Genome-wide association analysis identified quantitative trait loci (QTLs) underlying drought-related traits in cultivated peanut (Arachis hypogaea L.)

Authors: Dang, Phat; PATEL, JINESH - Auburn University; Sorensen, Ronald - Ron; Lamb, Marshall; CHEN, CHARLES - Auburn University

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/28/2024
Publication Date: 7/2/2024
Citation: Dang, P.M., Patel, J., Sorensen, R.B., Lamb, M.C., Chen, C. 2024. Genome-wide association analysis identified quantitative trait loci (QTLs) underlying drought-related traits in cultivated peanut (Arachis hypogaea L.). Genes. 15(7),868. https://doi.org/10.3390/genes15070868.
DOI: https://doi.org/10.3390/genes15070868

Interpretive Summary: Drought is a destructive environmental stress that affects all critical stages of peanut such as emergence, flowering, pegging, and pod filling. Development of drought tolerant variety is a sustainable strategy for long-term peanut production. The goal of this research is to identify important genomic components linked to drought tolerance trait assessing a diverse peanut germplasm collection. Drought evaluation studies were conducted in 2017 and 2018 utilizing environmental controlled plots to ensure drought treatment affectiveness. Physiological traits, such as relative water content and specific leaf area in leaves, were measured. Drought rating was performed at the peak of drought treatment to observe physical difference among different peanut lines. Yield related traits such as pod weight and pod count were measured at harvest. Association study was performed linking genomic components and evaluated traits. A total 144 genomic components were identified including 18 significant genomic locations in proximity of 317 candidate genes. Many genomic locations identified in this research are novel for the evaluated traits, with verification that pod weight shared a significant genomic location on chromosome B06 identified in other research. Identified potential genetic markers and the associated candidate genes provide a resource for molecular marker development. Verification of candidate genes surrounding significant genomic locations will facilitate application of marker-assisted peanut breeding for drought tolerance.

Technical Abstract: Drought is a destructive abiotic stress that affects all critical stages of peanut growth such as emergence, flowering, pegging, and pod filling. The development of a drought-tolerant variety is a sustainable strategy for long-term peanut production. The U.S. mini-core peanut germplasm collection was evaluated for drought tolerance to the middle-season drought treatment phenotyping for pod weight, pod count, relative water content (RWC), specific leaf area (SLA), leaf dry matter content (LDMC), and drought rating. A genome-wide association study (GWAS) was performed to identify minor and major QTLs. A total of 144 QTLs were identified, including 18 significant QTLs in proximity to 317 candidate genes. Ten significant QTLs on linkage groups (LGs) A03, A05, A06,A07, A08, B04, B05, B06, B09, and B10 were associated with pod weight and pod count. RWC stages 1 and 2 were correlated with pod weight, pod count, and drought rating. Six significant QTLs on LGs A04, A07, B03, and B04 were associated with RWC stages 1 and 2. Drought rating was negatively correlated with pod yield and pod count and was associated with a significant QTL on LG A06. Many QTLs identified in this research are novel for the evaluated traits, with verification that the pod weight shared a significant QTL on chromosome B06 identified in other research. Identified SNP markers and the associated candidate genes provide a resource for molecular marker development. Verification of candidate genes surrounding significant QTLs will facilitate the application of marker-assisted peanut breeding for drought tolerance.