Linkage mapping and genome-wide association study identified two peanut late leaf spot resistance loci, PLLSR-1 and PLLSR-2, using nested association mapping

Authors: GANGURDE, SUNIL - University Of Georgia; THOMPSON, ETHAN - University Of Georgia; YADURU, SHASIDHAR - University Of Georgia; WANG, HUI - University Of Georgia; FOUNTAIN, JAKE - University Of Georgia; CHU, YE - University Of Georgia; OZIAS-AKINS, PEGGY - University Of Georgia; ISLEIB, THOMAS - North Carolina State University; Holbrook Jr, C; DUTTA, BHABESH - University Of Georgia; CULBREATH, A - University Of Georgia; PANDEY, M - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Guo, Baozhu

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2024
Publication Date: 6/19/2024
Citation: Gangurde, S.S., Thompson, E., Yaduru, S., Wang, H., Fountain, J., Chu, Y., Ozias-Akins, P., Isleib, T.G., Holbrook Jr, C.C., Dutta, B., Culbreath, A.K., Pandey, M.K., Guo, B. 2024. Linkage mapping and genome-wide association study identified two peanut late leaf spot resistance loci, PLLSR-1 and PLLSR-2, using nested association mapping. Phytopathology. 114:1346-1355. https://doi.org/10.1094/PHYTO-04-23-0143-R.
DOI: https://doi.org/10.1094/PHYTO-04-23-0143-R

Interpretive Summary: Next-generation genetic mapping populations like nested-association mapping (NAM) provide an exciting avenue for establishing marker-trait associations. For peanut, the advent of new genomic resources including a complete genome sequence and SNP arrays allows for the rapid and accurate genotyping of breeding lines. Genotyping of NAM_Tifrunner population with peanut 58K SNP array and three years of field phenotyping allowed for this study to identify QTLs and SNP markers associated with late leaf spot resistance and shed light on the defense mechanisms employed by peanut against this disease. NAM_Tifrunner population identified two peanut late leaf spot resistance loci, ‘PLLSD-1’ on chromosome A02/B02 and ‘PLLSD-2’ on chromosome B03. PLLSR-1 has 10 NBS-LRR disease resistant genes on B02, and an NBS-LRR disease resistance gene was also identified on homeologous chromosome A02. This is a testament to the power of the NAM approach for genetic dissection of complex traits.

Technical Abstract: Identification of genetic markers linked to late leaf spot (LLS) disease resistance in peanut (Arachis hypogaea) has been a focus of molecular breeding for U.S. industry funded peanut genome project. Efforts have been hindered by limited mapping resolution due to low levels of genetic recombination and marker density available in traditional biparental mapping populations. To address this, a multi-parental nested association mapping (NAM) population has been used and genotyped with peanut 58 K SNP array. LLS severity was evaluated in the field for three years. Joint linkage-based QTL mapping identified nine QTLs with significant phenotypic variance explained (PVE) up to 47.7%. A genome-wide association study (GWAS) identified 13 SNPs consistently associated with resistance to LLS. Two genomic regions harboring the consistent QTLs and SNPs were identified from 1,336 Kb to 1,520 Kb (184 Kb) on chromosome B02 and from 1,026.9 Kb to 1,793.2 Kb (767 Kb) on chromosome B03, designed as peanut late leaf spot resistance locus PLLSR-1 and PLLSR-2, respectively. PLLSR-1 has 10 NBS-LRR disease resistant genes on B02, and an NBS-LRR disease resistance gene Arahy.VKVT6A was also identified on chromosome A02. PLLSR-2 has five significant SNPs associated with five different genes encoding callose synthase, pollen defective in guidance protein, pentatricopeptide repeat (PPR), acyl-activating enzyme, and C2 GRAM domains-containing protein, respectively. This study highlights the power of multi-parent populations such as NAM for genetic mapping and marker-trait association studies in peanut. Validation of these two LLS resistance loci will be needed for marker-assisted breeding.