Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f. sp. tritici in elite durum wheat

Non-invasive diagnosis of wheat stripe rust progression using hyperspectral reflectance

Wheat stripe rust (WSR), a fungal disease capable of inflicting severe crop loss, threatens most of global wheat production. Breeding for genetic resistance is the primary defense against stripe rust infection. Further development of rust-resistant wheat varieties depends on the ability to accurately and rapidly quantify rust resilience. In this study we demonstrate the ability of visible through shortwave infrared reflectance spectroscopy to effectively provide high-throughput classification of wheat stripe rust severity and identify important spectral regions for classification accuracy. Random forest models were developed using both leaf-level and canopy-level hyperspectral reflectance observations collected across a breeding population that was scored for WSR severity using 10 and 5 severity classes, respectively. The models were able to accurately diagnose scored disease severity class across these fine scoring scales between 45-52% of the time, which improved to 79-96% accuracy when allowing scores to be off-by-one. The canopy-level model demonstrated higher accuracy and distinct spectral characteristics relative to the leaf-level models, pointing to the use of this technology for field-scale monitoring. Leaf-level model performance was strong despite clear variation in scoring conducted between wheat growth stages. Two approaches to reduce predictor and model complexity, principal component dimensionality reduction and backward feature elimination, were applied here. Both approaches demonstrated that model classification skill could remain high while simplifying high-dimensional hyperspectral reflectance predictors, with parsimonious models having approximately 10 unique components or wavebands. Through the use of a high-resolution infection severity scoring methodology this study provides one of the most rigorous tests of the use of hyperspectral reflectance observations for WSR classification. We demonstrate that machine learning in combination with a few carefully-selected wavebands can be leveraged for precision remote monitoring and management of WSR to limit crop damage and to aid in the selection of resilient germplasm in breeding programs.

Genome-wide association study of common resistance to rust species in tetraploid wheat

Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.

Physiological specialization of Puccinia triticina and genome-wide association mapping provide insights into the genetics of wheat leaf rust resistance in Iran

Leaf rust caused by Puccinia triticina Erikss. (Pt) is the most widely distributed and important wheat disease worldwide. The objective of the present study was to determine the frequency of Iranian Pt races, their virulence to key resistance genes and map quantitative trait loci (QTL) for resistance to different Pt races from 185 globally diverse wheat genotypes using a genome-wide association study (GWAS) approach. The virulence pattern of the 33 Pt isolates from various wheat-growing areas of Iran on 55 wheat differentials showed that the FKTPS and FKTTS were relatively frequent pathotypes among the 18 identified races. The weighted average frequency of virulence on the resistance genes Lrb, Lr3bg, Lr14b, Lr16, Lr24, Lr3ka, Lr11 and Lr20 were high (> 90%). However, low virulence on the resistant genes Lr2a, Lr9, Lr19, Lr25, Lr28 and Lr29 indicates that these genes are still effective against the pathogen population in Iran at present. GWAS on a panel of 185 wheat genotypes against 10 Pt races resulted into 62 significant marker-trait associations (MTAs) belonged to 34 quantitative trait loci (QTL) across 16 chromosomes. Among them, 10 QTLs on chromosomes 1A, 1B, 3B, 3D, 4A, 6D, 7A and 7D were identified as potential novel QTLs, of which four QTLs (QLr.iau-3B-2, QLr.iau-7A-2, QLr.iau-7A-3 and QLr.iau-7D-2) are more interesting, as they are associated with resistance to two or more Pt races. The known and novel QTLs associated with different Pt races found here, can be used in future wheat breeding programs to recombine different loci for durable resistance against leaf rust races.

Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat

The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.

Genome-Wide QTL Mapping for Stripe Rust Resistance in Winter Wheat Pindong 34 Using a 90K SNP Array

Winter wheat cultivar Pindong 34 has both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust, which is caused by Puccinia striiformis f. sp. tritici (Pst). To map the quantitative trait loci (QTL) for stripe rust resistance, an F_6-10 recombinant inbred line (RIL) population from a cross of Mingxian 169 × Pingdong 34 was phenotyped for stripe rust response over multiple years in fields under natural infection conditions and with selected Pst races under controlled greenhouse conditions, and genotyping was performed with a 90K single nucleotide polymorphism (SNP) array chip. Inclusive composite interval mapping (ICIM) identified 12 APR resistance QTLs and 3 ASR resistance QTLs. Among the 12 APR resistance QTLs, QYrpd.swust-1BL (explaining 9.24-13.33% of the phenotypic variation), QYrpd.swust-3AL.1 (11.41-14.80%), QYrpd.swust-3AL.2 (11.55-16.10%), QYrpd.swust-6BL (9.39-12.78%), QYrpd.swust-6DL (9.52-16.36%), QYrpd.swust-7AL (9.09-17.0%), and QYrpd.swust-7DL (8.87-11.38%) were more abundant than in the five tested environments and QYrpd.swust-1AS (11.05-12.72%), QYrpd.swust-1DL (9.81-13.05%), QYrpd.swust-2BL.1 (9.69-10.57%), QYrpd.swust-2BL.2 (10.36-12.97%), and QYrpd.swust-2BL.3 (9.54-13.15%) were significant in some of the tests. The three ASR resistance QTLs QYrpd.swust-2AS (9.69-13.58%), QYrpd.swust-2BL.4 (9.49-12.07%), and QYrpd.swust-7AS (16.16%) were detected based on the reactions in the seedlings tested with the CYR34 Pst race. Among the 15 QTLs detected in Pindong 34, the ASR resistance gene QYrpd.swust-7AS mapped on the short arm of chromosome 7A was likely similar to the previously reported QTL Yr61 in the region. The QTLs identified in the present study and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.

Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust

Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.

Genome-Wide Association and Genomic Prediction for Stripe Rust Resistance in Synthetic-Derived Wheats

Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds.

Genome Wide Association Study Uncovers the QTLome for Osmotic Adjustment and Related Drought Adaptive Traits in Durum Wheat

Osmotic adjustment (OA) is a major component of drought resistance in crops. The genetic basis of OA in wheat and other crops remains largely unknown. In this study, 248 field-grown durum wheat elite accessions grown under well-watered conditions, underwent a progressively severe drought treatment started at heading. Leaf samples were collected at heading and 17 days later. The following traits were considered: flowering time (FT), leaf relative water content (RWC), osmotic potential (ψs), OA, chlorophyll content (SPAD), and leaf rolling (LR). The high variability (3.89-fold) in OA among drought-stressed accessions resulted in high repeatability of the trait (h² = 72.3%). Notably, a high positive correlation (r = 0.78) between OA and RWC was found under severe drought conditions. A genome-wide association study (GWAS) revealed 15 significant QTLs (Quantitative Trait Loci) for OA (global R² = 63.6%), as well as eight major QTL hotspots/clusters on chromosome arms 1BL, 2BL, 4AL, 5AL, 6AL, 6BL, and 7BS, where a higher OA capacity was positively associated with RWC and/or SPAD, and negatively with LR, indicating a beneficial effect of OA on the water status of the plant. The comparative analysis with the results of 15 previous field trials conducted under varying water regimes showed concurrent effects of five OA QTL cluster hotspots on normalized difference vegetation index (NDVI), thousand-kernel weight (TKW), and/or grain yield (GY). Gene content analysis of the cluster regions revealed the presence of several candidate genes, including bidirectional sugar transporter SWEET, rhomboid-like protein, and S-adenosyl-L-methionine-dependent methyltransferases superfamily protein, as well as DREB1. Our results support OA as a valuable proxy for marker-assisted selection (MAS) aimed at enhancing drought resistance in wheat.

Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies

Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.

Novel stripe rust all-stage resistance loci identified in a worldwide collection of durum wheat using genome-wide association mapping

Durumwheat [Triticum turgidum L. ssp. durum (Desf.)] production is constrained by fungal diseases including stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Continuous mining of germplasm for the discovery and deployment of stripe rust resistance (Yr) genes is needed to counter the impact of this disease. In this study, we evaluated a worldwide collection of 432 durum wheat accessions to seven U.S. Pst races that carry diverse virulence and avirulence combinations on wheat Yr genes. We found that 47-82% of the durum wheat accessions were susceptible to each of the tested Pst races. A total of 32 accessions were resistant to all seven races. Genome-wide association studies (GWAS) using over 97,000 single-nucleotide polymorphism markers generated from genotyping-by-sequencing of 364 accessions identified 56 quantitative trait loci (QTL) associated with all-stage stripe rust resistance located on all 14 durum wheat chromosomes. Six of these QTL were associated with resistance to 2-4 Pst races, and none were associated with resistance to all seven races. The remaining 50 QTL were race specific. Eighteen of the 56 identified QTL had relatively large effects against at least one of the races. A map-based comparison of the discovered QTL in this study with previously published Yr genes and QTL showed that 29 were previously identified, whereas the remaining 27 QTL appeared to be novel. This study reports effective sources of stripe rust resistance to contemporary races in the United States and shows that this durum wheat collection is abundant in novel resistance loci that can be transferred into adapted durum cultivars.

Evaluations of Genomic Prediction and Identification of New Loci for Resistance to Stripe Rust Disease in Wheat (Triticum aestivum L.)

Stripe rust is one of the most destructive diseases of wheat (Triticum aestivum L.), caused by Puccinia striiformis f. sp. tritici (Pst), and responsible for significant yield losses worldwide. Single-nucleotide polymorphism (SNP) diagnostic markers were used to identify new sources of resistance at adult plant stage to wheat stripe rust (YR) in 141 CIMMYT advanced bread wheat lines over 3 years in replicated trials at Borlaug Institute for South Asia (BISA), Ludhiana. We performed a genome-wide association study and genomic prediction to aid the genetic gain by accumulating disease resistance alleles. The responses to YR in 141 advanced wheat breeding lines at adult plant stage were used to generate G × E (genotype × environment)-dependent rust scores for prediction and genome-wide association study (GWAS), eliminating variation due to climate and disease pressure changes. The lowest mean prediction accuracies were 0.59 for genomic best linear unbiased prediction (GBLUP) and ridge-regression BLUP (RRBLUP), while the highest mean was 0.63 for extended GBLUP (EGBLUP) and random forest (RF), using 14,563 SNPs and the G × E rust score results. RF and EGBLUP predicted higher accuracies (∼3%) than did GBLUP and RRBLUP. Promising genomic prediction demonstrates the viability and efficacy of improving quantitative rust tolerance. The resistance to YR in these lines was attributed to eight quantitative trait loci (QTLs) using the FarmCPU algorithm. Four (Q.Yr.bisa-2A.1, Q.Yr.bisa-2D, Q.Yr.bisa-5B.2, and Q.Yr.bisa-7A) of eight QTLs linked to the diagnostic markers were mapped at unique loci (previously unidentified for Pst resistance) and possibly new loci. The statistical evidence of effectiveness and distribution of the new diagnostic markers for the resistance loci would help to develop new stripe rust resistance sources. These diagnostic markers along with previously established markers would be used to create novel DNA biosensor-based microarrays for rapid detection of the resistance loci on large panels upon functional validation of the candidate genes identified in the present study to aid in rapid genetic gain in the future breeding programs.

From Genetic Maps to QTL Cloning: An Overview for Durum Wheat

Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.

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.

Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most devastating foliar diseases in wheat. Host resistance is the most effective strategy for the management of the disease. To screen for accessions with stable resistance and identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using a panel of 140 Chinese wheat landraces. The panel was evaluated for stripe rust response at the adult-plant stage at six field-year environments with mixed races and at the seedling stage with two separate predominant races of the pathogen, and genotyped with the genome-wide Diversity Arrays Technology markers. The panel displayed abundant phenotypic variation in stripe rust responses, with 9 landraces showing stable resistance to the mixture of Pst races at the adult-plant stage in the field and 10 landraces showing resistance to individual races at the seedling stage in the greenhouse. GWAS identified 12 quantitative trait loci (QTL) significantly (P ≤ 0.001) associated to stripe rust resistance using the field data of at least two environments and 18 QTL using the seedling data with two races. Among these QTL, 10 were presumably novel, including 4 for adult-plant resistance mapped to chromosomes 1B (QYrcl.sicau-1B.3), 4A (QYrcl.sicau-4A.3), 6A (QYrcl.sicau-6A.2) and 7B (QYrcl.sicau-7B.2) and 6 for all-stage resistance mapped to chromosomes 2D (QYrcl.sicau-2D.1), 3B (QYrcl.sicau-3B.3), 3D (QYrcl.sicau-3D), 4B (QYrcl.sicau-4B), 6A (QYrcl.sicau-6A.1) and 6D (QYrcl.sicau-6D). The landraces with stable resistance can be used for developing wheat cultivars with effective resistance to stripe rust.

The potential of remote sensing and artificial intelligence as tools to improve the resilience of agriculture production systems

Modern agriculture and food production systems are facing increasing pressures from climate change, land and water availability, and, more recently, a pandemic. These factors are threatening the environmental and economic sustainability of current and future food supply systems. Scientific and technological innovations are needed more than ever to secure enough food for a fast-growing global population. Scientific advances have led to a better understanding of how various components of the agricultural system interact, from the cell to the field level. Despite incredible advances in genetic tools over the past few decades, our ability to accurately assess crop status in the field, at scale, has been severely lacking until recently. Thanks to recent advances in remote sensing and Artificial Intelligence (AI), we can now quantify field scale phenotypic information accurately and integrate the big data into predictive and prescriptive management tools. This review focuses on the use of recent technological advances in remote sensing and AI to improve the resilience of agricultural systems, and we will present a unique opportunity for the development of prescriptive tools needed to address the next decade's agricultural and human nutrition challenges.

Identification of Stripe Rust Resistance Loci in U.S. Spring Wheat Cultivars and Breeding Lines Using Genome-Wide Association Mapping and Yr Gene Markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a major threat to wheat production worldwide, especially in the United States. To identify loci for effective stripe rust resistance in U.S. wheat, a genome-wide association study (GWAS) was conducted using a panel of 616 spring wheat cultivars and breeding lines. The accessions in this panel were phenotyped for stripe rust response in the greenhouse at seedling stage with five predominant and highly virulent races of Pst and in different field environments at adult-plant stage in 2017 and 2018. In total, 2,029 single-nucleotide polymorphism markers that cover the whole genome were generated with genotyping by multiplexed sequencing and used in GWAS. In addition, 23 markers of previously reported resistance genes or quantitative trait loci (QTLs) were used to genotype the population. This spring panel was grouped into three subpopulations based on principal component analysis. A total of 37 genes or QTLs including 10 potentially new QTLs for resistance to stripe rust were detected by GWAS and linked marker tests. The frequencies of the resistance genes or QTLs in various nurseries were determined, indicating different intensities of these genes or QTLs used in breeding programs of different regions. These resistance loci and the information on their markers, effectiveness, and distributions should be useful for improving stripe rust resistance in wheat cultivars.

Association Analysis Identifies New Loci for Resistance to Chinese Yr26-Virulent Races of the Stripe Rust Pathogen in a Diverse Panel of Wheat Germplasm

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive fungal diseases of wheat worldwide. The expanding Yr26-virulent Pst race (V26) group overcomes almost all currently deployed resistance genes in China and has continued to accumulate new virulence. Investigating the genetic architecture of stripe rust resistance in common wheat is an important basis for a successful utilization of resistance in breeding programs. A panel of 410 exotic wheat germplasms was used for characterizing new stripe rust resistance loci. This panel was genotyped using high-density wheat 660K single-nucleotide polymorphism (SNP) array, and phenotypic evaluation of seedlings for stripe rust resistance was performed using multiple Pst races. Thirty-five loci conferring resistance were identified through genome-wide association mapping, and explained phenotypic variances ranged from 53 to 75%. Of these, 14 were colocated in the proximity of the known loci, including cataloged Yr genes Yr9, Yr10, Yr26, Yr33, Yr47, Yr56, Yr57, Yr64, Yr67, Yr72, and Yr81 and three temporarily designated as YrCen, YrNP63, and YrRC detected in our quantitative trait locus (QTL) mapping studies. Seven of them (Yr9, Yr10, Yr24/26, Yr81, YrCEN, YrNP63, and YrRC) were confirmed by molecular detection or genetic analysis. New loci that were identified to be different from reported Yr genes need further confirmation. Nine QTL with significantly large phenotypic effect on resistance to all tested races were considered as major loci for effective resistance. The identified loci enrich our stripe rust resistance gene pool, and the linked SNPs should be useful for marker-assisted selection in breeding programs.

Genetic characterization and genome-wide association mapping for dwarf bunt resistance in bread wheat accessions from the USDA National Small Grains Collection

Dwarf bunt-resistant bread wheat accessions and SNP markers associated with DB resistance identified in this study are valuable resources for characterization and deployment of DB resistance in bread wheat. Dwarf bunt (DB), caused by Tilletia controversa J.G. Kühn, can significantly reduce grain yield and quality on autumn-sown wheat in regions with prolonged snow cover. DB can be managed with the use of resistant cultivars. The objectives of the present study were to characterize DB resistance in a large set of bread wheat accessions from the National Small Grains Collection and use a genome-wide association study approach to identify genetic loci associated with DB resistance. A total of 292 accessions were selected using historical DB resistance data recorded across many trials and years in the Germplasm Resources Information Network (GRIN) and re-tested for DB resistance in replicated field nurseries in Logan, UT, in 2017, 2018, and 2019. Ninety-eight accessions were resistant with DB normalized incidence ≤ 10%, and twenty-eight of these were highly resistant with DB normalized incidence ≤ 1% in both GRIN and the field nurseries. Based on the presence of marker haplotypes of the four published dwarf bunt QTL on 6DS, 6DL, 7AL, and 7DS, highly resistant accessions identified in this study may provide novel resistance and should be further evaluated. This study validated one previously identified QTL on 6DS and identified an additional locus on 6DS. These loci explained 9-15% of the observed phenotypic variation. The resistant accessions and molecular markers identified in the present study may provide valuable resources for characterization and deployment of DB resistance in bread wheat.

Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding

Crops are the major source of food supply and raw materials for the processing industry. A balance between crop production and food consumption is continually threatened by plant diseases and adverse environmental conditions. This leads to serious losses every year and results in food shortages, particularly in developing countries. Presently, cutting-edge technologies for genome sequencing and phenotyping of crops combined with progress in computational sciences are leading a revolution in plant breeding, boosting the identification of the genetic basis of traits at a precision never reached before. In this frame, machine learning (ML) plays a pivotal role in data-mining and analysis, providing relevant information for decision-making towards achieving breeding targets. To this end, we summarize the recent progress in next-generation sequencing and the role of phenotyping technologies in genomics-assisted breeding toward the exploitation of the natural variation and the identification of target genes. We also explore the application of ML in managing big data and predictive models, reporting a case study using microRNAs (miRNAs) to identify genes related to stress conditions.

Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population (Triticum aestivum) via Genome-Wide Association Mapping

A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.

Genome-wide mapping of adult plant stripe rust resistance in wheat cultivar Toni

Two adult plant stripe rust resistance QTL, QYrto.swust-3AS and QYrto.swust-3BS, were identified and mapped in common wheat cultivar Toni. The two QTL were located to corresponding positions in the wheat physical map position based on flanking SNP markers. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important foliar diseases of wheat. Characterization and utilization of resistance genes are the most effective, economic and environmental-friendly way to control the disease. The wheat cultivar Toni resistant at the adult plant stage to predominant Chinese Pst races was crossed with the susceptible genotype Mingxian 169. A recombinant inbred line population comprising 171 lines was tested in the field at three locations in the 2016 and 2017 crop seasons. The Affymetrix Axiom^® 35 K single-nucleotide polymorphism (SNP) Wheat Breeder's Genotyping Array was used to map quantitative trait loci (QTL) for adult plant resistance to stripe rust. Inclusive composite interval mapping identified stable QTL QYrto.swust-3AS and QYrto.swust-3BS that explained 31.6-48.2% and 21.9-56.3% of the variation in stripe rust severity and infection type, respectively. The two QTL regions were anchored to the wheat IWGSC Ref Seq v1.0 sequence. QYrto.swust-3AS was localized to a 2.22-Mb interval flanked by SNP markers AX-95240191 and AX-94828890. Among 65 HC (high confidence) annotated genes in this region, 11 (16.9%) contained NB-ARC domains and 9 (13.8%) contained protein kinase domains and thus could contribute to disease resistance. QYrto.swust-3BS was localized to a 4.77-Mb interval flanked by SNP markers AX-94509749 and AX-94998050. One hundred and thirty three HC genes are annotated in this region. Among them, 14 (10.5%) protein kinase domain genes may contribute to disease resistance. The linked markers should be useful for marker-assisted selection in breeding for resistance.

Exploring and exploiting the genetic variation of Fusarium head blight resistance for genomic-assisted breeding in the elite durum wheat gene pool

KEY MESSAGE

Genomic selection had a higher selection response for FHB resistance than phenotypic selection, while association mapping identified major QTL on chromosome 3B unaffected by plant height and flowering date. Fusarium head blight (FHB) is one of the most destructive diseases of durum wheat. Hence, minimizing losses in yield, quality and avoiding contamination with mycotoxins are of pivotal importance, as durum wheat is mostly used for human consumption. While growing resistant varieties is the most promising approach for controlling this fungal disease, FHB resistance breeding in durum wheat is hampered by the limited variation in the elite gene pool and difficulties in efficiently combining the numerous small-effect resistance quantitative trait loci (QTL) in the same line. We evaluated an international collection of 228 genotyped durum wheat cultivars for FHB resistance over 3 years to investigate the genetic architecture and potential of genomic-assisted breeding for FHB resistance in durum wheat. Plant height was strongly positively correlated with FHB resistance and led to co-localization of plant height and resistance QTL. Nevertheless, a major QTL on chromosome 3B independent of plant height was identified in the same chromosomal interval as reported for the prominent hexaploid resistance QTL Fhb1, though haplotype analysis highlighted the distinctiveness of both QTL. Comparison between phenotypic and genomic selection for FHB resistance revealed a superior prediction ability of the former. However, simulated selection experiments resulted in higher selection responses when using genomic breeding values for early generation selection. An earlier identification of the most promising lines and crossing parents was feasible with a genomic selection index, which suggested a much faster short-term population improvement than previously possible in durum wheat, complementing long-term strategies with exotic resistance donors.

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

BACKGROUND

Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China.

RESULTS

Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage.

CONCLUSIONS

The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars.

Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces (Triticum aestivum L.) From the Yellow and Huai River Valleys

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker-trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.

QTL Mapping and Validation of Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Humai 15

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease that affects common wheat and barley throughout the world. The reasonable deployment of adult plant resistance (APR) wheat varieties is one of the best methods for controlling this disease. Wheat landraces are valuable resources for identifying the genes/QTLs responsible for disease resistance. Humai 15 is a Chinese spring wheat landrace and it has exhibited adequate levels of APR to the prevalent Pst races in field environments for many years. In this study, a population of 177 recombinant inbred lines (RILs) was derived from Humai 15 × Mingxian 169. After screening based on a 90K chip array using 45 RILs and Kompetitive Allelic Specific PCR marker genotyping for the population of RILs, a major effect QTL in Humai 15 was located on the centromere of chromosome 2B, where it accounted for up to 47.2% of the phenotypic variation. Two other minor QTL genes from Humai 15 were located on chromosome arms 3BS and 4BL. The Yr18 gene was identified on chromosome arm 7DS in Mingxian 169.

Comparative Aerial and Ground Based High Throughput Phenotyping for the Genetic Dissection of NDVI as a Proxy for Drought Adaptive Traits in Durum Wheat

High-throughput phenotyping platforms (HTPPs) provide novel opportunities to more effectively dissect the genetic basis of drought-adaptive traits. This genome-wide association study (GWAS) compares the results obtained with two Unmanned Aerial Vehicles (UAVs) and a ground-based platform used to measure Normalized Difference Vegetation Index (NDVI) in a panel of 248 elite durum wheat (Triticum turgidum L. ssp. durum Desf.) accessions at different growth stages and water regimes. Our results suggest increased ability of aerial over ground-based platforms to detect quantitative trait loci (QTL) for NDVI, particularly under terminal drought stress, with 22 and 16 single QTLs detected, respectively, and accounting for 89.6 vs. 64.7% phenotypic variance based on multiple QTL models. Additionally, the durum panel was investigated for leaf chlorophyll content (SPAD), leaf rolling and dry biomass under terminal drought stress. In total, 46 significant QTLs affected NDVI across platforms, 22 of which showed concomitant effects on leaf greenness, 2 on leaf rolling and 10 on biomass. Among 9 QTL hotspots on chromosomes 1A, 1B, 2B, 4B, 5B, 6B, and 7B that influenced NDVI and other drought-adaptive traits, 8 showed per se effects unrelated to phenology.

Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes

High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat. German wheat cultivar "Friedrichswerther" has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F_2:3 lines and F₆ recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F_2:3 lines and F₆ RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum)

KEY MESSAGE

SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.

Novel Sources of Stripe Rust Resistance Identified by Genome-Wide Association Mapping in Ethiopian Durum Wheat (Triticum turgidum ssp. durum)

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is a global concern for wheat production, and has been increasingly destructive in Ethiopia, as well as in the United States and in many other countries. As Ethiopia has a long history of stripe rust epidemics, its native wheat germplasm harbors potentially valuable resistance loci. Moreover, the Ethiopian germplasm has been historically underutilized in breeding of modern wheat worldwide and thus the resistance alleles from the Ethiopian germplasm represent potentially novel sources. The objective of this study was to identify loci conferring resistance to predominant Pst races in Ethiopia and the United States. Using a high-density 90 K wheat single nucleotide polymorphism array, a genome-wide association analysis (GWAS) was conducted on 182 durum wheat landrace accessions and contemporary varieties originating from Ethiopia. Landraces were detected to be more resistant at the seedling stage while cultivars were more resistant at the adult-plant stages. GWAS identified 68 loci associated with seedling resistance to one or more races. Six loci on chromosome arms 1AS, 1BS, 3AS, 4BL, and 5BL were associated with resistance against at least two races at the seedling stage, and five loci were previously undocumented. GWAS analysis of field resistance reactions identified 12 loci associated with resistance on chromosomes 1A, 1B, 2BS, 3BL, 4AL, 4B and 5AL, which were detected in at least two of six field screening nurseries at the adult-plant stage. Comparison with previously mapped resistance loci indicates that six of the 12 resistance loci are newly documented. This study reports effective sources of resistance to contemporary races in Ethiopia and the United States and reveals that Ethiopian durum wheat landraces are abundant in novel Pst resistance loci that may be transferred into adapted cultivars to provide resistance against Pst.

Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays

Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S. The maximum disease severity (MDS) data of F2:3 lines and the relative area under the disease progress curve (rAUDPC) data of RILs were collected during the 2014-2015 and 2015-2016 wheat growing seasons, respectively. Combined bulked segregant analysis and 90K single nucleotide polymorphism (SNP) arrays placed 275 of 511 polymorphic SNPs on chromosome 2B. Sixty four KASP markers selected from the 275 SNPs and 76 SSR markers on 2B were used to identify a chromosome region associated with rust response. A major effect QTL, named Qyrnap.nwafu-2BS, was identified by inclusive composite interval mapping and was preliminarily mapped to a 5.46 cM interval flanked by KASP markers 90K-AN34 and 90K-AN36 in chromosome 2BS. Fourteen KASP markers more closely linked to the locus were developed following a 660K SNP array analysis. The QTL region was finally narrowed to a 0.9 cM interval flanked by KASP markers 660K-AN21 and 660K-AN57 in bin region 2BS-1-0.53. The resistance of Napo 63 was stable across all environments, and as a QTL, explained an average 66.1% of the phenotypic variance in MDS of F2:3 lines and 55.7% of the phenotypic variance in rAUDPC of F5:6 RILs. The short genetic interval and flanking KASP markers developed in the study will facilitate marker-assisted selection, gene pyramiding, and eventual positional cloning of Qyrnap.nwafu-2BS.