Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes.
Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes.
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猪毛色候选基因中的逆转录转座子插入多态性 (RIP)
DOI：
10.3390/ani12080969
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发表时间：
2022-04-08
期刊：
影响因子：
3
通讯作者：
Song, Chengyi
中科院分区：
文献类型：
--
作者：
Du, Zhanyu;D'Alessandro, Enrico;Zheng, Yao;Wang, Mengli;Chen, Cai;Wang, Xiaoyan;Song, Chengyi
被毛颜色是猪品种的一项重要表型性状，有少数基因参与其调控。猪品种经过长期的选择，形成了多样化的毛色表型（如黑色、红色、白色、斑点、棕色、带状、两端黑色等）。迄今为止，已经确定了影响猪毛色表型的几个主要基因。在这方面，最近的研究提出了一种新的分子标记，称为反转录转座子插入多态性（RIPs）。该标记被认为是一种理想的分子标记，显示出用于猪群体遗传分析的潜力，并有可能扩展到其他家畜。我们在猪的20个毛色基因中发现了42个ripps，其中一些ripps可能有助于区分不同的品种。摘要家畜被毛颜色的多样性是人类积极选择的结果，是品种认同的重要组成部分。猪作为一种重要的生物多样性资源，具有许多独特的特征，包括最直观的特征，毛色，适应性好，毛色代表了猪品种的重要表型特征。由于家畜的能量代谢和色素沉着受到强烈选择的影响，探索表型特征和黑素皮质素系统的遗传机制具有相当大的意义。本研究选取了哺乳动物中与毛色相关的20个基因，通过对17个猪基因组的序列比对，鉴定了这些基因区域的结构变异（SVs），这些基因区域代表了不同类型的猪（微型、瘦肉型和肥肉型）。共获得167个与反转录转座子插入（>50 bp）重叠的大结构变异（>50 bp），并将其指定为推定的rip。最后，通过PCR检测确定了42个rip。此外，利用PCR方法对11个不同毛色家养品种的更多个体的11个RIP位点的基因型分布进行了进一步评估。在不同种群中观察到这些ripps的差异分布，其中一些ripps可能与品种差异有关。
Simple Summary Coat color is an important phenotypic trait of pig breeds, and a few genes are involved in its regulation. After long-term selection, pig breeds have formed diversified coat color phenotypes (e.g., black, red, white, spotted, brown, belted, two-end black, etc.). To date, several major genes affecting pig coat color phenotypes have been identified. In this view, recent studies suggested a new type of molecular marker known as retrotransposon insertion polymorphisms (RIPs). This marker is considered an ideal molecular marker, showing the potential to be used for population genetic analysis in pigs, with the possibility to be extended to other livestock animals as well. Here, we revealed 42 RIPs in 20 coat color genes in pigs, and some RIPs may be useful in distinguishing different breeds. Abstract The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.
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DOI：
10.1534/g3.114.013425
发表时间：
2014-08-01
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
David VA;Menotti-Raymond M;Wallace AC;Roelke M;Kehler J;Leighty R;Eizirik E;Hannah SS;Nelson G;Schäffer AA;Connelly CJ;O'Brien SJ;Ryugo DK
通讯作者：
Ryugo DK
影响因子：
4.6
作者：
Du Z;Huang K;Zhao J;Song X;Xing X;Wu Q;Zhang L;Xu C
通讯作者：
Xu C
影响因子：
2.4
作者：
Johnson, J. L.;Kozysa, A.;Kukekova, A. V.
通讯作者：
Kukekova, A. V.
正弦跳跃有助于猪基因组的大规模多态性
影响因子：
4.9
作者：
Chen C;D'Alessandro E;Murani E;Zheng Y;Giosa D;Yang N;Wang X;Gao B;Li K;Wimmers K;Song C
通讯作者：
Song C
对黑色素（MLPH）基因的新见解影响兔子的外套颜色稀释。
影响因子：
3.5
作者：
Demars J;Iannuccelli N;Utzeri VJ;Auvinet G;Riquet J;Fontanesi L;Allain D
通讯作者：
Allain D