Genetic mapping of time-to-maturity trait in hypogaea x fastigiata peanut background reveals a significant effect of pod-related and flowering pattern

Domesticated peanut (Arachis hypogaea L.) comprises two main subspecies, ssp. fastigiata and ssp. hypogaea, which differ in several characteristics, most notably time-to-maturation (TTM). Despite TTM‘s siginicance for adaptability, yield and quality, its genetic control in peanut remains largely unknown. Here, a recombinant inbred line (RIL) population, derived from a hypogaea (late-maturing) X fastigiata (early-maturing) cross, was used to dissect the genetics of TTM across three environments and to determine the associations with other traits such as plant architecture and pod/seed-related traits. A high-density genetic map that comprises 4671 SNP markers was used. Eighty-one quantitative trait loci (QTLs) were identified for all traits. Six loci were found for TTM, four of which (on A02, A05, A07 and A10) were stable and consistent across all three environments. Most TTM QTLs had small-to-medium effects except one QTL, qMIA07, which explained up to 14.3% PVE. Gene Onthology analyses showed that qMIA07 is enriched in processes that connected to pod/seed size. Indeed, qMIA07 and other three TTM QTLs were co-localized with pod/seed-related QTLs like pod/seed weight, number of double/multiple-seeded pods and number pods per plant. Flowering pattern, which is considered a TTM-affecting trait, was also co-localized with TTM on LG B02 but in only one environment. However, analysis of this QTL in a Near-Isogenic background confirmed a significant effect for flowering patern on TTM. This study demonstrates that seed/pod traits and flowering pattern are important factors that should be considered in introgressing early maturation from fastigiata background into hypogaea germplasm.