Identification of a stable major QTL for fresh-seed germination on chromosome Arahy.04 in cultivated peanut (Arachis hypogaea L.)

Fresh-seed germination (FSG) impairs peanut production, especially in areas where the peanut harvest season coincides with rainy weather. Developing FSG-resistant cultivars by molecular breeding is expected to mitigate yield loss and quality impairment caused by FSG. However, the genetic control of FSG awaits elucidation. In this study, FSG at 1, 3, 5, 7, and 9 days post-imbibition in three environments were tested, and quantitative-trait loci (QTL) associated with FSG were mapped in a peanut recombinant inbred line population by leveraging existing high-density peanut genetic maps. Of 24 QTL identified in 13 linkage groups, qFSGA04 was a stable major QTL on linkage group 04 (LG04). It was consistently detected in five germination stages and three environments. By designing and validating DNA markers in the confidence interval of qFSGA04, we identified one single-nucleotide polymorphism and one InDel closely associated with FSG that could be used as linked markers for FSG resistance in peanut breeding.