Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis

Authors: ZHANG, HUI - Auburn University; CHU, YE - University Of Georgia; Dang, Phat; TANG, YUEYI - Auburn University; JIANG, TAO - Auburn University; CLEVENGER, JOSH - University Of Georgia; OZIAS-AKINS, PEGGY - University Of Georgia; Holbrook, Carl - Corley; Wang, Ming; CAMPBELL, HOWARD - Auburn University; HAGAN, AUSTIN - Auburn University; CHEN, CHARLES - Auburn University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2020
Publication Date: 3/6/2020
Citation: Zhang, H., Chu, Y., Dang, P.M., Tang, Y., Jiang, T., Clevenger, J.P., Ozias-Akins, P., Holbrook Jr, C.C., Wang, M.L., Campbell, H., Hagan, A., Chen, C. 2020. Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. Theoretical and Applied Genetics. 133:2051-2061. https://doi.org/10.1007/s00122-020-03576-2.
DOI: https://doi.org/10.1007/s00122-020-03576-2

Interpretive Summary: Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. Due to strong environmental influences and involvement of many genetic components, breeding for high disease resistance has been limited. A genetics-based study called genome-wide association studies (GWAS) linking genetic differences of peanuts to ELS and LLS resistance using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core germplasm collection. The association of field resistance to variations in peanut genetic resulted in the identification of 46 quantitative trait loci (QTLs), both minor and major: 18 for ELS and 28 for LLS resistance. Of the 6 major QTLs, 5 were located on the B sub-genome and only 1 was on the A sub-genome, which suggested that the B sub-genome has more significantly resistance genomic regions than the A sub-genome. In addition, two genomic regions on linkage group B09 were found to provide significant resistance to both ELS and LLS. A total of 69 candidate genes were associated with the diseases, of which 2 candidate genes were highly correlated to both ELS and LLS and 10 only to ELS. Results provide insights into the complex interaction between cell response, disease regulated genes, and their regulatory networks. Research aids to pinpoint critical plant gene pathways and may provide gene-expression markers for applications in molecular breeding.

Technical Abstract: Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. However, the QTLs and genes underlying resistance to those diseases in peanut have not been well studied. We conducted a genome-wide association study (GWAS) for the two peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the U.S. peanut mini core collection. A total of 46 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.19% to 24.11%, in which 18 QTLs are for resistance to ELS and 28 QTLs for LLS. Among the 46 QTLs, there were four and two major QTLs with PVE higher than 16.99% for resistance ELS and LLS, respectively. Of the 6 major QTLs, 5 were located on the B sub-genome and only 1 was on the A sub-genome, which suggested that the B sub-genome has more significantly resistance genomic regions than the A sub-genome. In addition, two genomic regions on linkage group B09 were found to provide significant resistance to both ELS and LLS. A total of 69 non-redundant candidate genes were identified associated with diseases, among which, 12 candidate genes were in significant genomic regions including 2 candidate genes for both ELS and LLS, and other 10 candidate genes for ELS. The QTLs and candidate genes obtained from this study will be useful to breed peanut for resistances to the diseases.