种实践中得到应用。esr基因也被认为是影响猪繁殖性状的主要候选基因。猪的esr1和esr2基因均位于1号染色体,esr1基因全长274 592 bp,包括9个外显子(Exon) 和9个编码区(Coding sequence,CDS)。esr2全长184 401 bp,包括13个Exon和8个CDS区。有相关研究表明,esr基因影响猪生长性状及活体背膘厚[17]。鉴于esr基因在猪生长和生殖生理中的重要作用,本实验拟挖掘与鉴定猪esr基因的RIP,并与猪生长性状进行关联分析,以期为该分子标记在猪分子育种实践中的应用提供参考。
1 材料与方法1.1 材料本实验所用动物材料:大白猪(Large White pig) 耳样404个,2015年采自安徽省某种猪公司;苏姜猪(Sujiang pig) 耳样110个和姜曲海猪(Jiangquhai pig) 耳样24个,2015年采自江苏省泰州市姜曲海种猪场;杜洛克(Duroc pig) 和长白猪(Landrace pig) 耳样各24个,2015年由安徽省农业科学院提供;二花脸猪(Erhualian pig) 耳样24个、枫泾猪(Fengjing pig) 耳样24个和梅山猪(Meishan pig) 耳样24个,2014年采自江苏苏州苏太猪原种场;苏山猪(Sushan pig) 耳样24个,2019年采自江苏省靖江市绿野生态园;版纳猪(Banna pig) 耳样6个,2015年采自云南省西双版纳州滇南小耳猪保种场;五指山猪(Wuzhishan pig) 耳样6个,2015年采购于海南省五指山市;巴马小型猪(Bama minipig) 耳样6个,2016年采自广西巴马原种香猪农牧实业有限公司;藏猪(Tibetan pig) 耳样6个,2016年由云南省甘孜市畜牧所提供;野猪(Wild boar)耳样6个,2015年采购自安徽省。
1.2 方法1.2.1 猪esr基因序列的转座子注释从Ensembl (http://asia.ensembl.org/index.html)数据库中查找猪esr1基因(ENSSSCT000000351 47.2) 和esr2基因(ENSSSCT00000005632.3) 的参考序列,分别向上游延伸5 kb,下游延伸3 kb后下载,以此序列在NCBI的WGS库(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) 比对获得皮特兰猪、巴马猪、巴克夏猪、金华猪、杂交猪(杜长大)、汉普夏猪、长白猪、大白猪、藏猪、八眉猪、梅山猪、五指山猪、荣昌猪和哥廷根猪的esr1和esr2基因序列,ClustalX (version 2.0) 进行多序列比对,统计不同品种中esr1和esr2基因的大片段结构突变(Structural variations,SVs)。利用RepeatMasker (versions 4.0.7) 进行注释,仅保留比对得分超过1 000且序列长度超过50 bp的位点进行PCR鉴定。
1.2.2 DNA提取使用TIANamp Genomic DNA Kit (TIANGEN,中国北京) 提取上述猪耳组织,将获得的DNA使用分光光度计和琼脂糖凝胶电泳进行DNA浓度和质量检测,然后于?20 ℃保存备用。
1.2.3 引物设计及合成使用BatchPrimer3 (http://batchprimer3. bioinformatics.ucdavis.edu/cgi-bin/batchprimer3/ batchprimer3.cgi) 在线软件进行引物设计,使两侧引物分别位于猪esr基因含反转录转座子插入多态性位点左右侧翼序列中(表 1),引物由南京擎科生物科技有限公司合成。
表 1 esr1和esr2基因中验证有多态性的RIP位点引物Table 1 Primers for identifying RIP sites in the esr1 and esr2 genes
Primer name | Primer sequence (5'–3') | Annealing temperature (℃) |
esr1-SINE-RIP1 | F: ATTTAACCATGCGTCGGACT | 59 |
R: CCTTCTCAGAGAGCCTTTCC | 59 | |
esr1-LINE-RIP2 | F: GGGGTTGAACATGTTAGCAA | 58 |
R: ACTTCAAGCCCCATCATCTT | 58 | |
esr1-SINE-RIP3 | F: AAGGTAGGTCAGGGTTGCTG | 59 |
R: CTTTTTAGGGCCGCACTCTA | 59 | |
esr2-LINE- RIP | F: AATGGAGTGAGGAGCCTTTG | 59 |
R: AGCCCGCATCTGATTTAGAA | 59 |
表选项
1.2.4 PCR扩增与产物检测PCR扩增反应体系中包含猪DNA 1 μL,上、下游引物各1 μL,2×Taq Mix 10 μL,去离子水补足20 μL体系。
PCR反应程序为:95 ℃预变性5 min;95 ℃变性30 s,58–59 ℃退火1 min,72 ℃延伸30–60 s,34个循环;72 ℃最终延伸10 min后4 ℃保存。
PCR产物用1.0%琼脂糖凝胶进行电泳检测,溴化乙锭染色10 min后置于全自动数码凝胶图像分析系统中拍照。
1.2.5 统计分析利用Excel计算基因型频率和基因频率。多态性信息含量(Polymorphic information content,PIC) 的计算公式如下:
2 结果与分析2.1 猪esr1和esr2基因序列的反转录转座子注释Repeatmasker注释结果表明,esr1基因中共预测38个大片段结构突变(Structural variations, SVs),反转录转座子占47.37%;esr2中预测42个SVs,反转录转座子占69.05%,两个基因的反转录转座子总计占58.75% (表 2)。
表 2 预测猪esr1和esr2基因的结构变异Table 2 Predicted structural variations of the porcine esr1 and esr2 genes
esr1 | esr2 | Total | |
SVs | 38 | 42 | 80 |
SINE | 10 | 5 | 15 |
LINE | 7 | 22 | 29 |
LTR | 1 | 2 | 3 |
Retrotransposons/SVs (%) | 47.37% | 69.05% | 58.75% |
Note: the sequences of structural variation in this experiment were greater than or equal to 50 bp. |
表选项
2.2 PCR鉴定esr1中预测的18个反转录转座子多态性位点经PCR验证得到3个多态性位点,esr2中预测的29个多态性位点检测出1个多态性位点。图 1为esr1的3个位点和esr2的1个位点在杜洛克、长白猪、大白猪、苏姜猪、滇南小耳猪、二花脸猪、五指山猪、巴马香猪、藏猪、梅山猪、枫泾猪和野猪的12个品种池DNA中的多态性检测结果,其多态性位点分别命名为esr1-SINE-RIP1、esr1- LINE-RIP2、esr1-SINE-RIP3和esr2-LINE-RIP。
图 1 esr1和esr2 RIP位点在不同品种猪池DNA中的多态性检测 Fig. 1 Polymorphism of esr1 and esr2 RIP sites in DNA pool of different pig breeds. M: DL2000 DNA marker; 1: Duroc pig; 2: Landrace pig; 3: Large White pig; 4: Bama minipig; 5: Banna pig; 6: Fengjing pig; 7: Sujiang pig; 8: Wuzhishan pig; 9: Tibetan pig; 10: Meishan pig; 11: Erhualian pig; 12: wild boar. |
图选项 |
esr1-SINE-RIP1、esr1-LINE-RIP2、esr1-SINE- RIP3和esr2-SINE-RIP在基因中插入位置如图 2所示。插入的片段大小、转座子类型等信息如表 3所示。
图 2 esr1和esr2基因结构示意图 Fig. 2 Schematic diagram of the esr1 and esr2 genes. |
图选项 |
表 3 esr1和esr2基因反转录转座子插入序列信息Table 3 Analysis of retrotransposon sequences in the esr1 and esr2 genes
Name | Location | Length (bp) | Direction | Classification |
esr1-SINE-RIP1 | Intron 2 | 288 | + | SINEA1 |
esr1-LINE-RIP2 | Intron 5 | 202 | – | L1C7 |
esr1-SINE-RIP3 | Intron 5 | 290 | + | SINEA9 |
esr2-LINE-RIP | Intron 1 | 381 | – | L1A3 |
表选项
2.3 esr1和esr2 RIP位点群体多态性分析esr1和esr2 RIP位点在引入品种(大白猪、长白猪和杜洛克猪)、地方品种(梅山猪、二花脸猪、枫泾猪和姜曲海猪) 以及培育品种(苏姜猪和苏山猪) 中的基因型频率、等位基因频率、Hardy-Weinberg检验和PIC等如表 4所示。
表 4 不同品种猪esr1和esr2反转录转座子插入多态性分析Table 4 Analysis of the esr1 and esr2 RIP in different pig breeds
Polymorphic sites | Breeds | Number | Genotype frequency | Allele frequency | Hardy- Weinberg equilibrium | Polymorphic information content | |||
+/+ | +/– | –/– | + | – | |||||
esr1-SINE-RIP1 | Large White | 404 | 10.15 | 56.93 | 32.92 | 38.61 | 61.39 | 5.40e-5 | 0.36 |
Landrace | 24 | 4.17 | 95.83 | 2.08 | 97.92 | 0.92 | 0.04 | ||
Sushan | 24 | 29.17 | 70.83 | 14.58 | 85.42 | 0.40 | 0.22 | ||
esr1-LINE-RIP2 | Large White | 394 | 25.89 | 47.46 | 26.65 | 49.62 | 50.38 | 0.17 | 0.38 |
Landrace | 24 | 83.33 | 16.67 | 91.67 | 8.33 | 0.66 | 0.14 | ||
Duroc | 24 | 91.67 | 8.33 | 95.83 | 4.17 | 0.83 | 0.08 | ||
Fengjing | 24 | 100.00 | 100.00 | ||||||
Jiangquhai | 24 | 8.33 | 91.67 | 4.17 | 95.83 | 0.83 | 0.08 | ||
Sujiang | 106 | 33.02 | 38.68 | 28.30 | 52.36 | 47.64 | 0.02 | 0.37 | |
Sushan | 24 | 23.08 | 46.15 | 30.77 | 46.15 | 53.85 | 0.72 | 0.37 | |
esr1-SINE-RIP3 | Large White | 359 | 33.98 | 48.75 | 17.27 | 58.36 | 41.64 | 0.90 | 0.37 |
Meishan | 24 | 91.67 | 8.33 | 95.83 | 4.17 | 0.83 | 0.14 | ||
Fengjing | 24 | 100.00 | 100.00 | ||||||
Sushan | 24 | 66.67 | 33.33 | 83.33 | 16.67 | 0.33 | 0.24 | ||
esr2-LINE-RIP | Meishan | 24 | 0 | 79.17 | 20.83 | 39.58 | 60.42 | 0.001 | 0.36 |
Erhualian | 24 | 66.67 | 33.33 | 83.33 | 16.67 | 0.33 | 0.24 | ||
Fengjing | 24 | 70.83 | 29.17 | 85.42 | 14.58 | 0.40 | 0.22 | ||
Jiangquhai | 24 | 45.83 | 54.17 | 22.92 | 77.08 | 0.15 | 0.29 | ||
Sujiang | 110 | 17.27 | 41.82 | 40.91 | 38.18 | 61.82 | 0.23 | 0.36 | |
Sushan | 24 | 8.33 | 91.67 | 4.17 | 95.83 | 0.83 | 0.08 | ||
+/+: homozygote with retrotransposon insertion; +/–: heterozygote with retrotransposon insertion; –/–: homozygote without retrotransposon insertion; +: allele with retrotransposon insertion; –: allele without retrotransposon insertion. |
表选项
esr1-SINE-RIP1在大白猪、长白猪和苏山猪中有多态性且SINE–频率高于SINE+频率,地方品种中未检测到SINE插入。esr1-LINE-RIP2在被检测的9个品种中只有梅山猪、二花脸猪和枫泾猪没有多态性,长白猪和杜洛克猪中未检测到LINE–/–个体,姜曲海猪未检测到LINE+/+个体。esr1-SINE-RIP3在大白猪、梅山猪、苏山猪中有多态性,且SINE+频率高于SINE–频率,梅山猪中无SINE–/–型个体。esr2-LINE-RIP在引入品种中未检测到插入,培育品种苏山猪中纯合插入个体为0,LINE+频率也仅为4.17%。PIC结果显示,大白猪esr1-SINE-RIP1位点,大白猪、苏姜猪和苏山猪esr1-LINE-RIP2位点,大白猪esr1-SINE-RIP3位点,以及苏姜猪、姜曲海猪和梅山猪esr2-LINE- RIP2位点均为中度以上多态性,其他为低度多态性。
2.4 esr1-SINE-RIP1与大白猪性状关联分析将esr1-SINE-RIP1、esr1-LINE-RIP2、esr1-SINE-RIP3和RIP1-esr2-LINE 4个多态性位点与大白猪生长性状进行关联分析发现,大白猪esr1-SINE-RIP1位点的SINE+/+个体活体背膘厚和100 kg体重背膘厚显著高于SINE+/–个体(P < 0.05)。体重、眼肌厚度和达100 kg体重日龄与SINE是否插入无显著性关联(表 5)。
表 5 esr1-SINE-RIP1多态性与大白猪生长性状关联分析Table 5 Correlation analysis between esr1-SINE-RIP1 polymorphism and growth traits of Large White pigs
Genotype | Number | Body weight before slaughter (kg) | Thickness of back fat (mm) | Loin eye muscle thickness (mm) | Age at 100 kg body weight (d) | Back fat thickness at 100 kg body weight (mm) |
SINE+\+ | 39 | 104.16±1.62a | 12.74±0.64a | 58.39±0.91a | 161.04±1.60a | 12.23±0.57A |
SINE+\– | 224 | 104.42±0.79a | 11.38±0.20b | 56.67±0.34a | 161.28±0.68a | 10.93±0.17B |
SINE–\– | 133 | 103.89±0.56a | 11.57±0.24b | 57.40±0.42a | 161.23±0.88a | 11.28±0.22B |
Note: the same letter in the same column means that the difference between groups is not significant. Different superscript lowercase letters indicated significant difference between groups (P < 0.05). Different superscript capital letters indicated extremely significant difference between groups (P < 0.01). |
表选项
3 讨论1996年美国Rothschild研究组发现,雌激素受体基因(esr) 是猪产仔数的主效基因[18],此后,国内外众多研究者对esr基因在不同种群中的多态性及遗传效应进行了研究。大部分的研究结果证实了esr基因存在多个标记,对于繁殖性能特别是猪的头胎产仔数有一定的影响[19]。目前没有关于esr基因的转座子插入多态性的分子标记研究报道。
RIP是由Flevell等[20]提出的,是一种依据反转录转座子及其侧翼DNA序列设计的PCR引物的显性标记系统,可揭示某个基因座的不同等位状态(有无反转录转座子的插入)。其主要优点是可以用来进行大量的标记分析。目前RIP在植物和动物遗传进化与育种中得到了广泛应用。本研究采用比较基因组学预测了猪esr1和esr2的47个RIP位点,采用PCR证实了4个多态性位点,分别是位于esr1的SINEA1、L1C7、SINEA9插入和位于esr2的L1A3插入,依据Chen等[21]对猪反转录转座子的分类,上述均为年轻的反转录转座子。推测其可能有一定的活性,影响基因的表达或功能。
本研究对4个RIP位点在引入品种、地方品种和培育品种中的分布进行了检测。esr1-SINE-RIP1位点在地方品种中未检测到SINE插入,长白猪和苏山猪中插入频率较低。长白猪和杜洛克猪中esr1-LINE-RIP2位点的LINE+频率高于LINE–,姜曲海猪中LINE–频率高于LINE+,枫泾猪中未检测到LINE插入。以杜洛克猪、姜曲海猪和枫泾猪为亲本培育的苏姜猪中LINE+频率为52.36%,LINE–为47.64%,Hardy-Weinberg检验显示,苏姜猪中该位点偏离平衡(P < 0.05),说明人工选育影响了该位点的平衡。esr2-LINE-RIP位点在引入品种中未检测到插入。苏山猪中LINE+频率较低,可能是因为苏山猪的亲本为苏钟猪和大约克猪,而苏钟猪是以二花脸猪、梅山猪和长白猪为亲本[22]、地方猪种所占血缘较少的缘故。
因esr与雌激素结合在雌性动物的繁殖性状形成中发挥重要作用,本文前期对4个RIP位点与苏姜猪的繁殖性状如产仔数、仔猪初生重等性状进行关联分析,但未发现显著效应(数据未展示)。将这4个位点与大白猪的生长性状进行关联分析时,发现esr1-SINE-RIP1与大白猪的活体背膘厚和100 kg体重背膘厚紧密关联。有研究表明,esr除了在雌性生殖活动中的重要作用外,对动物的骨生长和脂肪合成也有影响[23-25]。在小鼠发育过程中,雌激素异常表达或esr1功能的缺失都会导致纵向骨生长减缓,雌激素被认为是通过减少软骨细胞的吸收、增殖和合成活性来减缓这一过程,从而导致骨骺板的成熟并进一步抑制纵向骨生长[23]。esr在脂肪中的作用机制目前尚不清楚,但有研究表明,脂肪组织具有esr1[24]和雌二醇合成所需的酶[25]。还有研究表明,性腺类固醇可以改变脂蛋白脂肪酶的活性,而脂蛋白脂肪酶是脂肪细胞生长和脂肪储存的关键酶[26]。也有相关报道证实猪esr基因突变与生长性状相关,如1997年Short等对4 262头母猪的esr位点进行基因分型,发现esr基因与活体背膘厚有一定的相关性,并分析到其与乳头数变异有关[27]。本研究通过性状关联分析发现esr1基因内含子2的SINE插入会影响猪的背膘沉积,其他性状未见明显变化,是否会对本文没有涉及的性状造成影响还有待进一步研究。因此该位点可以考虑作为分子标记辅助育种来调控猪的活体背膘厚,达到提高瘦肉率的目的。
4 结论对esr1和esr2基因进行多序列比对,转座子注释和PCR鉴定出4个反转录转座子多态性位点,分别是位于esr1的SINEA1、L1C7、SINEA9插入和位于esr2的L1A3插入。与大白猪的生长性状进行关联分析发现,esr1-SINE-RIP1位点的SINE+/+纯合插入个体的活体背膘厚和100 kg体重背膘厚显著高于SINE+/–个体和SINE–/–个体,可以考虑作为分子标记辅助选择大白猪瘦肉率。
参考文献
[1] | Zhang Z, Chen ZT, Ye SP, et al. Genome-wide association study for reproductive traits in a Duroc pig population. Animals (Basel), 2019, 9(10): 732. |
[2] | Crespo-Piazuelo D, Criado-Mesas L, Revilla M, et al. Indel detection from whole genome sequencing data and association with lipid metabolism in pigs. PLoS ONE, 2019, 14(6): e0218862. DOI:10.1371/journal.pone.0218862 |
[3] | Zhao Y, Wang K, Wang WL, et al. A high-throughput SNP discovery strategy for RNA-seq data. BMC Genomics, 2019, 20(1): 160. DOI:10.1186/s12864-019-5533-4 |
[4] | Wang H, Wang C, Yang K, et al. Genome-wide distributions and functional characterization of copy number variations between Chinese and Western pigs. PLoS ONE, 2015, 10(7): e0131522. DOI:10.1371/journal.pone.0131522 |
[5] | Xiong Y, Eickbush TH. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J, 1990, 9(10): 3353-3362. DOI:10.1002/j.1460-2075.1990.tb07536.x |
[6] | Lisch D. How important are transposons for plant evolution?. Nat Rev Genet, 2013, 14(1): 49-61. |
[7] | Xiao H, Jiang N, Schaffner E, et al. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science, 2008, 319(5869): 1527-1530. DOI:10.1126/science.1153040 |
[8] | Mirouze M, Reinders J, Bucher E, et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature, 2009, 461(7262): 427-430. DOI:10.1038/nature08328 |
[9] | Clark LA, Wahl JM, Rees CA, et al. Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. Proc Natl Acad Sci USA, 2006, 103(5): 1376-1381. DOI:10.1073/pnas.0506940103 |
[10] | Dall'Olio S, Scotti E, Fontanesi L, et al. Analysis of the 227 bp short interspersed nuclear element (SINE) insertion of the promoter of the myostatin (MSTN) gene in different horse breeds. Vet Ital, 2014, 50(3): 193-197. |
[11] | 陈伟. vrtn和ktn1基因转座子插入多态鉴定及其与生产性能的关联分析[D]. 扬州: 扬州大学, 2019. Chen W. Polymorphism identification of VRTN and KTN1 Gene transposon insertion and its association with production performance[D]. Yangzhou: Yangzhou University, 2019 (in Chinese). |
[12] | 陈才, 陈伟, 郑尧, 等. 转座子引起的猪ktn1基因结构变异及其与生产性能的关联分析. 生物工程学报, 2020, 36(2): 267-275. Chen C, Chen W, Zheng Y, et al. Structural variations caused by transposons in porcine ktn1 gene and their association with production traits. Chin J Biotech, 2020, 36(2): 267-275 (in Chinese). |
[13] | Han S, Khan MHU, Yang Y, et al. Identification and comprehensive analysis of the CLV3/esr-related (CLE) gene family in Brassica napus L. Plant Biol (Stuttg), 2020, 22(4): 709-721. DOI:10.1111/plb.13117 |
[14] | Tremblay GB, Tremblay A, Copeland NG, et al. Cloning, chromosomal localization, and functional analysis of the murine estrogen receptor β. Mol Endocrinol, 1997, 11(3): 353-365. |
[15] | Mosselman S, Polman J, Dijkema R. ER β beta: identification and characterization of a novel human estrogen receptor. FEBS Lett, 1996, 392(1): 49-53. DOI:10.1016/0014-5793(96)00782-X |
[16] | Rothschild MF, Messer LA, Vincent A. Molecular approaches to improved pig fertility. J Reprod Fertil Suppl, 1996, 52: 227-236. |
[17] | 王宵燕, 何庆玲, 经荣斌, 等. esr基因在苏姜猪世代选育中的遗传变异及与猪群繁殖性状的关联. 中国农业科学, 2012, 45(4): 768-773. Wang XY, He QL, Jing RB, et al. Genetic variation of ESR gene in different generations of Sujiang pigs and the impact on reproductive traits of pigs. Sci Agric Sin, 2012, 45(4): 768-773 (in Chinese). DOI:10.3864/j.issn.0578-1752.2012.04.018 |
[18] | Rothschild MF, Jacobson C, Vaske D, et al. The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc Natl Acad Sci USA, 1996, 93: 201-205. DOI:10.1073/pnas.93.1.201 |
[19] | 周梅, 张玉, 王重龙, 等. 猪产仔数性状候选基因研究进展. 家畜生态学报, 2020, 41(8): 1-6. Zhou M, Zhang Y, Wang CL, et al. Research progress on candidate genes for litter size traits in pigs. J Domest Anim Ecol, 2020, 41(8): 1-6 (in Chinese). DOI:10.3969/j.issn.1673-1182.2020.08.001 |
[20] | Flevell AJ, Knox MR, Pearce SR, et al. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J, 1998, 16(5): 643-650. DOI:10.1046/j.1365-313x.1998.00334.x |
[21] | Chen C, Wang W, Wang XY, et al. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mob DNA, 2019, 10: 19. DOI:10.1186/s13100-019-0161-8 |
[22] | 任守文, 李碧侠, 葛云山, 等. 苏山猪选育研究. 中国畜牧杂志, 2020, 56(11): 47-51. Ren SW, Li BX, Ge YS, et al. Study on breeding of Sushan pig. Chin J Anim Sci, 2020, 56(11): 47-51 (in Chinese). |
[23] | Lundeen SG, Carver JM, McKean ML, et al. Characterization of the ovariectomized rat model for the evaluation of estrogen effects on plasma cholesterol levels. Endocrinology, 1997, 138(4): 1552-1558. DOI:10.1210/endo.138.4.5083 |
[24] | Pedersen SB, B?rglum JD, M?ller-Pedersen T, et al. Effects of in vivo estrogen treatment on adipose tissue metabolism and nuclear estrogen receptor binding in isolated rat adipocytes. Mol Cell Endocrinol, 1992, 85(1/2): 13-19. |
[25] | Price TM, O'Brien SN. Determination of estrogen receptor messenger ribonucleic acid (mRNA) and cytochrome P450 aromatase mRNA levels in adipocytes and adipose stromal cells by competitive polymerase chain reaction amplification. J Clin Endocrinol Metab, 1993, 77(4): 1041-1045. |
[26] | Price TM, O'Brien SN, Welter BH, et al. Estrogen regulation of adipose tissue lipoprotein lipase—possible mechanism of body fat distribution. Am J Obstet Gynecol, 1998, 178(1): 101-107. DOI:10.1016/S0002-9378(98)70634-9 |
[27] | Short TH, Rothschild MF, Southwood OI, et al. Effect of the estrogen receptor locus on reproduction and production traits in four commercial pig lines. J Anim Sci, 1997, 75(12): 3138-3142. |