De novo transcriptome assembly and candidate gene discovery for high seedling vigor in cicer milkvetch ( Astragalus cicer L.)

Cicer milkvetch ( Astragalus cicer L.) (CMV) is a perennial, winter hardy forage legume for grazing in the temperate regions of world. Low seed germination and low seedling vigor of this species often reduce stand establishment success, limiting producer adoption. Objectives of this study were to identify the differentially expressed genes (DEGs) associated with seedling vigor in high‐vigor (AC Veldt and PI440143) and low‐vigor populations (PI206405) in CMV. Five, 7‐day‐old seedlings per population were randomly chosen for RNA extraction. Sequencing generated a total of 319 million clean reads, with 97.3% mapped to the de novo assembled transcriptome. A total of 3,322 DEGs were identified between the high and low seedling vigor populations. Of these, a total of 269 DEGs were mapped to the UniProt database, with 30 DEGs (11.2%) aligned to species in the Fabaceae family, and 146 DEGs (54.6%) with proteins associated with seedling vigor. A total of 427 significant gene ontology (GO) terms were identified in the high versus low seedling populations, with 366 terms successfully classified into three main GO categories: molecular function, biological process, and cellular component. Among these, 286 (70.0%) GO terms were associated with seedling vigor, which were mainly related to BPs related to seed size determination, energy provision, and the transport of energy and ion. Once validated, these candidate genes could be used to select plants with high seedling vigor in CMV genetic improvement.