RNA‐Seq analysis revealed differentially expressed genes linked to seed size variation in sainfoin

Abstract Sainfoin is a perennial forage legume with many desirable characteristics such as easy to establish, bloat‐free trait for grazing ruminants and providing pollinator habitat and biological nitrogen fixation to soil. However, adoption of this species is often hindered by high seed cost associated with its larger seed size compared to other forage legumes. One possible solution is to improve desirable sainfoin seed traits with an increased number of seeds per unit weight. This study was conducted using an RNA‐Seq technique to identify differentially expressed genes (DEGs) associated with sainfoin seed development at 7, 14 and 21 days after pollen fertilization from genotypes differing in seed size. More than 92.8% clean sequence reads were mapped to the sainfoin reference genome, and 771 DEGs were identified at the three time points. Certain DEGs were consistently expressed across all three seed developmental stages, and these genes were specific to each seed small group. Gene ontology analysis showed that the identified DEGs were significantly associated with 51 Gene Ontology (GO) terms across “biological process,” “cellular component” and “molecular function” domains. Two DEGs, LeOno04cG0222300 and LeOno01dG0039200, were highly expressed in small seed genotypes. These identified DEGs and related genomic resources may be useful for marker‐assisted breeding in sainfoin for a reduced seed size.