Multispectral and thermal infrared data, visual scores for severity of common rust symptoms, and genotypic single nucleotide polymorphism data of three F2-derived biparental doubled-haploid maize populations.

Three F2-derived biparental doubled haploid (DH) maize populations were generated for genetic mapping of resistance to common rust. Each of the three populations has the same susceptible parent, but a different resistance donor parent. Population 1 and 3 consist of 320 lines each, population 2 consists of 260 lines. The DH lines were evaluated for their susceptibility to common rust in two years and with two replications in each year. For phenotyping, a visual score (VS) for susceptibility was assigned. Additionally, unmanned aerial vehicle (UAV) derived multispectral and thermal infrared data was recorded and combined in different vegetation indices ("remote sensing", RS). The DH lines were genotyped with the DarTseq method, to obtain data on single nucleotide polymorphisms (SNPs). After quality control, 9051 markers remained. Missing values were "imputed" by the empirical mean of the marker scores of the respective locus. We used the data for comparison of genome-wide association studies and genomic prediction when based on different phenotyping methods, that is either VS or RS data. The data may be interesting for reuse for instance for benchmarking genomic prediction models, for phytopathological studies addressing common rust, or for specifications of vegetation indices.

Use of remote sensing for linkage mapping and genomic prediction for common rust resistance in maize.

Breeding for disease resistance is a central component of strategies implemented to mitigate biotic stress impacts on crop yield. Conventionally, genotypes of a plant population are evaluated through a labor-intensive process of assigning visual scores (VS) of susceptibility (or resistance) by specifically trained staff, which limits manageable volumes and repeatability of evaluation trials. Remote sensing (RS) tools have the potential to streamline phenotyping processes and to deliver more standardized results at higher through-put. Here, we use a two-year evaluation trial of three newly developed biparental populations of maize doubled haploid lines (DH) to compare the results of genomic analyses of resistance to common rust (CR) when phenotyping is either based on conventional VS or on RS-derived (vegetation) indices. As a general observation, for each population × year combination, the broad sense heritability of VS was greater than or very close to the maximum heritability across all RS indices. Moreover, results of linkage mapping as well as of genomic prediction (GP), suggest that VS data was of a higher quality, indicated by higher -logp values in the linkage studies and higher predictive abilities for genomic prediction. Nevertheless, despite the qualitative differences between the phenotyping methods, each successfully identified the same genomic region on chromosome 10 as being associated with disease resistance. This region is likely related to the known CR resistance locus Rp1. Our results indicate that RS technology can be used to streamline genetic evaluation processes for foliar disease resistance in maize. In particular, RS can potentially reduce costs of phenotypic evaluations and increase trialing capacities.

Occurrence and Distribution of Physiological Races of Exserohilum turcicum in Maize-Growing Regions of Mexico.

Turcicum leaf blight (TLB) is a common foliar disease of maize in Mexico that is caused by the fungal pathogen Exserohilum turcicum. The most effective management strategy against TLB is monogenic race-specific resistance. Among the 140 E. turcicum isolates from symptomatic leaves collected from maize fields in Mexico, 100 were obtained from tropical (Veracruz) and temperate areas (Estado de México) between 2010 and 2019, and 40 isolates were obtained from tropical (Sinaloa, Tamaulipas, Veracruz, and Chiapas), subtropical (Nayarit, Jalisco, and Guanajuato), and temperate areas (Estado de Mexico, Hidalgo, and Puebla) collected in 2019. All the isolates caused TLB symptoms on the positive control (ht4), showing that they were all pathogenic. Six physiological races of E. turcicum (2, 3, 23, 3N, 23N, and 123N) were identified based on resistant or susceptible responses displayed by five maize differential genotypes (A619Ht1, A619Ht2, A619Ht3, B68HtN, and A619ht4). The most common was race 23, accounting for 68% of the isolates, followed by races 23N, 123N, 3, 2, and 3N at 15, 8, 6, 2, and 1%, respectively. Race 123N was able to infect the greatest number of maize differential genotypes used in the study. Race 123N was detected in Sinaloa and Estado de México. Race 3 was detected in Nayarit and Jalisco. Race 2 was detected in Jalisco, Estado de México, and Veracruz, and race 3N was detected in Tamaulipas. Race 23 was equally dominant in the tropical, subtropical, and temperate regions, while race 123N was more common in the tropical environment, and race 23N was more common in the tropical and temperate environments. There was no evidence for shifts in the races between 2010 and 2019.

Mapping of Genetic Loci Conferring Resistance to Leaf Rust From Three Globally Resistant Durum Wheat Sources.

Genetic resistance in the host plant is the most economical and environmentally friendly strategy for controlling wheat leaf rust, caused by Puccinia triticina Eriks. The durum wheat lines Gaza (Middle East), Arnacoris (France) and Saragolla (Italy) express high levels of resistance to the Mexican races of P. triticina. Three recombinant inbred line (RIL) populations, derived from crosses of each of these resistance sources to the susceptible line ATRED #2, were evaluated for leaf rust reactions at CIMMYT's leaf rust nurseries in Mexico. Genetic analyses of host reactions suggested oligogenic control of resistance in all populations. The F8 RILs from each cross were genotyped using the Illumina iSelect 90K array, and high-density genetic maps were constructed for each population. Using composite interval mapping, a total of seven quantitative trait loci (QTL) that provide resistance to leaf rust were identified. Two QTL designated as QLr.usw-6BS and QLr.usw-6BL were identified on chromosome 6B in Gaza, which explained up to 78.5% and 21.3% of the observed leaf rust severity variance, respectively. A major QTL designated as QLr.usw-7BL was detected on the long arm of chromosome 7B in Arnacoris, which accounted for up to 65.9% of the disease severity variance. Arnacoris also carried a minor QTL on chromosome 1BL, designated as QLr.usw-1BL.1 that explained up to 17.7% of the phenotypic variance. Three QTL conferred leaf rust resistance in Saragolla, namely QLr.usw-2BS, QLr.usw-3B, and QLr.usw-1BL.2, which accounted for up to 42.3, 9.4, and 7.1% of the phenotypic variance, respectively. Markers flanking each QTL were physically mapped against the durum wheat reference sequence and candidate genes involved in disease resistance were identified within the QTL intervals. The QTL identified in this study and their closely linked markers are useful resources for gene pyramiding and breeding for durable leaf rust resistance in durum wheat.

Application of Remote Sensing for Phenotyping Tar Spot Complex Resistance in Maize.

Tar spot complex (TSC), caused by at least two fungal pathogens, Phyllachora maydis and Monographella maydis, is one of the major foliar diseases of maize in Central and South America. P. maydis was also detected in the United States of America in 2015 and since then the pathogen has spread in the maize growing regions of the country. Although remote sensing (RS) techniques are increasingly being used for plant phenotyping, they have not been applied to phenotyping TSC resistance in maize. In this study, several multispectral vegetation indices (VIs) and thermal imaging of maize plots under disease pressure and disease-free conditions were tested using an unmanned aerial vehicle (UAV) over two crop seasons. A strong relationship between grain yield, a vegetative index (MCARI2), and canopy temperature was observed under disease pressure. A strong relationship was also observed between the area under the disease progress curve of TSC and three vegetative indices (RDVI, MCARI1, and MCARI2). In addition, we demonstrated that TSC could cause up to 58% yield loss in the most susceptible maize hybrids. Our results suggest that the RS techniques tested in this study could be used for high throughput phenotyping of TSC resistance and potentially for other foliar diseases of maize. This may help reduce the cost and time required for the development of improved maize germplasm. Challenges and opportunities in the use of RS technologies for disease resistance phenotyping are discussed.

Genetic analysis of resistance to stripe rust in durum wheat (Triticum turgidum L. var. durum).

Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to stripe rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for stripe rust resistance were identified on chromosome 7B (LOD 6.87-11.47) and chromosome 5B (LOD 3.88-9.17). The QTL for stripe rust resistance on chromosome 7B was supported in the breeding panel. Both QTL were anchored to the genome sequence of wild emmer wheat, which identified gene candidates involved in disease resistance. Exome capture sequencing identified variation in the candidate genes between Kofa and W9262-260D3. These genetic insights will be useful in durum breeding to enhance resistance to stripe rust.

Detection of Aflatoxigenic and Atoxigenic Mexican Aspergillus Strains by the Dichlorvos⁻Ammonia (DV⁻AM) Method.

The dichlorvos⁻ammonia (DV⁻AM) method is a sensitive method for distinguishing aflatoxigenic fungi by detecting red (positive) colonies. In this study, the DV⁻AM method was applied for the isolation of aflatoxigenic and atoxigenic fungi from soil samples from a maize field in Mexico. In the first screening, we obtained two isolates from two soil subsamples of 20 independent samples and, in the second screening, we obtained two isolates from one subsample of these. Morphological and phylogenic analyses of the two isolates (MEX-A19-13, MEX-A19-2nd-5) indicated that they were Aspergillus flavus located in the A. flavus clade. Chemical analyses demonstrated that one isolate could produce B-type aflatoxins, while the other produced no aflatoxins. These results demonstrate that the DV⁻AM method is useful for the isolation of both aflatoxigenic and atoxigenic Aspergilli.

Characterization and mapping of leaf rust resistance in four durum wheat cultivars.

Widening the genetic basis of leaf rust resistance is a primary objective of the global durum wheat breeding effort at the International Wheat and Maize Improvement Center (CIMMYT). Breeding programs in North America are following suit, especially after the emergence of new races of Puccinia triticina such as BBG/BP and BBBQD in Mexico and the United States, respectively. This study was conducted to characterize and map previously undescribed genes for leaf rust resistance in durum wheat and to develop reliable molecular markers for marker-assisted breeding. Four recombinant inbred line (RIL) mapping populations derived from the resistance sources Amria, Byblos, Geromtel_3 and Tunsyr_2, which were crossed to the susceptible line ATRED #2, were evaluated for their reaction to the Mexican race BBG/BP of P. triticina. Genetic analyses of host reactions indicated that leaf rust resistance in these genotypes was based on major seedling resistance genes. Allelism tests among resistant parents supported that Amria and Byblos carried allelic or closely linked genes. The resistance in Geromtel_3 and Tunsyr_2 also appeared to be allelic. Bulked segregant analysis using the Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified two genomic regions for leaf rust resistance; one on chromosome 6BS for Geromtel_3 and Tunsyr_2 and the other on chromosome 7BL for Amria and Byblos. Polymorphic SNPs identified within these regions were converted to kompetitive allele-specific PCR (KASP) assays and used to genotype the RIL populations. KASP markers usw215 and usw218 were the closest to the resistance genes in Geromtel_3 and Tunsyr_2, while usw260 was closely linked to the resistance genes in Amria and Byblos. DNA sequences associated with these SNP markers were anchored to the wild emmer wheat (WEW) reference sequence, which identified several candidate resistance genes. The molecular markers reported herein will be useful to effectively pyramid these resistance genes with other previously marked genes into adapted, elite durum wheat genotypes.

Genome-Wide Analysis of Tar Spot Complex Resistance in Maize Using Genotyping-by-Sequencing SNPs and Whole-Genome Prediction.

Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Association mapping revealed four quantitative trait loci (QTL) on chromosome 2, 3, 7, and 8. All the QTL, except for the one on chromosome 3, were further validated by linkage mapping in different genetic backgrounds. Additional QTL were identified by linkage mapping alone. A major QTL located on bin 8.03 was consistently detected with the largest phenotypic explained variation: 13% in association-mapping analysis and 13.18 to 43.31% in linkage-mapping analysis. These results indicated that TSC resistance in maize was controlled by a major QTL located on bin 8.03 and several minor QTL with smaller effects on other chromosomes. Genomic prediction results showed moderate-to-high prediction accuracies in different populations using various training population sizes and marker densities. Prediction accuracy of TSC resistance was >0.50 when half of the population was included into the training set and 500 to 1,000 SNPs were used for prediction. Information obtained from this study can be used for developing functional molecular markers for marker-assisted selection (MAS) and for implementing genomic selection (GS) to improve TSC resistance in tropical maize.

Genome-Wide Association Mapping of Leaf Rust Response in a Durum Wheat Worldwide Germplasm Collection.

Leaf rust (caused by Erikss. []) is increasingly impacting durum wheat ( L. var. ) production with the recent appearance of races with virulence to widely grown cultivars in many durum producing areas worldwide. A highly virulent race on durum wheat was recently detected in Kansas. This race may spread to the northern Great Plains, where most of the US durum wheat is produced. The objective of this study was to identify sources of resistance to several races from the United States and Mexico at seedling stage in the greenhouse and at adult stage in field experiments. Genome-wide association study (GWAS) was used to identify single-nucleotide polymorphism (SNP) markers associated with leaf rust response in a worldwide durum wheat collection of 496 accessions. Thirteen accessions were resistant across all experiments. Association mapping revealed 88 significant SNPs associated with leaf rust response. Of these, 33 SNPs were located on chromosomes 2A and 2B, and 55 SNPs were distributed across all other chromosomes except for 1B and 7B. Twenty markers were associated with leaf rust response at seedling stage, while 68 markers were associated with leaf rust response at adult plant stage. The current study identified a total of 14 previously uncharacterized loci associated with leaf rust response in durum wheat. The discovery of these loci through association mapping (AM) is a significant step in identifying useful sources of resistance that can be used to broaden the relatively narrow leaf rust resistance spectrum in durum wheat germplasm.

Genetic analysis of leaf rust resistance in six durum wheat genotypes.

Leaf rust, caused by Puccinia triticina, is one of the main fungal diseases limiting durum wheat production. This study aimed to characterize previously undescribed genes for leaf rust resistance in durum wheat. Six different resistant durum genotypes were crossed to two susceptible International Maize and Wheat Improvement Center (CIMMYT) lines and the resulting F1, F2, and F3 progenies were evaluated for leaf rust reactions in the field and under greenhouse conditions. In addition, allelism tests were conducted. The results of the study indicated that most genotypes carried single effective dominant or recessive seedling resistance genes; the only exception to this was genotype Gaza, which carried one adult plant and one seedling resistance gene. In addition, it was concluded that the resistance genes identified in the current study were neither allelic to LrCamayo or Lr61, nor were they related to Lr3 or Lr14a, the genes that already are either ineffective or are considered to be vulnerable for breeding purposes. A complicated allelic or linkage relationship between the identified genes is discussed. The results of the study will be useful for breeding for durable resistance by creating polygenic complexes.