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

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.

Mapping and Validation of Major Quantitative Trait Loci for Resistance to Northern Corn Leaf Blight Along With the Determination of the Relationship Between Resistances to Multiple Foliar Pathogens of Maize (Zea mays L.)

Among various foliar diseases affecting maize yields worldwide, northern corn leaf blight (NCLB) is economically important. The genetics of resistance was worked out to be quantitative in nature thereby suggesting the need for the detection of quantitative trait loci (QTL) to initiate effective marker-aided breeding strategies. From the cross CML153 (susceptible) × SKV50 (resistant), 344 F_{2 : 3} progenies were derived and screened for their reaction to NCLB during the rainy season of 2013 and 2014. The identification of QTL affecting resistance to NCLB was carried out using the genetic linkage map constructed with 194 polymorphic SNPs and the disease data recorded on F_{2 : 3} progeny families. Three QTL for NCLB resistance were detected on chromosomes 2, 5, and 8 with the QTL qNCLB-8-2 explaining the highest phenotypic variation of 16.34% followed by qNCLB-5 with 10.24%. QTL for resistance to sorghum downy mildew (SDM) and southern corn rust (SCR) were also identified from one season phenotypic data, and the co-location of QTL for resistance to three foliar diseases was investigated. QTL present in chromosome bins 8.03, 5.03, 5.04, and 3.04 for resistance to NCLB, SDM, and SCR were co-localized, indicating their usefulness for the pyramiding of quantitative resistance to multiple foliar pathogens. Marker-assisted selection was practiced in the crosses CM212 × SKV50, HKI162 × SKV50, and CML153 × SKV50 employing markers linked to major QTL on chromosomes 8, 2, and 10 for NCLB, SDM, and SCR resistance, respectively. The populations were advanced to F₆ stage to derive multiple disease-resistant inbred lines. Out of the 125 lines developed, 77 lines were tested for their combining ability and 39 inbred lines exhibited high general combining ability with an acceptable level of resistance to major diseases.

Genetic Dissection of Quantitative Resistance to Common Rust (Puccinia sorghi) in Tropical Maize (Zea mays L.) by Combined Genome-Wide Association Study, Linkage Mapping, and Genomic Prediction

Common rust is one of the major foliar diseases in maize, leading to significant grain yield losses and poor grain quality. To dissect the genetic architecture of common rust resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid (DH) population, DH1, were used to perform GWAS and linkage mapping analyses. The GWAS results revealed six single-nucleotide polymorphisms (SNPs) significantly associated with quantitative resistance of common rust at a very stringent threshold of P-value 3.70 × 10^-6 at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04. Linkage mapping identified five quantitative trait loci (QTL) at bins 1.03, 2.06, 4.08, 7.03, and 9.00. The phenotypic variation explained (PVE) value of each QTL ranged from 5.40 to 12.45%, accounting for the total PVE value of 40.67%. Joint GWAS and linkage mapping analyses identified a stable genomic region located at bin 4.08. Five significant SNPs were only identified by GWAS, and four QTL were only detected by linkage mapping. The significantly associated SNP of S10_95231291 detected in the GWAS analysis was first reported. The linkage mapping analysis detected two new QTL on chromosomes 7 and 10. The major QTL on chromosome 7 in the region between 144,567,253 and 149,717,562 bp had the largest PVE value of 12.45%. Four candidate genes of GRMZM2G328500, GRMZM2G162250, GRMZM2G114893, and GRMZM2G138949 were identified, which played important roles in the response of stress resilience and the regulation of plant growth and development. Genomic prediction (GP) accuracies observed in the GWAS panel and DH1 population were 0.61 and 0.51, respectively. This study provided new insight into the genetic architecture of quantitative resistance of common rust. In tropical maize, common rust could be improved by pyramiding the new sources of quantitative resistance through marker-assisted selection (MAS) or genomic selection (GS), rather than the implementation of MAS for the single dominant race-specific resistance gene.

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.

Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm

Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F₃ biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h²) estimates were moderate with 0.37-0.45 for the individual F₃ populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6-10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14-40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F₃ populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize.

Identification and Fine Mapping of qSCR4.01, a Novel Major QTL for Resistance to Puccinia polysora in Maize

Southern corn rust (SCR) is a prevalent foliar disease that can lead to severe yield losses in maize. Growing SCR-resistant varieties is the most effective way to control the disease. To identify major quantitative trait loci (QTLs) for SCR resistance, a recombinant inbred line population derived from a cross between CIMBL83 (resistant) and Lx9801 (susceptible) was analyzed. The resistance to SCR had high heritability within the population, and a major QTL on chromosome 4 (qSCR4.01), which can explain 48 to 65% of the total phenotypic variation, was consistently detected across multiple environments. Using a progeny-based fine-mapping strategy, we delimited qSCR4.01 to an interval of ∼770 kb. In contrast to other major QTLs for SCR resistance previously reported on the short arm of chromosome 10, qSCR4.01 is a novel QTL and, therefore, a desirable source of SCR resistance in maize breeding programs.

Dominant, Heritable Resistance to Stewart's Wilt in Maize Is Associated with an Enhanced Vascular Defense Response to Infection with Pantoea stewartii

Vascular wilt bacteria such as Pantoea stewartii, the causal agent of Stewart's bacterial wilt of maize (SW), are destructive pathogens that are difficult to control. These bacteria colonize the xylem, where they form biofilms that block sap flow leading to characteristic wilting symptoms. Heritable forms of SW resistance exist and are used in maize breeding programs but the underlying genes and mechanisms are mostly unknown. Here, we show that seedlings of maize inbred lines with pan1 mutations are highly resistant to SW. However, current evidence suggests that other genes introgressed along with pan1 are responsible for resistance. Genomic analyses of pan1 lines were used to identify candidate resistance genes. In-depth comparison of P. stewartii interaction with susceptible and resistant maize lines revealed an enhanced vascular defense response in pan1 lines characterized by accumulation of electron-dense materials in xylem conduits visible by electron microscopy. We propose that this vascular defense response restricts P. stewartii spread through the vasculature, reducing both systemic bacterial colonization of the xylem network and consequent wilting. Though apparently unrelated to the resistance phenotype of pan1 lines, we also demonstrate that the effector WtsE is essential for P. stewartii xylem dissemination, show evidence for a nutritional immunity response to P. stewartii that alters xylem sap composition, and present the first analysis of maize transcriptional responses to P. stewartii infection.

Combined linkage and association mapping reveal QTL for host plant resistance to common rust (Puccinia sorghi) in tropical maize

BACKGROUND

Common rust, caused by Puccinia sorghi, is an important foliar disease of maize that has been associated with up to 50% grain yield loss. Development of resistant maize germplasm is the ideal strategy to combat P. sorghi.

RESULTS

Association mapping performed using a mixed linear model (MLM), integrating population structure and family relatedness identified 25 QTL (P < 3.12 × 10- 5) that were associated with resistance to common rust and distributed on chromosomes 1, 3, 5, 6, 8, and 10. We identified three QTLs associated with all three disease parameters (final disease rating, mean disease rating, and area under disease progress curve) located on chromosomes 1, 3, and 8. A total of 5 QTLs for resistance to common rust were identified in the RIL population. Nine candidate genes located on chromosomes 1, 5, 6, 8, and 10 for resistance to common rust associated loci were identified through detailed annotation.

CONCLUSIONS

Using a diverse set of inbred lines genotyped with high density markers and evaluated for common rust resistance in multiple environments, it was possible to identify QTL significantly associated with resistance to common rust and several candidate genes. The results point to the need for fine mapping common rust resistance by targeting regions identified in common between this study and others using diverse germplasm.

Pest categorisation of Pantoea stewartii subsp. stewartii

Following a request from the European Commission, the EFSA Plant Health Panel performed a pest categorisation of Pantoea stewartii subsp. stewartii (hereafter P. s. subsp. stewartii). P. s. subsp. stewartii is a Gram-negative bacterium that causes Stewart's vascular wilt and leaf blight of sweet corn and maize, a disease responsible for serious crop losses throughout the world. The bacterium is endemic to the USA and is now present in Africa, North, Central and South America, Asia and Ukraine. In the EU, it is reported from Italy with a restricted distribution and under eradication. The bacterium is regulated according to Council Directive 2000/29/EC (Annex IIAI) as a harmful organism whose introduction and spread in the EU is banned on seeds of Zea mays. Other reported potential host plants include various species of the family Poaceae, including weeds, rice (Oryza sativa), oat (Avena sativa) and common wheat (Triticum aestivum), as well as jackfruit (Artocarpus heterophyllus), the ornamental Dracaena sanderiana and the palm Bactris gasipaes, but there is uncertainty about whether these are hosts of P. s. subsp. stewartii or of the other subspecies. The pest could enter the EU via host plants for planting (including seed) and via insect vectors from neighbouring countries. Host plants are widely distributed and climatic conditions are conducive in the EU. P. s. subsp. stewartii could spread by movement of host plants for planting (including seeds) and insect vectors. Impacts could occur on maize and rice. Methods to certify pest freedom of maize seeds are available. The main knowledge gaps concern the availability of vectors in the EU, the level of susceptibility of the maize cultivars grown in the EU, the virulence of strains in recent outbreaks, and the host range of the bacterium. The criteria assessed by the Panel for consideration as a potential quarantine pest are met.

Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize

Southern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. Upon previous study with the nested association mapping (NAM) population, which consist of 5,000 recombinant inbred lines from 25 parents crossed with B73, we expanded the phenotyping environments from the United States (US) to China, and increased the marker densities from 1106 to 7386 SNPs for linkage mapping, and from 1.6 to 28.5 million markers for association mapping. We identified 49 SLB and 48 NLB resistance-related unique QTLs in linkage mapping, and multiple loci in association mapping with candidate genes involved in known plant disease-resistance pathways. Furthermore, an independent natural population with 282 diversified inbred lines were sequenced for four candidate genes selected based on their biological functions. Three of them demonstrated significant associations with disease resistance. These findings provided valuable resources for further implementations to develop varieties with superior resistance for NLB and SLB.

Large-scale Maize Seedling Infection with Exserohilum turcicum in the Greenhouse

Northern corn leaf blight (NCLB) is a serious foliar disease of maize (Zea mays) worldwide and breeding for resistance is of primary importance for maize crop protection. Phenotyping for NCLB resistance is well established in the field, but such experiments depend on suitable environmental conditions and are seasonal. Here we describe a greenhouse seedling approach that is suitable for testing thousands of seedling plants in a single experiment with a duration of 37 days. Three scoring methods were used to quantify the disease severity: the area under the disease progress curve (AUDPC), the primary diseased leaf area of the inoculated leaves at 16 days post inoculation (PrimDLA at 16 dpi) and the incubation period (IP) that was determined as days from inoculation to symptom appearance. By testing a diverse panel of maize genotypes, a high correlation between the three different methods was observed (81.9% to 94.1%), indicating that each of scoring methods can be applied for disease quantification. Thus, the seedling assay developed served as a relatively simple and high-throughput method for phenotyping NCLB disease resistance under greenhouse condition.

Genetics of Resistance and Pathogenicity in the Maize/Setosphaeria turcica Pathosystem and Implications for Breeding

Northern corn leaf blight (NCLB), the most devastating leaf pathogen in maize (Zea mays L.), is caused by the heterothallic ascomycete Setosphaeria turcica. The pathogen population shows an extremely high genetic diversity in tropical and subtropical regions. Varietal resistance is the most efficient technique to control NCLB. Host resistance can be qualitative based on race-specific Ht genes or quantitative controlled by many genes with small effects. Quantitative resistance is moderately to highly effective and should be more durable combatting all races of the pathogen. Quantitative resistance must, however, be analyzed in many environments (= location × year combinations) to select stable resistances. In the tropical and subtropical environments, quantitative resistance is the preferred option to manage NCLB epidemics. Resistance level can be increased in practical breeding programs by several recurrent selection cycles based on disease severity rating and/or by genomic selection. This review aims to address two important aspects of the NCLB pathosystem: the genetics of the fungus S. turcica and the modes of inheritance of the host plant maize, including successful breeding strategies regarding NCLB resistance. Both drivers of this pathosystem, pathogen, and host, must be taken into account to result in more durable resistance.

A Genome-Wide Association Study for Partial Resistance to Maize Common Rust

Quantitative resistance to maize common rust (causal agent Puccinia sorghi) was assessed in an association mapping population of 274 diverse inbred lines. Resistance to common rust was found to be moderately correlated with resistance to three other diseases and with the severity of the hypersensitive defense response previously assessed in the same population. Using a mixed linear model accounting for the confounding effects of population structure and flowering time, genome-wide association tests were performed based at 246,497 single-nucleotide polymorphism loci. Three loci associated with maize common rust resistance were identified. Candidate genes at each locus had predicted roles, mainly in cell wall modification. Other candidate genes included a resistance gene and a gene with a predicted role in regulating accumulation of reactive oxygen species.

Two distinct classes of QTL determine rust resistance in sorghum

BACKGROUND

Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments.

RESULTS

In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust.

CONCLUSIONS

The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.

Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield. Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar 'GPBD 4' into three rust susceptible varieties ('ICGV 91114', 'JL 24' and 'TAG 24') through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2-3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56-96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.

Evidence of Multiple Disease Resistance (MDR) and implication of meta-analysis in marker assisted selection

Meta-analysis was performed for three major foliar diseases with the aim to find out the total number of QTL responsible for these diseases and depict some real QTL for molecular breeding and marker assisted selection (MAS) in maize. Furthermore, we confirmed our results with some major known disease resistance genes and most well-known gene family of nucleotide binding site (NBS) encoding genes. Our analysis revealed that disease resistance QTL were randomly distributed in maize genome, but were clustered at different regions of the chromosomes. Totally 389 QTL were observed for these three major diseases in diverse maize germplasm, out of which 63 QTL were controlling more than one disease revealing the presence of multiple disease resistance (MDR). 44 real-QTLs were observed based on 4 QTL as standard in a specific region of genome. We also confirmed the Ht1 and Ht2 genes within the region of real QTL and 14 NBS-encoding genes. On chromosome 8 two NBS genes in one QTL were observed and on chromosome 3, several cluster and maximum MDR QTL were observed indicating that the apparent clustering could be due to genes exhibiting pleiotropic effect. Significant relationship was observed between the number of disease QTL and total genes per chromosome based on the reference genome B73. Therefore, we concluded that disease resistance genes are abundant in maize genome and these results can unleash the phenomenon of MDR. Furthermore, these results could be very handy to focus on hot spot on different chromosome for fine mapping of disease resistance genes and MAS.

Characterization and fine-mapping of a resistance locus for northern leaf blight in maize bin 8.06

As part of a larger effort to capture diverse alleles at a set of loci associated with disease resistance in maize, DK888, a hybrid known to possess resistance to multiple diseases, was used as a donor in constructing near-isogenic lines (NILs). A NIL pair contrasting for resistance to northern leaf blight (NLB), caused by Setosphaeria turcica, was identified and associated with bin 8.06. This region of the maize genome had been associated in previous studies with both qualitative and quantitative resistance to NLB. In addition, bins 8.05-8.06 had been associated with quantitative resistance to several other diseases, as well as resistance gene analogs and defense response gene homologs. To test the hypothesis that the DK888 allele at bin 8.06 (designated qNLB8.06 ( DK888 )) conditions the broad-spectrum quantitative resistance characteristic of the donor, the NILs were evaluated with a range of maize pathogens and different races of S. turcica. The results revealed that qNLB8.06 (DK888) confers race-specific resistance exclusively to NLB. Allelism analysis suggested that qNLB8.06 (DK888) is identical, allelic, or closely linked and functionally related to Ht2. The resistance conditioned by qNLB8.06 was incompletely dominant and varied in effectiveness depending upon allele and/or genetic background. High-resolution breakpoint analysis, using approximately 2,800 individuals in F(9)/F(10) heterogeneous inbred families and 98 F(10)/F(11) fixed lines carrying various recombinant events, delimited qNLB8.06 ( DK888 ) to a region of approximately 0.46 Mb, spanning 143.92-144.38 Mb on the B73 physical map. Three compelling candidate genes were identified in this region. Isolation of the gene(s) will contribute to better understanding of this complex locus.

Resistance loci affecting distinct stages of fungal pathogenesis: use of introgression lines for QTL mapping and characterization in the maize--Setosphaeria turcica pathosystem

BACKGROUND

Studies on host-pathogen interactions in a range of pathosystems have revealed an array of mechanisms by which plants reduce the efficiency of pathogenesis. While R-gene mediated resistance confers highly effective defense responses against pathogen invasion, quantitative resistance is associated with intermediate levels of resistance that reduces disease progress. To test the hypothesis that specific loci affect distinct stages of fungal pathogenesis, a set of maize introgression lines was used for mapping and characterization of quantitative trait loci (QTL) conditioning resistance to Setosphaeria turcica, the causal agent of northern leaf blight (NLB). To better understand the nature of quantitative resistance, the identified QTL were further tested for three secondary hypotheses: (1) that disease QTL differ by host developmental stage; (2) that their performance changes across environments; and (3) that they condition broad-spectrum resistance.

RESULTS

Among a set of 82 introgression lines, seven lines were confirmed as more resistant or susceptible than B73. Two NLB QTL were validated in BC4F2 segregating populations and advanced introgression lines. These loci, designated qNLB1.02 and qNLB1.06, were investigated in detail by comparing the introgression lines with B73 for a series of macroscopic and microscopic disease components targeting different stages of NLB development. Repeated greenhouse and field trials revealed that qNLB1.06(Tx303) (the Tx303 allele at bin 1.06) reduces the efficiency of fungal penetration, while qNLB1.02(B73) (the B73 allele at bin 1.02) enhances the accumulation of callose and phenolics surrounding infection sites, reduces hyphal growth into the vascular bundle and impairs the subsequent necrotrophic colonization in the leaves. The QTL were equally effective in both juvenile and adult plants; qNLB1.06(Tx303) showed greater effectiveness in the field than in the greenhouse. In addition to NLB resistance, qNLB1.02(B73) was associated with resistance to Stewart's wilt and common rust, while qNLB1.06(Tx303) conferred resistance to Stewart's wilt. The non-specific resistance may be attributed to pleiotropy or linkage.

CONCLUSIONS

Our research has led to successful identification of two reliably-expressed QTL that can potentially be utilized to protect maize from S. turcica in different environments. This approach to identifying and dissecting quantitative resistance in plants will facilitate the application of quantitative resistance in crop protection.

Selection mapping of loci for quantitative disease resistance in a diverse maize population

The selection response of a complex maize population improved primarily for quantitative disease resistance to northern leaf blight (NLB) and secondarily for common rust resistance and agronomic phenotypes was investigated at the molecular genetic level. A tiered marker analysis with 151 simple sequence repeat (SSR) markers in 90 individuals of the population indicated that on average six alleles per locus were available for selection. An improved test statistic for selection mapping was developed, in which quantitative trait loci (QTL) are identified through the analysis of allele-frequency shifts at mapped multiallelic loci over generations of selection. After correcting for the multiple tests performed, 25 SSR loci showed evidence of selection. Many of the putatively selected loci were unlinked and dispersed across the genome, which was consistent with the diffuse distribution of previously published QTL for NLB resistance. Compelling evidence for selection was found on maize chromosome 8, where several putatively selected loci colocalized with published NLB QTL and a race-specific resistance gene. Analysis of F2 populations derived from the selection mapping population suggested that multiple linked loci in this chromosomal segment were, in part, responsible for the selection response for quantitative resistance to NLB.

Selection for quantitative trait loci associated with resistance to Stewart's wilt in sweet corn

The objectives of this research were to identify quantitative trait loci (QTL) for Stewart's wilt resistance from a mapping population derived from a sweet corn hybrid that is highly resistant to Pantoea stewartii and to determine if marker-based selection for those QTL could substantially improve Stewart's wilt resistance in a population derived from a cross of resistant lines and a highly susceptible sweet corn inbred. Three significant QTL for Stewart's wilt resistance on chromosomes 2 (bin 2.03), 5 (bin 5.03), and 6 (bin 6.06/6.07) explained 31% of the genetic variance in a population of 110 F(3:4) families derived from the sweet corn hybrid Bonus. The three QTL appeared to be additive in their effects on Stewart's wilt ratings. Based on means of families that were either homozygous or heterozygous for marker alleles associated with the resistance QTL, the QTL on chromosomes 2 and 6 appeared to have dominant or partially dominant gene action, while the QTL on chromosome 5 appeared to be recessive. A population of 422 BC(2)S(2) families was derived from crosses of a sweet corn inbred highly susceptible to Stewart's wilt, Green Giant Code 88 (GG88), and plants from two F(3:4) families (12465 and 12467) from the Bonus mapping population that were homozygous for marker alleles associated with Stewart's wilt resistance at the three QTL. Mean Stewart's wilt ratings for BC(2)S(2) families were significantly (P < 0.05) lower for families that were homozygous for the bnlg1902 marker allele (bin 5.03) from resistant lines 12465 or 12467 than for families that were heterozygous at this marker locus or homozygous for the bnlg1902 marker allele from GG88. Resistance associated with this QTL was expressed only if F(3:5) or BC(2)S(2) families were homozygous for marker alleles associated with the resistant inbred parent (P(1)). Marker alleles identified in the F(3:5) mapping population that were in proximity to the resistance QTL on chromosomes 2 and 6 were not polymorphic in crosses of GG88 with 12465 and 12467. Selection for other polymorphic marker loci adjacent to these two regions did not improve Stewart's wilt resistance of BC(2)S(2) families.

Analysis of quantitative trait Loci for resistance to southern leaf blight in juvenile maize

ABSTRACT A set of 192 maize recombinant inbred lines (RILs), derived from a cross between the inbred lines Mo17 and B73, were evaluated as 3-week-old seedlings in the greenhouse for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O. Six significant (LOD >3.1) quantitative trait loci (QTL) were identified for disease resistance, located on chromosomes 1, 2, 3, 6, 7, and 8. Results were compared with a previous study that had used the same RIL population and pathogen isolate, but had examined resistance in mature rather than juvenile plants. There was a very weak but significant correlation between the overall resistance phenotypes of the RILs scored as mature and juvenile plants. Two QTL were found in similar positions on chromosomes 1 and 3 at both growth stages. Other QTL were specific to one growth stage or the other. Twenty-three of these RILs, together with the parental lines, were inoculated in the greenhouse with four C. heterostrophus isolates. Results indicated that the quantitative resistance observed was largely isolate non-specific.

The genetic architecture of disease resistance in maize: a synthesis of published studies

ABSTRACT Fifty publications on the mapping of maize disease resistance loci were synthesized. These papers reported the locations of 437 quantitative trait loci (QTL) for disease (dQTL), 17 resistance genes (R-genes), and 25 R-gene analogs. A set of rules was devised to enable the placement of these loci on a single consensus map, permitting analysis of the distribution of resistance loci identified across a variety of maize germplasm for a number of different diseases. The confidence intervals of the dQTL were distributed over all 10 chromosomes and covered 89% of the genetic map to which the data were anchored. Visual inspection indicated the presence of clusters of dQTL for multiple diseases. Clustering of dQTL was supported by statistical tests that took into account genome-wide variations in gene density. Several novel clusters of resistance loci were identified. Evidence was also found for the association of dQTL with maturity-related QTL. It was evident from the distinct dQTL distributions for the different diseases that certain breeding schemes may be more suitable for certain diseases. This review provides an up-to-date synthesis of reports on the locations of resistance loci in maize.

Recombination events generating a novel Rp1 race specificity

Genes at the maize Rp1 rust resistance complex often mispair in meiosis, which allows genes to recombine unequally, creating recombinant haplotypes. Four recombinant haplotypes were identified from progeny of an Rp1-D/Rp1-I heterozygote that conferred a nonparental resistance specificity designated Rp1-I*. Sequence comparisons of paralogs in the recombinant and parental haplotypes demonstrated that all four recombinants were derived from intergenic (between gene) recombination events. The sequence of paralogs in the HRp1-I parental haplotype indicated this haplotype includes 41 or more rp1 genes, at least 31 of which are transcribed. The results indicate that most of the novel resistance specificities that have arisen spontaneously at Rp1 are the result of reassort ment of existing Rp1 genes.

Frequency of the Ht1 Gene in Populations of Sweet Corn Selected for Resistance to Exserohilum turcicum Race 1

ABSTRACT The possibility that the Ht1 gene or genes tightly linked to Ht1 convey general resistance to races of Exserohilum turcicum that are virulent against Ht1 (i.e., residual resistance) could be useful in sweet corn where the Ht1 gene is present in many commercial hybrids and breeding populations. The objective of this study was to determine if the frequency of the Ht1 gene changed in populations of sweet corn selected for general resistance to E. turcicum race 1, thus conveying residual resistance. Four populations were developed with theoretical initial frequencies of the Ht1 gene of 0, 0.25, 0.25, and 0.5. The populations were advanced by recurrent mass selection with parental control through four or five cycles of selection following inoculation with an Ht-virulent race of E. turcicum (i.e., race 1). Plants from each cycle of each population were evaluated for severity of northern corn leaf blight (NCLB) and chlorotic lesion reactions following inoculation in field and greenhouse trials with either race 0 or 1 of E. turcicum. Recurrent mass selection for general resistance to E. turcicum race 1 reduced the severity of NCLB in all four populations of sweet corn, although the change in the most susceptible population was minimal. Percent gain per cycle was 14.5, 12.3, 14, and 3.7% for populations I, II, III, and IV, respectively. The Ht1 gene did not convey levels of general resistance to E. turcicum race 1 that were substantial enough to be selected for in this population improvement program. There was no apparent selection advantage for resistance to E. turcicum race 1 in the populations that contained the Ht1 gene. The frequency of the Ht1 gene did not differ among cycles of selection within any of the populations in response to improved levels of general resistance to NCLB. The lack of change in frequency of Ht1 in these populations and the similarity in gain per cycle among populations with and without Ht1 lead us to conclude that the Ht1 gene itself did not have a residual effect on resistance.