Widespread Occurrence of Common Rust, Caused by Puccinia sorghi, on Rp-Resistant Sweet Corn in the Midwestern United States

Dissection of Common Rust Resistance in Tropical Maize Multiparent Population through GWAS and Linkage Studies

Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as the male parent crossed with three resistant tropical maize inbred lines (CML312, D39, and Y32) to generate 627 F7 recombinant inbred lines (RILs), with the aim of identifying maize disease-resistant loci and candidate genes for common rust. Phenotypic data showed good segregation between resistance and susceptibility, with varying degrees of resistance observed across different subpopulations. Significant genotype effects and genotype × environment interactions were observed, with heritability ranging from 85.7% to 92.2%. Linkage and genome-wide association analyses across the three environments identified 20 QTLs and 62 significant SNPs. Among these, seven major QTLs explained 66% of the phenotypic variance. Comparison with six SNPs repeatedly identified across different environments revealed overlap between qRUST3-3 and Snp-203,116,453, and Snp-204,202,469. Haplotype analysis indicated two different haplotypes for CR resistance for both the SNPs. Based on LD decay plots, three co-located candidate genes, Zm00001d043536, Zm00001d043566, and Zm00001d043569, were identified within 20 kb upstream and downstream of these two SNPs. Zm00001d043536 regulates hormone regulation, Zm00001d043566 controls stomatal opening and closure, related to trichome, and Zm00001d043569 is associated with plant disease immune responses. Additionally, we performed candidate gene screening for five additional SNPs that were repeatedly detected across different environments, resulting in the identification of five candidate genes. These findings contribute to the development of genetic resources for common rust resistance in maize breeding programs.

Genetic dissection of maize disease resistance and its applications in molecular breeding

Disease resistance is essential for reliable maize production. In a long-term tug-of-war between maize and its pathogenic microbes, naturally occurring resistance genes gradually accumulate and play a key role in protecting maize from various destructive diseases. Recently, significant progress has been made in deciphering the genetic basis of disease resistance in maize. Enhancing disease resistance can now be explored at the molecular level, from marker-assisted selection to genomic selection, transgenesis technique, and genome editing. In view of the continuing accumulation of cloned resistance genes and in-depth understanding of their resistance mechanisms, coupled with rapid progress of biotechnology, it is expected that the large-scale commercial application of molecular breeding of resistant maize varieties will soon become a reality.

Identification and diversity of tropical maize inbred lines with resistance to common rust (Puccinia sorghi Schwein)

Common rust (CR) caused by Puccinia sorghi Schwein is one of the major foliar diseases of maize (Zea mays L.) in Eastern and Southern Africa. This study was conducted to (i) evaluate the response of elite tropical adapted maize inbred lines to Puccinia sorghi and identify resistant lines (ii) examine associations between CR disease parameters and agronomic traits, and (iii) assess the genetic diversity of the inbred lines. Fifty inbred lines were evaluated in field trials for three seasons (2017-2019) in Uganda under artificial inoculation. Disease severity was rated on a 1-9 scale at 21 (Rust 1), 28 (Rust 2), and 35 (Rust 3) days after inoculation. Area under disease progress curve (AUDPC) was calculated. The genetic diversity of the lines was assessed using 44,975 single nucleotide polymorphism markers. Combined ANOVA across seasons showed significant (P < .001) line mean squares for the three rust scores and AUDPC. Heritability was high for Rust 2 (0.90), Rust 3 (0.83), and AUDPC (0.93). Of the 50 lines, 12 were highly resistant to CR. Inbred lines CKL1522, CKL05010, and CKL05017 had significantly lower Rust 3 scores and AUDPC compared to the resistant check CML444 and are potential donors of CR resistance alleles. The genetic correlations between CR disease resistance parameters were positive and strong. A neighbor-joining (NJ) tree and STRUCTURE suggested the presence of three major groups among the lines, with lines highly resistant to CR spread across the three groups. The genetic diversity among the highly resistant lines can be exploited by recycling genetically distant lines to develop new multiple disease resistant inbred lines for hybrid development and deployment.

Quantitative Disease Resistance: Dissection and Adoption in Maize

Maize is the world's most produced crop, providing food, feed, and biofuel. Maize production is constantly threatened by the presence of devastating pathogens worldwide. Characterization of the genetic components underlying disease resistance is a major research area in maize which is highly relevant for resistance breeding programs. Quantitative disease resistance (QDR) is the type of resistance most widely used by maize breeders. The past decade has witnessed significant progress in fine-mapping and cloning of genes controlling QDR. The molecular mechanisms underlying QDR remain poorly understood and exploited. In this review we discuss recent advances in maize QDR research and strategy for resistance breeding.

Resistance to Puccinia polysora in Maize Accessions

A number of potential sources of general and specific resistance to southern corn rust were identified from 1,890 plant introduction accessions that were screened for reactions to Puccinia polysora race 9. Resistance appeared to differ among four accessions on which uredinia were not observed in initial screenings. Resistance to P. polysora in PI 186215 (Argentine inbred 2-687) was a chlorotic fleck, hypersensitive reaction that was conditioned by a single, dominant gene that was allelic with or very closely linked to the Rpp9 gene based on tests of allelism. All but 3 of 2,357 testcross progeny, (inbred 2-687 × Rpp9) × P_S were resistant. Resistance in Ames 19016 (Va59) was effective in F₁ progeny and appeared to be dominant and simply inherited; however, this resistance appeared to be a slow-rusting or incomplete resistance that was effective in adult plants but not in young seedlings. Severity of southern rust was less than 10% on resistant progeny from crosses with Va59 compared with severity exceeding 70% on susceptible progeny. Resistance in plant introduction (PI) 186209 (Venezuelan flint) and NSL 75976 (IA DS61) were not effective in F₁ hybrid combination and, thus, probably have limited value in commercial maize. Resistance in PI 186209 may be conditioned by a single recessive gene and resistance in NSL 75976 may be co-dominant.

Reduction in Common Rust Severity Conferred by the Rp1D Gene in Sweet Corn Hybrids Infected by Mixtures of Rp1D-Virulent and Avirulent Puccinia sorghi

The Rp1D gene confers a hypersensitive, chlorotic-fleck, resistant reaction to Puccinia sorghi, the casual agent of common rust of corn. About 40% of commercial sweet corn hybrids carry the Rp1D gene. Sine 1999, Rp1D-virulent (D-virulent) isolates of P. sorghi have occurred regularly in populations of P. sorghi in North America. Observations from sweet corn hybrid nurseries and other trials indicate that the frequency of D-virulent isolates affects severity of rust on Rp1D hybrids; however, the frequency of D-virulence at which the Rp1D gene is rendered completely ineffective is not known. The objective of this study was to assess whether common rust severity is reduced by the Rp1D gene in sweet corn hybrids infected by mixtures of D-virulent and Rp1D-avirulent (avirulent) P. sorghi. Forty pairs of Rp1D-resistant and susceptible (rp1d) versions of sweet corn hybrids from six different commercial breeding programs were evaluated in 2003 and 2004 in trials inoculated with one of five different ratios of avirulent:D-virulent inocula: 100:0, 90:10, 80:20, 60:40, or 0:100. When D-virulent P. sorghi was 100% of initial inoculum, common rust was equally severe on Rp1D and rp1d versions of the same hybrid. Thus, the Rp1D gene did not confer partial or residual resistance in these trials. When initial inocula consisted of 40% or less D-virulent P. sorghi, rust was significantly less severe on Rp1D versions than on rp1d versions of the same hybrids. Relationships between rust severity on Rp1D and rp1d versions of hybrids were explained by linear regressions in all trials. Slope coefficients (i.e., rust severity on Rp1D hybrids as a proportion of that on rp1d hybrids) were related to the percentage of D-virulent P. sorghi in the initial inoculum and were 0.21, 0.29, 0.51, 0.64, and 0.93 in 2003 and 0.25, 0.50, 0.67, 0.76, and 1.0 in 2004 for trials inoculated with 0, 10, 20, 40, and 100% D-virulent P. sorghi, respectively. Thus, the Rp1D gene may convey levels of control in proportion to the frequency of virulence in mixed populations of D-virulent and avirulent P. sorghi when the frequency of virulent isolates is less than 40%.

Yield Loss in Sweet Corn Caused by Puccinia sorghi: A Meta-Analysis

Data sets meeting established criteria were included in a meta-analysis of the relationship between percent common rust severity and percent relative yield loss in sweet corn (processing: 20 data sets; fresh market: 14 data sets). The slope of the linear, zero intercept relationship was estimated from each data set. Overall slopes and their respective 95% confidence intervals for the processing and fresh market situations were estimated by a random effects meta-analysis. Results indicated that for processing sweet corn, every 10% increase in rust severity reduced yield by 2.4 to 7.0%; the corresponding reduction for fresh market sweet corn was between 3.0 and 6.2%. A meta-regression analysis did not identify any factors that could account for the observed variability between data sets. An expression was then obtained for Δ_s, the reduction in rust severity a single strobilurin fungicide spray ought to cause for the cost of the treatment to be offset by the value of the resulting yield improvement. The empirical distribution of Δ_s,was derived by stochastic simulation, which showed that fungicide usage could be cost effective 90% of the time when rust severity is reduced by 12% in processing sweet corn and by 5% in fresh market sweet corn.

Quantitative Trait Loci in Sweet Corn Associated with Partial Resistance to Stewart's Wilt, Northern Corn Leaf Blight, and Common Rust

ABSTRACT Partial resistance to Stewart's wilt (Erwina stewartii, syn. Pantoea stewartii), northern corn leaf blight (NCLB) (Exserohilum turcicum), and common rust (Puccinia sorghi) was observed in an F(2:3) population developed from a cross between the inbred sweet corn lines IL731a and W6786. The objective of this study was to identify quantitative trait loci (QTL) associated with partial resistance using restriction fragment length polymorphic markers. Phenotypic data were collected for 2 years for Stewart's wilt, NCLB, and common rust but, due to significant family-environment interaction, analysis was conducted individually on data from each year. In 2 years of evaluation for the three diseases, a total of 33 regions in the maize genome were associated with partial resistance describing from 5.9 to 18% of the total phenotypic variability. Of six regions common in both years, three were associated with partial resistance to Stewart's wilt (chromosomes 4:07, 5:03, and 6:04), one was associated with NCLB (chromosome 9:05), and two were associated with common rust (chromosomes 2:04 and 3:04). The rust QTL on 3S mapped to within 20 cM of the rp3 locus and explained 17.7% of the phenotypic variability. Some of the QTL associated with partial resistance to the three diseases have been reported previously, and some are described here for the first time. Results suggest it may be possible to consolidate QTL from various elite backgrounds in a manner analogous to the pyramiding of major resistance genes. We also report here on two QTL associated with anthocyanin production on chromosomes 10:6 and 5:03 in the general location of the a2 gene.

Resistance Genes in the rp1 Region of Maize Effective Against Puccinia sorghi Virulent on the Rp1-D Gene in North America

Resistance in sweet corn conferred by the Rp1-D gene has controlled common rust, caused by Puccinia sorghi, in North American corn for nearly 15 years. Eleven isolates of P. sorghi virulent on corn with the Rp1-D gene were collected from Rp-resistant corn in 1999 from Wiscon-sin, Illinois, New York, and Minnesota. Isolates were increased on susceptible sweet corn. Urediniospores of nine isolates were bulked. Reactions of individual Rp genes in the rp1 region and reactions of linked combinations of Rp genes in the rp1 region (i.e., compound rust resistance genes) were evaluated against the bulked population of P. sorghi in several greenhouse trials. Reactions of individual and compound Rp genes also were evaluated against individual isolates of P. sorghi. Each trial contained at least two replicates of several lines with Rp genes and one susceptible check. Five to 10 two-leaved seedlings per line were inoculated at least twice with a suspension of urediniospores. Ten days after inoculation, rust reactions were rated:+ = sporulating uredinia, - = no sporulating uredinia, and I = chlorotic or necrotic tissue surrounding small uredinia. Four single genes, Rp1-E, Rp-G, Rp1-I, and Rp1-K, and eight compound genes, Rp1-JFC, Rp1-JC, Rp-GI, Rp-G5, Rp-GDJ, Rp-G5JD, Rp-G5JC, and Rp-GFJ, conferred resistance. Additional characterization of virulence in North American populations of P. sorghi that are avirulent against Rp1-D is necessary to determine if these genes will be as widely effective as the Rp1-D gene has been. Two subpopulations of P. sorghi were detected from the bulked population after it was sequentially cultured for at least five cycles on seedlings with Rp1-C or with Rp1-J. The subpopulation cultured on Rp1-J was avirulent on lines with Rp1-C/L/N, Rp1-B, and Rp1-M; whereas the subpopulation cultured on Rp1-C was virulent on lines with each of these genes. Both subpopulations were virulent on lines with Rp1-D.