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ARS Home » Plains Area » El Reno, Oklahoma » Oklahoma and Central Plains Agricultural Research Center » Peanut and Small Grains Research Unit » Research » Publications at this Location » Publication #403845
Research Project: Genetic Improvement of Peanut for Production in the Southwest United States Region

Location: Peanut and Small Grains Research Unit

Title: Discovery of a resistance gene cluster associated with smut resistance in peanut

Author
item Chamberlin, Kelly
item Bennett, Rebecca
item BALDESSARI, JORGE - Instituto Nacional De Tecnologia Agropecuaria
item DE LA BARRERA, GUILLERMO - Instituto Nacional De Tecnologia Agropecuaria
item CORDES, GUILLERMO - Instituto Nacional De Tecnologia Agropecuaria
item GRANDON, NANCY - Instituto Nacional De Tecnologia Agropecuaria
item MAMANI, EVA - Instituto Nacional De Tecnologia Agropecuaria
item RODRIGUEZ, ANA - Instituto Nacional De Tecnologia Agropecuaria
item MORICHETTI, SERGIO - Aceitera General Deheza
item Holbrook, Carl - Corley
item OZIAS-AKINS, PEGGY - University Of Georgia
item CHU, YE - University Of Georgia
item Tallury, Shyamalrau - Shyam
item CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology
item KORANI, WALID - Hudsonalpha Institute For Biotechnology
item Scheffler, Brian
item YOUNGBLOOD, RAMEY - Mississippi State University
item Simpson, Sheron

Submitted to: Peanut Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2024
Publication Date: 6/14/2024
Citation: Chamberlin, K.D., Bennett, R., Baldessari, J., De La Barrera, G., Cordes, G., Grandon, N.G., Mamani, E., Rodriguez, A.V., Morichetti, S., Holbrook Jr, C.C., Ozias-Akins, P., Chu, Y., Tallury, S.P., Clevenger, J.P., Korani, W., Scheffler, B.E., Youngblood, R., Simpson, S.A. 2024. Discovery of a resistance gene cluster associated with smut resistance in peanut. Peanut Science. 51(1):58-65.

Interpretive Summary: Peanut smut is a fungal disease that is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching 30%. Because fungicides have shown moderate but highly variable levels of control levels, development and deployment of smut resistant cultivars are the best strategies for disease management. Screening for smut-resistant germplasm requires years of field trials and is currently the only option for breeders because genetic markers for resistance have not yet been developed. In this study, we analyzed recombinant inbred line (RIL) populations that had been field tested for smut resistance to identify regions of the peanut genome associated with that resistance. Results identified and validated a strong quantitative loci (QTL) located on peanut chromosome 12. The identified region will be used to develop molecular markers that will be used by many to screen germplasm collections and breeding materials for smut resistance.

Technical Abstract: Peanut smut, caused by Thecaphora frezzii Carranza & J.C. Lindq., is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching 30%. Because fungicides have shown moderate but highly variable levels of control levels, development and deployment of smut resistant cultivars are the best strategies for disease management. Screening for smut-resistant germplasm requires years of field trials and is currently the only option for breeders because genetic markers for resistance have not yet been developed. The objectives of this study were to perform whole genome sequencing (WGS) on a recombinant inbred line (RIL) population developed for smut resistance mapping and subsequently fine map discovered QTL associated with smut resistance. An expedited strategy was employed by phenotyping in the F3 generation. We phenotyped 200 families with 3 plants per family for smut resistance in infested fields during the 2019/2020 season in General Deheza (32°45'23'S 63°47'20'W), Argentina. Each individual was sequenced using iGenomXRipTide library preparation and Illumina NovaSeq sequencing to yield approximately 1 times genome coverage. Analysis of the phenotype and genotype data using Khufu resulted in the identification of a single major smut resistance QTL on chromosome 12 (B02). Chromosome level genome sequences were assembled for the resistant parent (Ascasubi) and susceptible parent (Granoleico) using PacBio HIFI sequencing. A validation population was sequenced using Khufu to validate the QTL region and analysis confirmed the major locus on chromosome 12. The identified variation will be used to develop smut resistant varieties quickly using molecular assisted breeding strategies.