基于简化基因组测序的不同干形云南松遗传分析  

Genetic Analysis on Different Stem Forms of Pinus yunnanensis by Reduced-representation Genome Sequencing

作　　者：吴治洋 纵丹[1,2,3] 甘沛华 刘子腾 朱梅彩 何承忠[1,2,3] WU Zhiyang;ZONG Dan;GAN Peihua;LIU Ziteng;ZHU Meicai;HE Chengzhong(Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province,Southwest Forestry University,Kunming 650224,China;Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China,Southwest Forestry University,Kunming 650224,China;Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China,Ministry of Education,Southwest Forestry University,Kunming 650224,China)

机构地区：[1]西南林业大学,云南省高校林木遗传改良与繁育重点实验室,云南昆明650224 [2]西南林业大学,西南地区生物多样性保育国家林业和草原局重点实验室,云南昆明650224 [3]西南林业大学,西南山地森林资源保育与利用教育部重点实验室,云南昆明650224

出　　处：《云南农业大学学报（自然科学版）》2022年第2期285-293,共9页Journal of Yunnan Agricultural University:Natural Science

基　　金：云南省专家工作站建设项目(202005AF150020);云南省产业技术领军人才培养项目(81210420);中央引导地方科技发展专项(YDZX201953000002845)。

摘　　要：【目的】研究直干形和扭干形云南松遗传差异,揭示其遗传变异特点。【方法】分别以胚乳和针叶为材料,采用简化基因组测序技术对直干形和扭干形云南松22份样本进行单核苷酸多态型(SNP)位点挖掘及遗传分析。【结果】样本间共获得772240个变异,其中SNP变异762699个,InDel变异9541个。在SNP变异中,颠换(38.28%)类型小于转换(61.72%)类型;而InDel变异中,缺失型变异与插入型变异数量大致相等。遗传差异分析结果显示:直干形云南松胚乳组(ES)、直干形云南松针叶组(NS)、扭干形云南松胚乳组(ET)和扭干形云南松针叶组(NT)中SNP位点的多态性信息含量(PIC)、基因多样性指数(N;)以及Shannon信息指数(Ⅰ)分别在0.1633~0.1837、0.2345~0.2625和0.3043~0.3448之间,云南松分析样本具有较低的遗传差异水平。直干形和扭干形云南松之间具有中度的遗传分化(F;=0.1071,F;=0.1437)和较高水平的基因流(N;=2.0839,N;=1.4893)。位于27条序列上的39个SNP位点能够很好地区分不同干形云南松。SNP注释结果表明:多向耐药性蛋白(PDR3)、乙烯响应转录因子(ERF017和RAP2)及MYB相关蛋白340(MYB340)等可能在云南松直干形和扭干形的发育中发挥着调控作用。【结论】云南松干形扭曲变异主要受遗传因素调控,但环境因素的协同作用增强了该特征的显著性。[Purpose]To study the genetic differences between straight and twisted stems of Pinus yunnanensis,revealing its genetic variation characteristics.[Method]Endosperm and needles of total 22 samples used as materials,reduced-representation genome sequencing technology was employed to develop single nucleotide polymorphism (SNP) markers and analyze genetic differences between straight and twisted stems of P.yunnanensis.[Results]After detection of genetic variation,a total of 772 240 variable sites were obtained.Of which,762 699 variable sites were SNPs,and the variation type of transversion (38.28%) was lower than that of transitions (61.72%);9 541 variable sites were InDels,and the variation type of insertion and deletion were roughly equal.Genetics analyses results showed that:among endosperm group in straight stem (ES),needle group in straight stem (NS),endosperm group in twisted stem (ET) and needle group in twisted stem (NT),the polymorphism information content (PIC),Nei’s diversity index (N;) and the information index of Shannon (Ⅰ) ranged from 0.163 3 to 0.183 7,0.234 5 to 0.262 5 and 0.304 3 to 0.344 8,respectively.These genetic variation indexes indicated that there were lower levels of genetic variation in tested samples of P.yunnanensis.However,there was moderate genetic differentiation (F;=0.107 1,F;=0.143 7) and frequent gene flow (N;=2.083 9,N;=1.489 3) between straight and twisted stems of P.yunnanensis.Furthermore,straight and twisted stems of P.yunnanensis could be completely identified by 39 SNPs located in 27 selected sequences.The SNP annotation results suggested that pleiotropic drug resistance protein 3 (PDR3),ethylene-responsive transcription factors (ERF017and RAP2) and MYB-related protein 340 (MYB340) maybe played a role in the regulation on straight and twisted stems development of P.yunnanensis.[Conclusion]The main stem twisted variation of P.yunnanensis is mainly regulated by genetic factors,but the synergistic effect of environmental factors enhances the significance of this feature.

关 键 词：云南松 干形变异 遗传基础 简化基因组测序 双酶切基因分型 单核苷酸多态性 

分 类 号：S791.257.08[农业科学—林木遗传育种]