EST-SSR Markers’ Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of <i>Eleusine indica</i> in China
Jingchao Chen | Hailan Cui | Hongjuan Huang | Shouhui Wei | Yan Liu | Haiyan Yu | Yan Ma | Xiangju Li | Xiaoyan Ma
Goosegrass (<i>Eleusine indica</i>) 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 <i>E. indica.</i> 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 (<i>N<sub>a</sub></i>) ranging from two to eleven per locus, and the effective number of alleles (<i>N<sub>e</sub></i>) ranged from 1.07 to 4.53. The average polymorphic information content (<i>PIC</i>) was 0.36. Genetic structure analysis (K = 2) and principal coordinate analysis divided 59 <i>E. indica</i> 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 <i>E. indica</i> and successfully analyzed the diversity and population genetic structures of 59 <i>E. indica</i> populations in China.
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