EST-SSR Markers' Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of Eleusine indica in China
文献类型： 外文期刊
第一作者： Chen, Jingchao
作者： Chen, Jingchao;Cui, Hailan;Huang, Hongjuan;Wei, Shouhui;Yu, Haiyan;Li, Xiangju;Liu, Yan;Ma, Yan;Ma, Xiaoyan
作者机构： Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Beijing 100193, Peoples R China;Chinese Acad Trop Agr Sci, Environm & Plant Protect Inst, Haikou 571101, Peoples R China;Chinese Acad Agr Sci, Inst Cotton Res, Anyang 455000, Peoples R China
关键词： Eleusine indica; microsatellite markers; population structure; RNA-Seq
期刊名称：CURRENT ISSUES IN MOLECULAR BIOLOGY （ 2022影响因子：3.1； 五年影响因子：3.3 ）
ISSN： 1467-3037
年卷期： 2023 年 45 卷 1 期
收录情况： SCI
摘要： Goosegrass (Eleusine indica) is one of the worst agricultural weeds in China. Molecular markers were developed for genetic diversity and population structure analyses. In this study, we identified 8391 expressed sequence tag-simple sequence repeat (EST-SSR) markers from the de novo assembled unigenes of E. indica. Mononucleotides were the most abundant type of repeats (3591, 42.79%), followed by trinucleotides (3162, 37.68%). The most dominant mononucleotide and trinucleotide repeat motifs were A/T (3406, 40.59%) and AAT/ATT (103, 1.5%), respectively. Fourteen pairs of EST-SSR primers were verified and used to analyze the genetic diversity and population structure of 59 goosegrass populations. A total of 49 alleles were amplified, with the number of alleles (N-a) ranging from two to eleven per locus, and the effective number of alleles (N-e) ranged from 1.07 to 4.53. The average polymorphic information content (PIC) was 0.36. Genetic structure analysis (K = 2) and principal coordinate analysis divided 59 E. indica populations into two groups in a manner similar to the unweighted pair-group method (Dice genetic similarity coefficient = 0.700). This study developed a set of EST-SSR markers in E. indica and successfully analyzed the diversity and population genetic structures of 59 E. indica populations in China.
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