卵形鲳鲹基因组调研及其SSR分子标记的开发应用  

Genome survey and development of SSR molecular markers for Trachinotus ovatus

作　　者：张永德 文露婷 罗洪林 林勇 杜雪松 余艳玲 韦孜娜 黄姻 ZHANG Yong-de;WEN Lu-ting;LUO Hong-lin;LIN Yong;DU Xue-song;YU Yan-ling;WEI Zi-na;HUANG Yin(Guangxi Academy of Fishery Sciences/Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture,Nanning 530021,China)

机构地区：[1]广西水产科学研究院/广西水产遗传育种与健康养殖重点实验室,南宁530021

出　　处：《南方农业学报》2020年第5期983-994,共12页Journal of Southern Agriculture

基　　金：广西创新驱动发展专项(桂科AA17204080-3,桂科AA18242031-2);广西公益性科研院所基本科研业务费专项(CXIF-2016-03)。

摘　　要：[目的]通过高通量测序技术调研卵形鲳鲹基因组数据并开发SSR分子标记,为卵形鲳鲹全基因组测序与组装、种质资源保护利用及良种选育提供技术支撑。[方法]通过Illumina Hiseq 2500测序平台对卵形鲳鲹基因组进行调研,采用K-mer方法对基因组大小、杂合率、G+C含量及序列重复性等进行分析,从调研数据中分析SSR的分布特征,筛选出多态性SSR位点,并对卵形鲳鲹养殖群体进行遗传多样性分析。[结果]卵形鲳鲹基因组大小为642.68 Mb,杂合率为0.31%,重复序列比例为30.19%,G+C含量为41.45%,提示卵形鲳鲹基因组为简单基因组。基因组初步组装结果显示,Contig总长度为627.23 Mb,N50、N90分别为8.21和1.71 Mb;Scalffold总长度为628.19 Mb,N50、N90分别为10.19和2.04 Mb。从卵形鲳鲹基因组调研数据中共检测出190121条SSR序列,SSR序列分布密度为295.8条/Mb。在所有SSR序列中,以二核苷酸重复基元最多(115557条),占60.78%;其次是三核苷酸重复基元(54839条),占28.84%;六核苷酸重复基元最少(1172条),占0.62%。在二核苷酸重复基元中以TG和AC的重复数较多,分别占二核苷酸重复基元总数的22.99%和21.76%。从合成的50对SSR引物中筛选获得29对多态性SSR引物,采用这29对SSR引物对卵形鲳鲹群体进行遗传多样性分析,结果发现29个SSR位点共检测到98个等位基因,其有效等位基因数(Ne)为1.3998~3.9123(平均为2.6690),期望杂合度(He)为0.2856~0.7444(平均为0.5965),多态信息含量(PIC)为0.2647~0.6968(平均为0.5195);在29个SSR位点中,高度多态性位点(PIC>0.50)有15个,其余14个为中度多态性位点(0.25<PIC≤0.50),说明卵形鲳鲹群体遗传多样性较丰富。[结论]卵形鲳鲹基因组为简单基因组,利用基因组调研数据可实现SSR分子标记大规模开发,且新开发的SSR分子标记可用于卵形鲳鲹群体遗传多样性分析。【Objective】High throughput sequencing was used to survey the genome data of Trachinotus ovatus and develop SSR molecular markers to provide an effective basis for whole genome sequencing and assembling,protection and utilization of germplasm resources and selective breeding of T.ovatus.【Method】Illumina Hiseq 2500 sequencing platform was used to survey the T.ovatus genome,and K-mer was used to analyze the genome size,heterozygosity rate,G+C content and sequence repeatability.The distribution characteristics of SSR were analyzed from the survey data.The polymorphic SSR loci were screened and the genetic polymorphism of T.ovatus population was analyzed.【Result】The genome size of T.ovatus was 642.68 Mb,with a 0.31%heterozygosity rate and 30.19%repeated sequence proportion,and the G+C content was 41.45%,indicating that the T.ovatus genome was a simple genome.Preliminary genome assembly results showed that the total length of contig was 627.23 Mb,N50 and N90 were 8.21 Mb and 1.71 Mb,respectively,while the total length of Scalffold was 628.19 Mb,N50 and N90 were 10.19 Mb and 2.04 Mb,respectively.A total of 190121 SSR sequences were detected from the genomic survey data,with a SSR sequence distribution density of 295.8 SSRs/Mb.Among all SSR sequences,dinucleotide repeat motifs were the most common SSRs,accounting for 60.78%(115557)of the total SSR sequences;followed by trinucleotide repeat motifs,accounting for 28.84%(54839);hexanucleotide repeat motifs were the least,accounting for 1.96%(1172).Among the dinucleotide repeating motifs,TG and AC had the highest frequency in dinucleotide motifs,accounting for 22.99%and 21.76%of the total number of dinucleotiderepeating motifs,respectively.A total of 29 polymorphic SSR primers were screened from 50 SSR primers,and the genetic polymorphism analysis was conducted on 64 T.ovatus with these 29 SSR primers.The results showed that a total of 98 alleles were detected in 29 SSR loci.The effective allele number(Ne)was 1.3998-3.9123(average 2.6690),the expected heterozygos

关 键 词：卵形鲳鲹 基因组 核苷酸重复基元 SSR分子标记 遗传多样性 

分 类 号：S965.331[农业科学—水产养殖]