刀状黑黄檀基因组特征与种群遗传变异分析  

Genomic Characteristics and Population Genetic Variation of Dalbergia cultrata Graham ex Benth in China

作　　者：刘宇 郑勇奇[1] 李长红 林富荣[1] 黄平[1] LIU Yu;ZHENG Yong-qi;LI Chang-hong;LIN Fu-rong;HUANG Ping(State Key Laboratory of Tree Genetics and Breeding,Research Institute of Forestry,Chinese Academy of Forestry,Laboratory of Forest Silviculture and Tree Cultivation,Beijing 100091,China;Wenzhou Key Laboratory of Resource Plant Innovation and Utilization,Zhejiang Institute of Subtropical Crops,Zhejiang Academy of Agricultural Sciences,Wenzhou 325005,Zhejiang,China)

机构地区：[1]林木遗传育种国家重点实验室,中国林业科学研究院林业研究所,国家林业和草原局森林培育重点实验室,北京100091 [2]温州市资源植物创新利用重点实验室,浙江省农业科学院浙江省亚热带作物研究所,浙江温州325005

出　　处：《林业科学研究》2022年第4期44-53,共10页Forest Research

基　　金：国家自然科学基金项目(31761143002);国家林业与草原种质资源库(2005DKA21003)。

摘　　要：[目的]本研究旨在分析刀状黑黄檀基因组基本特征,发掘一套多态性好、重现性高的基因组SSR分子标记并用于评估其野生种群遗传变异程度。[方法]利用二代测序(NGS)方法初步评估刀状黑黄檀基因组大小、杂合度和重复序列;利用MISA对基因组上潜在的SSR位点进行检索,解析SSR类型与特征;利用Primer Premier v 5.0设计合成300对引物,通过琼脂糖凝胶电泳、非变性聚丙烯酰胺凝胶电泳对潜在的SSR位点进行初筛与复筛,最后采用荧光标记毛细管电泳进行SSR位点多态性与种群遗传多样性分析。[结果]刀状黑黄檀基因组特征分析结果显示:其基因组大小约为706.92 Mb,杂合度为1.26%,重复序列比率为55.74%。通过筛选实验,发掘了27个具有良好多态性的SSR标记,并进行了验证。结果显示27个SSR位点共扩增得到117个等位基因,多态性信息含量(PIC)介于0.149~0.803。对3个野生种群遗传多样性分析结果显示:种群水平的平均期望杂合度(H_(e))为0.504,遗传分化系数(F_(ST))为0.034;AMOVA分析显示:种群间变异占比3.46%,种群内变异占比96.54%,这表明遗传变异主要来源于种群内。[结论]刀状黑黄檀基因组属于高杂合、高重复的复杂基因组,研究结果为制定基因组精细组装策略提供了参考依据;发掘与验证的27个SSR标记具有较好的多态性与扩增稳定性;3个野生种群具有中等遗传多样性和较低的遗传分化,本研究为开展刀状黑黄檀的种质资源收集保存与分析评价提供科学依据。[Objective]To analyze the characterization of Dalberiga cultrata genome,and develop a set of high polymorphic SSR molecular markers for assessment of genetic variation of wild population.[Method]Next Generation Sequencing(NGS)was performed to evaluate the characteristic of genome,and MISA was used to mine candidate genomic SSR loci from the assembled data.The franking primers of candidate SSR loci were designed by Primer Premier v 5.0,and screened by polyacrylamide gel electrophoresis(PAGE).The polymorphic and population genetic analysis was performed by capillary electrophoresis(CE).[Result]The genome size of D.cultrata was about 706.92 Mb and the heterozygosity was about 1.26%.The rate of repetitive sequence was 55.74%.A total of 27 polymorphic SSR loci were screened and117 alleles were amplified on 27 SSR loci.The value of the polymorphism information content(PIC)varied from 0.149 to 0.803.The population genetic analysis showed the mean expected heterozygosity(He)and the coefficient of genetic differentiation(FST)was 0.504 and 0.034,respectively.AMOVA analysis revealed the genetic variation within the populations(96.54%)was much higher than that among the populations(3.46%).[Conclusion]The genome of D.cultrata belongs to high heterozygosity and highly repetitive complex genome,which provides important basic data to make a fine assembly strategy.A set of novel genomic SSR markers shows good polymorphism,and stability.Moderate genetic diversity and low genetic differentiation of wild populations of D.cultrata are revealed by SSR markers.This study would facilitate to conserve and assess wild germplasms of D.cultrata.

关 键 词：刀状黑黄檀 下一代测序技术 基因组SSR 多态性 遗传多样性 

分 类 号：S722.3[农业科学—林木遗传育种]