Cicer milkvetch (Astragalus cicer L.) (CMV) is a promising legume forage crop for grazing in western Canada. CMV is characterized by perennial, winter hardy, rhizomatous herbaceous plant with aggressive creeping root, but poor seedling vigor has limited its use. In this study, an RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with seedling vigor in three CMV populations: rapid seedling vigor of AC Veldt (Veldt) and PI440143 (PI143), and slow seedling vigor of PI206405 (PI405). Five whole seedlings per population were randomly chosen 7 days after germination for RNA extraction. Sequencing generated a total of 351.2 million raw sequence reads and 97.3% of clean reads were mapped to the de novo assembled transcriptome. A total of 115 DEGs were identified between rapid and slow seedling vigor group, 76.5% (88 out of 115) were aligned to plant species in the Fabaceae family, and 15.7% (18 out of 115) DEGs were assigned to ontology categories. A group of 61 significant GO terms were identified for rapid vs slow seedling groups. These terms were mainly related to pathways associated with methylglyoxal, methyltransferase activity, inositol, phenylpropanoids, and IAA-amino acid conjugate hydrolase. The listed compounds play important roles in seed aging and vigor, seed longevity, seed germination vigor, seed germination rate, and seedling vigor in many crops. These proteins play key roles in seed and seedling vigor in many crops. Once validated, these genes could be used for selection for higher seedling vigor in CMV.
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