Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel

Abstract

Southern rust is a severe foliar disease of maize resulting from infection with the obligate biotrophic fungus, Puccinia polysora. The disease reduces photosynthetic productivity which reduces yields with the greatest yield losses (up to 50 %) associated with earlier onset infections. Puccinia polysora urediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season, combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the US corn belt. In summer 2020, a severe outbreak of Southern Rust was observed in eastern Nebraska (NE), USA. Disease incidence severity showed significant variation among maize genotypes. A replicated maize association panel planted in Lincoln, NE was scored for disease severity. Genome wide association studies identified four loci associated with significant quantitative variation in disease severity which were associated with candidate genes with plausible links to quantitative disease resistance and a transcriptome wide association study conducted identified additional associated genes. Together these results indicate substantial diversity in resistance to southern rust exists among current temperate adapted maize germplasm, including several candidate loci which may explain observed variation in resistance to southern rust.

A role for heritable transcriptomic variation in maize adaptation to temperate environments

“…The SNPs in this peak were strongly linked to a gene encoding trehalose-6-phosphate synthase 9 (ZmTRPS9) whose exprssion and activity is altered in maize tb1 mutant 55 . Moreover, TRP9 was also involved in disease responses in tomato (Solanum lycopersicum) and southern rust 56,57 in agreement with IC32 being functionally enriched for phytohormone signaling and plant pathogen interactions (Figure 4b,c). A peak represented by the lead SNP located at 281 Mb on chromosome 1 (1:280,872,052) was associated with variation in the expression of 45 out of 743 genes expression module IC96 with an enrichment p-value of 1.33e -5 .…”

“…Although TRRS and TRPP homologs are expressed differently in response to the same stress in plants, in maize, the trehalose metabolic pathway is uniformly repressed while trehalose-6 phosphate levels are elevated, linking plant hormone signaling and trehalose metabolism 55 . In addition to the involvement of TRPS9 in the tb1 mutant 55 , TRP9 was also reported to be involved in disease responses in tomato (Solanum lycopersicum) and southern rust 56,57 . TRPS catalyzes the formation of T6P; IC32 was associated with TRPS9 and was enriched for phytohormone signaling and plant pathogen interactions, providing another piece of evidence that trehalose metabolism is involved in plant hormone sensing and disease response.…”

Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize

“…Apparent PCR duplicates were marked within the resulting BAM alignments using picard (v2.22) 19 . A priori segregating genetic markers identified in maize HapMap3 7,9 scored for each individual using GATK toolkit (v5.1) 20 . Missing values were imputed using beagle/5.01 with the HapMap3 population treated as a reference panel and parameters settings: ‘window=1 overlap=0.1 ne=1200’ 21 .…”

“…We speculate that this difference may result from the inclusion of local checks or lines-of-interest or changes in naming convention or transcription errors which we were unable to resolve. For the 1,014 unique genotypes named as part of the SAM population 3 or WiDiv population 6 , raw whole-genome sequencing or RNA-seq sequence data was aggregated from a number of sources (Table S2) 6,7,12 as described in Sun et al 2021 9 . Alignment of published sequence data from these sources to the maize reference genome (B73_RefGen_V4) 15,16 , scoring of a priori segregating SNPs from HapMap3 7 , imputation, and filtering resulted in a set of 17,717,568 with minor allele frequency >0.01 and heterozygosity rate of <0.1, leading to an average of one SNP per 120 bp (see Methods).…”

“…A set of 752 maize genotypes, which were a strict subset of the WiDiv panel, and included 254 of 369 genotypes from the SAM diversity panel were evaluated in a field experiment conducted in Lincoln, Nebraska in the summer of 2020. The experimental design of this field experiment has been previously described 9 . Briefly, the field was laid out in a randomized complete block design with two blocks of 840 plots including a repeated check genotype (B97).…”