Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes.
Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes.
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猪繁殖候选基因中的逆转录转座子插入多态性 (RIP)
DOI：
10.3390/genes13081359
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发表时间：
2022-07-28
期刊：
影响因子：
3.5
通讯作者：
Song, Chengyi
中科院分区：
文献类型：
--
作者：
Du, Zhanyu;D'Alessandro, Enrico;Asare, Emmanuel;Zheng, Yao;Wang, Mengli;Chen, Cai;Wang, Xiaoyan;Song, Chengyi
反转录转座子占猪参考基因组的三分之一以上。由于不同品种的基因组变异性，由反转录转座产生的缺失或插入（indel）引起的结构变异（SV）可能在基因组中具有功能。窝产仔数是最重要的繁殖性状之一，对养猪生产的盈利能力有着重要的影响。本研究运用生物信息学、遗传学和分子生物学的方法，对不同猪种的基因组进行了分析。预测的100个SV在20个与繁殖性能相关的基因中被注释为反转录转座子indel。基于这些预测的SV的PCR检测在20个基因中发现了20个RIP，其中大多数RIP（12个）由SINE indel产生，8个RIP由ERV indel产生。从9个猪种中筛选出12个RIPs对24个个体进行了第二轮PCR检测。PCR检测结果表明，RIP-A1 CF-4插入片段在巴马、大白色和梅山猪中仅存在纯合基因型，在其他猪种中存在低至中度多态性。我们发现RIP-CWH 43 -9、RIP-IDO 2 -9、RIP-PRLR-6、RIP-VMP 1 -12和RIP-OPN-1在大白色猪品种中具有丰富的多态性。统计分析表明，RIP-CWH 43 -9的SINE插入有利于大白猪的总产仔数和窝产仔数的繁殖性状，但对大白猪的窝产仔数影响显著（p < 0.01）和（p < 0.05）。另一方面，IDO 2 -9中的SINE插入可能对LW的繁殖性状不利，这在大白色中受到显著影响（p < 0.05）。这两个RIPs在猪基因组研究中具有重要意义，可作为育种体系中有用的分子标记。
Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotranspos-on-generated deletion or insertion (indel) may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive traits of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.
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影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.
影响因子：
50.3
作者：
Garsed, Dale W.;Marshall, Owen J.;Thomas, David M.
通讯作者：
Thomas, David M.
影响因子：
2.4
作者：
Li, K.;Ren, J.;Huang, L.
通讯作者：
Huang, L.
影响因子：
1.9
作者：
Baumgartner, W;Weiss, P;Schindler, H
通讯作者：
Schindler, H
DOI：
10.18699/vj17.231
发表时间：
2017-01-01
期刊：
Vavilovskij Zbreve~urnal Genetiki i Selekcii / Vavilov Journal of Genetics and Breeding
影响因子：
--
作者：
Kalendar, R. N.;Aizharkyn, K. S.;Tagimanova, D. S.
通讯作者：
Tagimanova, D. S.