Population genomic analyses based on 1 million SNPs in commercial egg layers.
Population genomic analyses based on 1 million SNPs in commercial egg layers.
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DOI：
10.1371/journal.pone.0094509
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Simianer H
中科院分区：
文献类型：
--
作者：
Gholami M;Erbe M;Gärke C;Preisinger R;Weigend A;Weigend S;Simianer H
识别选择的特征可以提供关于处于或已经处于选择压力下的基因或基因组区域的有价值的见解，这可以导致更好地理解基因型-表型关系。选择标记检测的一种常见策略是比较来自多个种群的样本，并搜索具有显著遗传分化的基因组区域。Wright固定指数FST是评价居群间遗传分化的有效指标。本研究的目的是检测不同鸡群之间的SNP-wise FST计算的基础上的选择性签名。采用3种不同的600 K SNP芯片对3个商品蛋鸡品种和14个非商品花式品种的96个个体进行基因分型。过滤后，总共有100万个SNP可用于FST计算。计算重叠窗口的FST值的平均值。然后在商业产蛋鸡和非商业产花式品种之间，以及在白色产蛋鸡和棕色产蛋鸡之间进行这些比较。比较非商业和商业品种导致630个选择性标记的检测，而656个选择性标记的检测在商业蛋鸡品种之间的比较。选择标记区域的注释揭示了对应于生产性状的各种基因，选择了蛋鸡品种。其中NCOA 1、SREBF 2和RALGAPA 1与繁殖性状、就巢性和产蛋量相关。此外，检测到的几个基因与生长和胴体性状相关，包括POMC，PRKAB 2，SPP 1，IGF 2，CAPN 1，TGF β 2和IGFBP 2。我们的方法表明，包括具有特定育种历史的不同种群可以为更好地理解农场动物选择提供独特的机会。
Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.
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影响因子：
14.9
作者：
Kanehisa M;Goto S;Sato Y;Furumichi M;Tanabe M
通讯作者：
Tanabe M
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM
影响因子：
4.4
作者：
Bennett, A. K.;Hester, P. Y.;Spurlock, D. M.
通讯作者：
Spurlock, D. M.
影响因子：
4.5
作者：
Johansson AM;Pettersson ME;Siegel PB;Carlborg O
通讯作者：
Carlborg O
影响因子：
5.8
作者：
Jombart, Thibaut;Ahmed, Ismail
通讯作者：
Ahmed, Ismail