Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2012

Study of the Spectral Characteristics of Crops of Winter Wheat Varieties Infected with Pathogens of Leaf Diseases

Studying the influence of the host plant genotype on the spectral reflectance of crops infected by a pathogen is one of the key directions in the development of precision methods for monitoring the phytosanitary state of wheat agrocenoses. The purpose of this research was to study the influence of varietal factors and disease development on the spectral characteristics of winter wheat varieties of different susceptibility to diseases during the growing seasons of 2021, 2022 and 2023. The studied winter wheat crops were represented by three varieties differing in susceptibility to phytopathogens: Grom, Svarog and Bezostaya 100. Over three years of research, a clear and pronounced influence of the varietal factor on the spectral characteristics of winter wheat crops was observed, which in most cases manifested itself as an immunological reaction of specific varieties to the influence of pathogen development. The nature of the influence of the pathogenic background and the spectral characteristics of winter wheat crops were determined by the complex interaction of the development of individual diseases under the conditions of a particular year of research. A uniform and clear division of the spectral characteristics of winter wheat according to the intensity of the disease was recorded only at a level of pathogen development of more than 5%. Moreover, this gradation was most clearly manifested in the spectral channels of the near-infrared range and at a wavelength of 720 nm.

Characterization of Quantitative Trait Loci for Leaf Rust Resistance in the Uzbekistani Wheat Landrace Teremai Bugdai

Leaf rust, caused by Puccinia triticina, is a major cause of wheat yield losses globally, and novel leaf rust resistance genes are needed to enhance wheat leaf rust resistance. Teremai Bugdai is a landrace from Uzebekistan that is highly resistant to many races of P. triticina in the United States. To unravel leaf rust resistance loci in Teremai Bugdai, a recombinant inbred line (RIL) population of Teremai Bugdai × TAM 110 was evaluated for response to P. triticina race Pt54-1 (TNBGJ) and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). Quantitative trait loci (QTL) analysis using 5,130 high-quality GBS-SNPs revealed three QTLs, QLr-Stars-2DS, QLr-Stars-6BL, and QLr.Stars-7BL, for leaf rust resistance in two experiments. QLr-Stars-2DS, which is either a new Lr2 allele or a new resistance locus, was delimited to an ∼19.47-Mb interval between 46.4 and 65.9 Mb on 2DS and explained 31.3 and 33.2% of the phenotypic variance in the two experiments. QLr-Stars-6BL was mapped in an ∼84.0-kb interval between 719.48 and 719.56 Mb on 6BL, accounting for 33 to 36.8% of the phenotypic variance in two experiments. QLr.Stars-7BL was placed in a 350-kb interval between 762.41 and 762.76 Mb on 7BL and explained 4.4 to 5.3% of the phenotypic variance. Nine GBS-SNPs flanking these QTLs were converted to kompetitive allele specific PCR (KASP) markers, and these markers can be used to facilitate their introgression into locally adapted wheat lines.

Development of Methods for Remote Monitoring of Leaf Diseases in Wheat Agrocenoses

The development of remote methods for diagnosing the state of crops using spectral equipment for remote sensing of the Earth and original monitoring tools is the most promising solution to the problem of monitoring diseases of wheat agrocenoses. A research site was created on the experimental field of the Federal Research Center of Biological Plant Protection. Within the experimental field with a total area of 1 ha, test plots were allocated to create an artificial infectious background, and the corresponding control plots were treated with fungicides. The research methodology is based on the time synchronization of high-precision ground-based spectrometric measurements with satellite and unmanned remote surveys and the comparison of the obtained data with phytopathological field surveys. Our results show that the least-affected plants predominantly had lower reflectance values in the green, red, and red-edge spectral ranges and high values in the near-infrared range throughout the growing season. The most informative spectral ranges when using satellite images and multispectral cameras placed on UAVs are the red and IR ranges. At the same time, the high frequency of measurements is of key importance for determining the level of pathogenic background. We conclude that information acquisition density does not play as significant of a role as the repetition of measurements when carrying out ground-based spectrometry. The use of vegetation indices in assessing the dynamics of the spectral images of various survey systems allows us to bring them to similar values.

Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii

The wheat wild relative Aegilops tauschii was previously used to transfer the Lr42 leaf rust resistance gene into bread wheat. Lr42 confers resistance at both seedling and adult stages, and it is broadly effective against all leaf rust races tested to date. Lr42 has been used extensively in the CIMMYT international wheat breeding program with resulting cultivars deployed in several countries. Here, using a bulked segregant RNA-Seq (BSR-Seq) mapping strategy, we identify three candidate genes for Lr42. Overexpression of a nucleotide-binding site leucine-rich repeat (NLR) gene AET1Gv20040300 induces strong resistance to leaf rust in wheat and a mutation of the gene disrupted the resistance. The Lr42 resistance allele is rare in Ae. tauschii and likely arose from ectopic recombination. Cloning of Lr42 provides diagnostic markers and over 1000 CIMMYT wheat lines carrying Lr42 have been developed documenting its widespread use and impact in crop improvement.

Genome-Wide Association Studies Reveal All-Stage Rust Resistance Loci in Elite Durum Wheat Genotypes

Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.

Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing

The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied for genotype were similar to groups from other regions, which indicated past and recent migration across regions. Isolates from tetraploid durum wheat in five different regions were highly related with distinct genotypes compared to isolates from hexaploid common wheat. Based on a molecular clock, isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the divergence of isolates found worldwide that are virulent to durum wheat, and then by isolates found on common wheat.

Fine Mapping of the Wheat Leaf Rust Resistance Gene Lr42

Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both recessive and dominant in hexaploid wheat; however, in diploid Aegilops tauschii (TA2450), we found Lr42 to be dominant by studying segregation in two independent F₂ and their F_2:3 populations. We further fine-mapped Lr42 in hexaploid wheat using a KS93U50/Morocco F₅ recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers TC387992 and WMC432. The 3.7 cM Lr42 region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the Ae. tauschii reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in Ae. tauschii, respectively, and these are the likely candidates for Lr42. Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers (SNP113325 and TC387992) flanking Lr42 to facilitate marker-assisted selection for rust resistance in wheat breeding programs.

Genetic and Molecular Characterization of Leaf Rust Resistance in Two Durum Wheat Landraces

Leaf rust, caused by Puccinia triticina, is a constraint to durum wheat (Triticum turgidum subsp. durum) production, and landraces are reported to be an important source of resistance. Two Portuguese landraces (Aus26582 and Aus26579) showed resistance against durum-specific P. triticina races and were crossed with a susceptible landrace (Bansi) to develop recombinant inbred line (RIL) populations. Monogenic segregation for leaf rust resistance was observed among both RIL populations. The underlying locus, temporarily named LrAW2, was mapped to the short arm of chromosome 6B in the Aus26582/Bansi population and five DArTseq markers cosegregated with LrAW2. Simple sequence repeat markers sun683 and sun684, developed from the chromosome survey sequence (CSS) contig 6BS_2963854, identified through BlastN search of cosegregating DArTseq markers in the International Wheat Genome Sequencing Consortium database, cosegregated with LrAW2. Comparison of the CSS contig 6BS_2963854-based sequences amplified from parental genotypes led to the development of marker sunKASP_60, which also showed close linkage with LrAW2. Markers sun684 and sunKASP_60 showed close association with LrAW2 in both RIL populations. The amplification of LrAW2-specific products by linked markers in Aus26582, Aus26579, and Guayacan (Lr61) indicated that LrAW2 may be Lr61. The alternate amplicon or haplotype produced with LrAW2-linked markers in Australian durum cultivars demonstrated their effectiveness in marker-assisted selection.

Pathotype Diversity of Phytophthora sojae in Eleven States in the United States

Pathotype diversity of Phytophthora sojae was assessed in 11 states in the United States during 2012 and 2013. Isolates of P. sojae were recovered from 202 fields, either from soil samples using a soybean seedling bioassay or by isolation from symptomatic plants. Each isolate was inoculated directly onto 12 soybean differentials; no Rps gene or Rps 1a, 1b, 1c, 1k, 3a, 3b, 3c, 4, 6, 7, or 8. There were 213 unique virulence pathotypes identified among the 873 isolates collected. None of the Rps genes were effective against all the isolates collected but Rps6 and Rps8 were effective against the majority of isolates collected in the northern regions of the sampled area. Virulence toward Rps1a, 1b, 1c, and 1k ranged from 36 to 100% of isolates collected in each state, while virulence to Rps6 and Rps8 was less than 36 and 10%, respectively. Depending on the state, the effectiveness of Rps3a ranged from totally effective to susceptible to more than 40% of the isolates. Pathotype complexity has increased in populations of P. sojae in the United States, emphasizing the increasing importance of stacked Rps genes in combination with high partial resistance as a means of limiting losses to P. sojae.

Genetically Divergent Types of the Wheat Leaf Fungus Puccinia triticina in Ethiopia, a Center of Tetraploid Wheat Diversity

Collections of Puccinia triticina, the wheat leaf rust fungus, were obtained from tetraploid and hexaploid wheat in the central highlands of Ethiopia, and a smaller number from Kenya, from 2011 to 2013, in order to determine the genetic diversity of this wheat pathogen in a center of host diversity. Single-uredinial isolates were derived and tested for virulence phenotype to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes and for molecular genotypes with 10 simple sequence repeat (SSR) primers. Nine virulence phenotypes were described among the 193 isolates tested for virulence. Phenotype BBBQJ, found only in Ethiopia, was predominantly collected from tetraploid wheat. Phenotype EEEEE, also found only in Ethiopia, was exclusively collected from tetraploid wheat and was avirulent to the susceptible hexaploid wheat 'Thatcher'. Phenotypes MBDSS and MCDSS, found in both Ethiopia and Kenya, were predominantly collected from common wheat. Phenotypes CCMSS, CCPSS, and CBMSS were found in Ethiopia from common wheat at low frequency. Phenotypes TCBSS and TCBSQ were found on durum wheat and common wheat in Kenya. Four groups of distinct SSR genotypes were described among the 48 isolates genotyped. Isolates with phenotypes BBBQJ and EEEEE were in two distinct SSR groups, and isolates with phenotypes MBDSS and MCDSS were in a third group. Isolates with CCMSS, CCPSS, CBMSS, TCBSS, and TCBSQ phenotypes were in a fourth SSR genotype group. The diverse host environment of Ethiopia has selected and maintained a genetically divergent population of P. triticina.

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2013

Collections of Puccinia triticina were obtained from rust-infected leaves provided by cooperators throughout the United States and from wheat fields and breeding plots by USDA-ARS personnel and cooperators in the Great Plains, Ohio River Valley, and southeastern states in order to determine the virulence of the wheat leaf rust population in 2013. Single uredinial isolates (490 total) were derived from the collections and tested for virulence phenotype on 20 lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes. In 2013, 79 virulence phenotypes were described in the United States. Virulence phenotypes MBTNB, TNBGJ, and MCTNB were the three most common phenotypes. Phenotypes MBTNB and MCTNB are both virulent to Lr11, and MCTNB is virulent to Lr26. MBTNB and MCTNB were most common in the soft red winter wheat region of the southeastern states and Ohio Valley. Phenotype TNBGJ is virulent to Lr39/41 and was widely distributed throughout the hard red winter wheat region of the Great Plains. Isolates with virulence to Lr11, Lr18, and Lr26 were common in the southeastern states and Ohio Valley region. Isolates with virulence to Lr21, Lr24, and Lr39/41 were frequent in the hard red wheat region of the southern and northern Great Plains.