Seed vigor is an important agronomic trait, and wide variation exists among peanut accessions. However, the detailed regulatory mechanisms underlying differences in seed vigor between varieties are not known in peanut yet. Here, we performed a comparative transcriptome analysis of germinating seeds in two contrasting peanut accessions, namely A86 (high-vigor variety) and A279 (low-vigor variety). A total of 583 and 860 differentially expressed genes (DEGs) were identified at two imbibition stages between A86 and A279, respectively. Pathway enrichment tests highlighted the cell wall remodeling-, hormone signaling-, transcriptional regulation-, and oxidative stress-related DEGs, which may explain to a certain extent the difference in seed vigor between the two cultivars. Among them, the largest number of cell wall remodeling-related DEGs were extensions followed by cellulose synthases, fasciclin-like arabinogalactan proteins, polygalacturonases, expansins, and pectinesterases and the hormone signaling-related DEGs belonged mainly to the auxin and ethylene signaling pathway. The majority of transcriptional regulation-related DEGs were MYB, FAR1, and bHLH transcription factors, and the oxidative stress-related DEGs were mainly peroxidases. Further physiological analyses indicated that differences in seed vigor between A86 and A279 may be associated with differences in the ROS-scavenging abilities mediated by peroxidases. Moreover, we identified 16 DEGs homologous to known Arabidopsis regulators of seed dormancy and germination, suggesting that these DEGs would play similar functional roles during peanut seed germination. Our results not only provide important insights into the difference in seed vigor between varieties, but offer candidate genes that are worth investigating in future studies.

Seed germination is a key contributing factor to the yield of direct seeding cultivation in rice. Unraveling the genetic architecture underlying rice seed germination is pivotal for breeding elite direct-seeded rice varieties. However, only a limited number of genes regulating seed germination have been characterized in rice. In this study, we implemented a genome-wide association study (GWAS) to dissect the genetic structure of seed germination by using 131 Japonica rice accessions. We identified six stable loci (qGR1.1, qGR2.1, qGR3.1, qGR7.1, qGR8.1 and qGR9) associated with seed germination in two consecutive years, all of which were co-localized with previously reported quantitative trait loci (QTLs). OsGA2ox5, encoding a gibberellin 2-oxidase, was identified as the most plausible candidate gene of the major locus qGR7.1. Knockout of OsGA2ox5 led to delayed seed germination and retarded seedling growth. A non-synonymous variant (Chr7-218,245) within the coding region of OsGA2ox5 might be closely associated with variation in seed germination among Japonica accessions. Low nucleotide diversity at the OsGA2ox5 locus in Japonica could be a result of selection during rice improvement. Taken together, our results provide an important foundation for elucidating the molecular mechanism underlying seed germination and genetic improvement of rice seed vigor in the future.