金定鸭全基因组选择信号检测

Detection of whole-genome selection signal in Jinding duck

在自然选择和人工选择协同作用下,中国地方鸭品种表型具有多样性。选择信号是生物进化过程中产生的基因型标记,通过选择信号检测可揭示物种进化方向。对4个福建地方鸭品种进行简化基因组测序,以连城白鸭、莆田黑鸭和山麻鸭为参考背景,检测金定鸭选择信号,探求该品种进化方向。基于SNP数据,利用群体遗传分化指数(Fst)和核苷酸多样性比值(πratio)进行选择性清除分析,根据top 5%确定Fst和πratio阈值,将两个阈值结合以确定受选择基因组区域。3个比较组的受选择区域分别检测出349、185、316个候选基因;对候选基因进行GO和KEGG富集分析,结果显示这3组候选基因中分别有129、27、77个基因显著富集在20、6、14条通路上(P<0.05)。从这些显著富集的候选基因中挑选出可能与金定鸭重要经济性状相关的功能基因;候选基因主要参与代谢途径、PI3K-Akt信号通路、趋化因子信号通路、淀粉和蔗糖代谢等,提示金定鸭在产蛋性能、肌肉生长发育、热应激、免疫和脂肪代谢等方面经历较强人工选择。研究结果为金定鸭遗传资源保护与开发利用提供参考。

Chinese indigenous ducks shape the phenotypic diversities of varieties under the influence of natural selection and artificial selection.Selection signatures are genotypic markers formation in the process of species evolution.The detection of selection signatures can reveal the evolutionary direction of species.In this study,restriction-site associated DNA sequencings was performed on four local duck breeds in Fujian Province,and selection signal detection was performed on Jinding duck with Liancheng White duck,Putian black duck and Shanma duck as the reference background to explore the evolutionary direction of this breed.Based on SNP data,selective sweep analysis was performed using population genetic differentiation coefficient(Fst)and nucleotide diversity ratio(πratio).The top 5%value was used as the threshold for Fst andπratio,and the two thresholds were combined to identify selected genomic regions.In the selected regions of the three comparison groups,349,185 and 316 candidate genes were detected,respectively.The candidate genes were analyzed by gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG).The results showed that 129,27 and 77 genes were significantly enriched in 20,6 and 14 pathways,respectively(P<0.05).The functional genes that may be related to the important economic traits of Jinding ducks were selected from these significantly enriched candidate genes.These candidate genes were mainly involved in metabolic pathways,PI3K-Akt signaling pathways,starch and sucrose metabolism,chemo kine signaling pathways and so on,suggesting that Jinding duck has experienced strong artificial selection in egg laying performance,muscle growth and development,heat stress,immunity and fat metabolism.The results of this study provided a reference for the protection and development of genetic resources of Jinding duck.