Genetic and genomic characterization of a multiparent advanced generation inter-cross (MAGIC) population of peanut (Arachis hypogea L.)

Authors: THOMPSON, ETHAN - University Of Georgia; WANG, HUI - University Of Georgia; KORANI, WALID - Hudsonalpha Institute For Biotechnology; FOUNTAIN, JAKE - University Of Georgia; CULBREATH, ALBERT - University Of Georgia; Holbrook, Carl - Corley; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology; Guo, Baozhu

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Cultivated peanut is an important legume crop grown worldwide. However, cultivated peanut has a narrow genetic base with limited genetic diversity. Multiparent populations allow for the combination of several diverse lines into one population, thus increasing recombination and diversity. Multiparental advanced generation inter-cross (MAGIC) populations facilitate a mosaic of all founders equally within the population through multiple crossing generations, resulting in the capability to dissect complex genetic traits and support plant breeding by broadening the genetic base. Here we describe a peanut MAGIC population (PeanutMAGIC) with 2,775 RILs derived from eight diverse peanut cultivars and breeding lines through a simple funnel design. PeanutMAGIC is a new mapping population and offering an additional resource for peanut germplasm improvement. We randomly selected a subset of 310 RILs from PeanutMAGIC, called MAGIC Core, and conducted phenotyping for pod and seed traits and performed whole genome resequencing for genotyping. The PeanutMAGIC or the MAGIC Core will be made available for research and breeding purposes upon request.

Technical Abstract: Multiparent advanced generation inter-cross (MAGIC) populations are a new type of genetic resource for both high-resolution mapping of quantitative traits and breeding selection as germplasm or improved cultivars. We have developed an eight parent MAGIC population for peanut (Arachis hypogea L.). These eight diverse founders were inter-crossed using a structured funnel mating design to ensure that the MAGIC population would possess a balanced representation from each parent, followed by small family plot and single-seed descent, resulting in 2,775 F7 recombinant inbred lines (RILs). The objectives of this study were to introduce a peanut MAGIC population (PeanutMAGIC) as a new resource for genetic and genomic studies. We selected a subset of 310 MAGIC RILs, called MAGIC Core, and conducted two-year phenotyping for seed and pod traits, and genotyping by whole genome resequencing. The characterization of MAGIC Core demonstrated that PeanutMAGIC harbors a balance and evenly differentiated mosaic of genome blocks from the eight founders, providing unique recombination events for high-definition mapping of quantitative traits. Using the two years of phenotypic data, we showed that PeanutMAGIC can achieve high-definition mapping of a spectrum of qualitative to quantitative traits such as seed coat color, pod weight, seed weight, shelling percentage, pod constriction, and pod reticulation. Genetic and genomic characterization suggests that PeanutMAGIC could be used as a new resource for genetic mapping and breeding.