我国地方鸡品种资源丰富,且在长期的选择进化过程中形成了各异的种质特性.科学评估群体遗传多样性,明确品种间遗传结构,对地方鸡品种资源的保护与创新利用具有重要价值.为了评估23K SNP芯片"酉芯一号"在地方鸡遗传多样性和遗传结构分析中的应用效力,本文利用RADseq鉴定21个地方鸡种基因组遗传变异,并研发23K芯片"酉芯一号".基于两组SNP数据集计算各品种的遗传统计量,开展相关性、拟合及系统发育分析,以评估芯片的应用效力.结果表明,基于两组SNP数据集计算的观察杂合度(Ho)、多态信息含量(PIC)、近交系数(FROH)和遗传分化系数(Fst),在21个地方鸡种中趋势基本一致.琅琊鸡(LA)、瓢鸡(PJ)、文昌鸡(WC)的遗传多样性较为丰富;边鸡(BJ)、狼山鸡(LS)、固始鸡(GS)、东乡绿壳蛋鸡(DX)和北京油鸡(BY)的遗传多样性相对匮乏,两组Ho、PIC、FROH和平均Fst的相关系数分别为0.794、0.901、0.926和0.984,均达到极显著水平(P＜0.01),且拟合度较高(P＜0.001),R2分别为0.644、0.827、0.916和0.927.针对两组SNP数据集,采用邻接法(NJ)和极大似然法(ML)构建的进化树较为合理,将21个地方鸡种总体上分为6大类,与品种的形成历史和地理分布相吻合;23K芯片对5个新增品种亦实现有效聚类,没有出现个体偏离.利用不同密度的SNP估算遗传统计量会存在一定差异,需要进行数据和分析方法的标准化,23K芯片在地方鸡遗传多样性和结构分析中具有较好的效力.

Double-digested Restriction Site Associated DNA Sequencing (ddRAD) through next-generation sequencing (NGS) generates large numbers of loci for characterizing genomewide variation among multiple samples using next-generation sequencing.Different combinations of restriction endonucleases (REs) may produce varying size distributions of digested fragments,which affect the number of genotyped loci.Understanding digestion profiles across different species will help in selecting REs for digestion in a particular organism.In this study,we use ofgenome sequences to compare the in silico digestion profile of 26 combinations of REs in 131 insect species with two simulation programs.The number of digested fragments in the 300-450 bp range increases linearly with the size of the genome.Different species and insect orders showed similar profiles when digested by different combinations of REs in silico,indicating the conservation of digestion by double enzymes in insect genomes.Combinations with NlaⅢ or TaqαⅠ usually produced higher number of fragments in the range 300-450 bp,while combinations with EcoRI or MluCI produced fewer fragments.The proportion of fragments with the same overhangs at the two ends of digested DNA was higher than those with different overhangs.The two four-base enzyme pairs produced more fragments in the 300-450 bp range than pairs of four-base + six-base enzymes.Experimental digestion of three species from Hymenoptera,Lepidoptera and Thysanoptera showed profiles congruent with in silico expectations.Our results shed light on understanding the digestion profiles of insect genomes and provide guidance on selecting REs for ddRAD projects.

The Hawaiian radiation of Myrsine(primrose family,Primulaceae)is the only one among the ten most species-rich Hawaiian plant lineages that has never been included in a phylogenetic analysis.Our study is based on a RADseq dataset of nearly all Hawaiian Myrsine species and a Sanger sequencing dataset based on a worldwide sampling of Myrsine and related genera.Myrsine as a whole might be paraphyletic with respect to the monotypic Macaronesian genera Heberdenia and Pleiomeris,whereas Hawaiian Myrsine is resolved as monophyletic.The Sanger sequencing proved to be insufficient to resolve the Hawaiian lineage,whereas RADseq fully resolved the relationships with high support.Hawaiian Myrsine consists of three main lineages,of which one contains the majority of species and is mainly confined to Kaua'i,and the other two lineages primarily consist of few widespread species.Although phylogenetic reconstructions delivered fully resolved and supported tree topologies,Quartet Sampling and HyDe analyses reveal phylogenetic incongruence throughout the phylogeny and provide the first molecular evidence of extensive hybridization in the lineage.