CUI Xueqiang,DENG Jieling,HUANG Changyan,et al.SNP Molecular Markers Development and Population Genetic Diversity Analysis of Liparis gigantea[J].Northern Horticulture,2023,(21):101-108.[doi:10.11937/bfyy.20231659]
紫花羊耳蒜SNP标记开发及居群遗传多样性分析
- Title:
- SNP Molecular Markers Development and Population Genetic Diversity Analysis of Liparis gigantea
- 文章编号:
- 1001-0009(2023)21-0101-08
- Keywords:
- Liparis gigantea; SLAF-seq; SNP marker; populations; genetic diversity
- 分类号:
- S 682.31
- 文献标志码:
- A
- 摘要:
- 以广西乐业县4个紫花羊耳蒜地理居群共44份样本为试材，采用特异性位点扩增片段测序（SLAF-seq）方法开发了紫花羊耳蒜SNP标记，利用开发的标记研究了紫花羊耳蒜不同地理居群间的遗传多样性及亲缘关系，以期为紫花羊耳蒜的开发利用及野生居群保护提供参考依据。结果表明：测试样本共获得152 Mb Clean Reads数据，各样本Reads数据在2 098 129~5 169 592。样本平均GC含量为35.67%，平均测序质量值Q30为94.19%。通过测序数据分析，共获得1 428 438个SLAF标签，标签的平均测序深度为13.12×，其中具多态性的SLAF标签有210 148个。共开发得到574 866个群体SNP标记，每个样本的SNP 标记数目介于232 156~420 019，SNP标记完整度40.38%~73.06%，杂合率为2.51%~5.47%。对群体SNP 过滤，共获得52 450个高度一致性的有效SNP 标记。使用相关软件计算遗传多样性指数，平均最小等位基因频率（MAF）为0.314 6；平均观察杂合度（Ho）为0.160 1；平均Nei′s基因多样性指数（H）为0.436 8；平均多态性信息含量（PIC）为0.312 6；平均Shannon多样性信息指数（I）为0.580 8，表明紫花羊耳蒜居群间遗传多样性较丰富。利用筛选获得的SNP标记构建系统发育进化树，44份紫花羊耳蒜样本资源被分为4个类群，分析发现居群的遗传多样性及聚类结果与其生长海拔高度有一定相关性。
- Abstract:
- A total of 44 samples from 4 geographical populations of Liparis gigantea in Leye county，Guangxi were used as test materials.Specific site amplified fragment sequencing (SLAF-seq) was used to develop SNP markers for Liparis gigantea.The genetic diversity and genetic relationships among different geographical populations of Liparis gigantea were studied by using the developed markers，in order to provide reference for the development，utilization and wild population protection of Liparis gigantea.The results showed that a total of 152 Mb of Clean Reads data were obtained from the test samples.The Reads data of each sample ranged from 2 098 129 to 5 169 592.The average GC content and sequencing quality value (Q30) of samples was 35.67% and 94.19%.Through sequencing data analysis，a total of 1 428 438 SLAF tags and 210 148 polymorphic SLAF tags were obtained.The average sequencing depth of the tags was 13.12×.A total of 574 866 population SNP markers were developed.The number of SNP markers in each sample ranged from 232 156 to 420 019.The integrity ratio was 40.38% to 73.06%，and the hetloci ratio was 2.51% to 5.47%.The population SNPs were filtered，and a total of 52 450 highly consistent and effective SNP markers were obtained.Using relevant software to calculate the genetic diversity index.The average minimum allele frequency (MAF) was 0.314 6.The average observed heterozygosity (Ho) was 0.160 1.The average Nei′s gene diversity index (H) was 0.436 8.The average polymorphism information content (PIC) was 0.312 6.The average Shannon diversity information index (I) was 0.580 8，indicating that the genetic diversity among populations of Liparis gigantea was relatively rich.The phylogenetic tree was constructed by using the SNP markers obtained.The 44 Liparis gigantea resources were divided into 4 groups.Analysis revealed that the genetic diversity and clustering results of the population were correlated with their growth altitude.
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备注/Memo
第一作者简介：崔学强（1991-），男，硕士，助理研究员，现主要从事兰科植物分子育种等研究工作。E-mail：yncuixueqiang@126.com.责任作者：张自斌（1978-），男，博士，副研究员，现主要从事兰科植物分子育种等研究工作。E-mail：candou154@126.com.基金项目：广西自然科学基金资助项目(2020GXNSFAA297090)；广西重点研发计划资助项目(桂科AB21220056)；广西农业科学院基本科研业务专项资助项目(桂农科2021YT133)。收稿日期：2023-05-15