Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.
Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.
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在肉类和鸡蛋型鸡系中选择的遗传变异和推定区域的全基因组表征。
DOI：
10.1186/s12864-018-4444-0
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发表时间：
2018-01-25
期刊：
影响因子：
4.4
通讯作者：
Coutinho LL
中科院分区：
文献类型：
--
作者：
Boschiero C;Moreira GCM;Gheyas AA;Godoy TF;Gasparin G;Mariani PDSC;Paduan M;Cesar ASM;Ledur MC;Coutinho LL
肉用型和蛋用型鸡已经根据不同的性状进行了几代选择。针对不同表型的人工和自然选择可以改变遗传变异的频率，在基因组中留下特定的基因组足迹。因此，本研究的目的是从两个巴西系（肉和白色蛋型）的28只鸡的序列，并使用这些信息来表征全基因组的遗传变异，确定推定的区域选择下使用Fst方法，并找到推定的选择下的途径。共鉴定出1393万个SNP和136万个INDEL，其中从肉鸡（肉型）品系中检测到更多的变异。虽然大多数位于非编码区，我们确定了7255个不耐受的非同义SNPs，512个stopgain/loss SNPs，1381个移码和1094个非移码INDEL，可能会改变蛋白质功能。携带不耐受性非同义SNPs的基因影响代谢途径，主要涉及白蛋蛋鸡系的生殖和内分泌系统，以及肉鸡系的脂质代谢和代谢性疾病。滑动窗口的Fst分析，分别使用SNPs和INDEL，确定了超过300个假定的选择区域与超过250个基因重叠。首次在鸡中，INDEL变体被考虑用于选择标记分析，显示SNP和INDEL数据之间的结果的高度相关性。选择标记的推定区域揭示了与鸡的重要表型性状（如脂质代谢、生长、繁殖和心脏发育）相关的有趣的候选基因和途径。本研究应用Fst方法确定了高置信度的选择区域，为揭示选择足迹提供了新的视角，有助于阐明与肉用和蛋用鸡品系相关的不同表型性状的功能机制。此外，我们从巴西肉鸡和白色蛋鸡品系中产生了一个大的品系特异性和常见遗传变异的目录，这些遗传变异可用于基因组研究，包括与家禽业经济利益表型的关联分析。本文的在线版本（10.1186/s12864-018-4444-0）包含补充材料，可供授权用户使用。
Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry. The online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Johnson JL;Wittgenstein H;Mitchell SE;Hyma KE;Temnykh SV;Kharlamova AV;Gulevich RG;Vladimirova AV;Fong HW;Acland GM;Trut LN;Kukekova AV
通讯作者：
Kukekova AV
影响因子：
3.7
作者：
Gholami M;Erbe M;Gärke C;Preisinger R;Weigend A;Weigend S;Simianer H
通讯作者：
Simianer H
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
全基因组 mRNA 筛选和功能分析显示 FOXO3 是鸡生长的候选基因
影响因子：
3.7
作者：
Chen B;Xu J;He X;Xu H;Li G;Du H;Nie Q;Zhang X
通讯作者：
Zhang X
DOI：
10.1093/bioinformatics/btv562
发表时间：
2016-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Díez-Villanueva A;Serra E;Buschbeck M;Peinado MA;Malinverni R
通讯作者：
Malinverni R