芯片检测家禽繁殖和适应性特征候选基因的选择特征（英文）

In silico detection of signatures of selection at candidate genes for productive and adaptive traits in poultry

家禽是非常重要的农业资源,对妇女和青年占较高人口比例的发展中国家的农村贫困人口具有重要意义。然而,家禽养殖业正受到全球气候变化引起的低产量、低繁殖和致命的疾病暴发和热应激条件的威胁。基于公共数据库中的候选基因序列,及开源的BLASTp软件和程序可用于物种间的同源染色体基因选择比较分析。MUSCLE软件的FastMe命令可以执行多个序列比对之前的系统发育史重建。为探测候选基因的特征,采用PAML包的嵌套密码替换模型,通过似然比检验(LRTs)和贝叶斯(BEB)后验概率来计算非同义的替换率。该计算方法检测了蛋白质激酶(PKR)、2',5'-寡腺苷酸合成酶(OAS)、toll样受体7(TLR7)和toll样受体3(TLR3)免疫基因的适应和纯化选择的特征。热休克蛋白70(HSP70)、热休克蛋白90(HSP90)和小热休克蛋白(sH SP)基因中也检测到了纯化选择。在vipr1和生长激素受体中,所有的品系均证明发生了催乳素中的纯化选择,而品系导致家禽和其他鸟类物种受到积极的正选择。对于生长激素基因,在偶蹄类中检测到正向选择。胰岛素生长因子I受体基因在位于受体L域的460位置处的异亮氨酸上具有正选择。这些结果为后续的体外和体内研究的统计检测和实验验证奠定了基础,对发展中国家家禽养殖业的分子标记和品种的遗传改良的深入研究非常重要。

Pouhry represent a valuable micro-livestock resource that is important to the rural poor in developing counties who are mostly women and the youth. However, the poultry industry is threatened by low production, productivity and virulent disease outbreaks and heat-stress conditions associated with the ongoing climate change. Gene sequences of can- didate genes in public databases were selected and a reciprocal BLASTp was performed to select inter-species homotogs for comparative analysis. MUSCLE software was used to perform Multiple Sequence Alignments prior to phylogeny recon- struction using FastMe. To detect signatures of selection, the nested codon substitution models of PAML package was used to compute the rate of non-synonymous （dN） to synonymous （dS） substitutions in different lineages and amino acid sites through likelihood Ratio Tests （LRTs） and Bayes Empirical Bayes （BEB） posterior probabilities. The Com- putational approach detected signatures of adaptive and purifying selection at Protein KinaseR （PKR） , 2＇,5＇-oligoadeny- late synthetase （OAS） , Toll-like Receptor 7 （ TLR7 ） and Toll-like Receptor3 （ TLR3 ） immune genes. Predominant pu- rifying selection was detected at Heat Shock Protein 70 （ HSP70）, Heat Shock Protein 90 （ HSP90）, and Small Heat Shock Protein （SHSP） genes. In viprl and growth hormone receptor, all the lineages were shown to be under purifying selection while in prolactin, the lineages leading to poultry and other avian species were under positive selection. For the growth hormone gene, positive selection was detected in the artiodactyls. The insulin like growth factor I receptor gene had positive selection on amino acid isoleucine at position 460 located on receptor L domain. These results form an im- portant foundation for further statistical testing and experimental validation through in vitro and in vivo studies. The downstream results are important towards the development of molecular markers for the genetic improvement of poultry in developing countries.