Identification and mapping of Sr46 from Aegilops tauschii accession CIae 25 conferring resistance to race TTKSK (Ug99) of wheat stem rust pathogen

k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives

Genome-wide association studies (GWAS) have allowed the discovery of marker-trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation.

Advances in the Mining of Disease Resistance Genes from Aegilops tauschii and the Utilization in Wheat

Aegilops tauschii is one of the malignant weeds that affect wheat production and is also the wild species ancestor of the D genome of hexaploid wheat (Triticum aestivum, AABBDD). It contains many disease resistance genes that have been lost in the long-term evolution of wheat and is an important genetic resource for the mining and utilization of wheat disease resistance genes. In recent years, the genome sequence of Aegilops tauschii has been preliminarily completed, which has laid a good foundation for the further exploration of wheat disease resistance genes in Aegilops tauschii. There are many studies on disease resistance genes in Aegilops tauschii; in order to provide better help for the disease resistance breeding of wheat, this paper analyzes and reviews the relationship between Aegilops tauschii and wheat, the research progress of Aegilops tauschii, the discovery of disease resistance genes from Aegilops tauschii, and the application of disease resistance genes from Aegilops tauschii to modern wheat breeding, providing a reference for the further exploration and utilization of Aegilops tauschii in wheat disease resistance breeding.

Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat

Stem rust resistance genes, SrRL5271 and Sr672.1 as well as SrCPI110651, from Aegilops tauschii, the diploid D genome progenitor of wheat, are sequence variants of Sr46 differing by 1-2 nucleotides leading to non-synonymous amino acid substitutions. The Aegilops tauschii (wheat D-genome progenitor) accessions RL 5271 and CPI110672 were identified as resistant to multiple races (including the Ug99) of the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt). This study was conducted to identify the stem rust resistance (Sr) gene(s) in both accessions. Genetic analysis of the resistance in RL 5271 identified a single dominant allele (SrRL5271) controlling resistance, whereas resistance segregated at two loci (SR672.1 and SR672.2) for a cross of CPI110672. Bulked segregant analysis placed SrRL5271 and Sr672.1 in a region on chromosome arm 2DS that encodes Sr46. Molecular marker screening, mapping and genomic sequence analysis demonstrated SrRL5271 and Sr672.1 are alleles of Sr46. The amino acid sequence of SrRL5271 and Sr672.1 is identical but differs from Sr46 (hereafter referred to as Sr46_h1 by following the gene nomenclature in wheat) by a single amino acid (N763K) and is thus designated Sr46_h2. Screening of a panel of Ae. tauschii accessions identified an additional allelic variant that differed from Sr46_h2 by a different amino acid (A648V) and was designated Sr46_h3. By contrast, the protein encoded by the susceptible allele of Ae. tauschii accession AL8/78 differed from these resistance proteins by 54 amino acid substitutions (94% nucleotide sequence gene identity). Cloning and complementation tests of the three resistance haplotypes confirmed their resistance to Pgt race 98-1,2,3,5,6 and partial resistance to Pgt race TTRTF in bread wheat. The three Sr46 haplotypes, with no virulent races detected yet, represent a valuable source for improving stem resistance in wheat.

Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance

The powdery mildew resistance gene Pm58 was traced to a 141.3-kb interval with the co-segregating marker Xkasp68500 in wheat breeding. Pm58 is a powdery mildew resistance gene identified in Aegilops tauschii accession TA1662 and effective in a common wheat background. To finely map Pm58, an F₂ population of 676 plants derived from the cross T093 × TA1662 was used for recombinant screening. We obtained 13 recombinants that occurred between the flanking markers Xhnu670 and Xhnu186. Genotyping and phenotyping these recombinant F_2:3 families delimited Pm58 to a 0.22-cM interval (Xsts20220-Xkasp61553) on chromosome arm 2DS. The region carrying the Pm58 locus was approximately 141.3-kb, which contained eight annotated genes according to the reference genome sequence of Ae. tauschii AL8/78. Haplotype analysis of 178 Ae. tauschii accessions using the candidate gene-specific markers identified a disease resistance gene AET2Gv20068500 as a candidate for Pm58. Comparative mapping of the Pm58-containing interval revealed two presence/absence variations (PAVs) between AL8/78 and common wheat Chinese Spring. PAV-1 resides in the 3'-end of AET2Gv20068500. The majority of 158 common wheat cultivars (84.8%) displayed the absence of a 14.1-kb fragment in the PAV-1 region, which was confirmed by aligning the targeted genome sequences of the other sequenced Ae. tauschii accessions and common wheat cultivars. A co-segregating marker Xkasp68500 developed from AET2Gv20068500 can distinguish TA1662 from all randomly selected common wheat cultivars and will be instrumental for tracking Pm58 in breeding programs.

Variability in Physiological Traits Reveals Boron Toxicity Tolerance in Aegilops Species

Boron (B) is an important micronutrient required for the normal growth and development of plants. However, its excess in the soil causes severe damage to plant tissues, which affects the final yield. Wheat, one of the main staple crops, has been reported to be largely affected by B toxicity stress in arid and semi-arid regions of the world. The prevalence of B toxicity stress can be addressed by utilizing wild wheat genotypes with a variant level of stress tolerance. Wild wheat relatives have been identified as a prominent source of several abiotic stress-tolerant genes. However, Aegilops species in the tertiary gene pool of wheat have not been well exploited as a source of B toxicity tolerance. This study explores the root and shoot growth, proline induction, and extent of lipid peroxidation in 19 Aegilops accessions comprising 6 different species and the B-tolerant check wheat cultivar Bolal 2973 grown under Control (3.1 μM B), toxic (1 mM B), and highly toxic (10 mM B) B stress treatment. B toxicity stress had a more decisive impact on growth parameters as compared to the malondialdehyde (MDA) and proline content. The obtained results suggested that even the genotypes with high shoot B (SB) accumulation can be tolerant to B toxicity stress, and the mechanism of B redistribution in leaves should be studied in detail. It has been proposed that the studied Aegilops accessions can be potentially used for genetically improving the B toxicity-tolerance trait due to a high level of variation in the response toward high B toxicity. Though a number of accessions showed suppression in the root and shoot growth, very few accessions with stress adaptive plasticity to B toxicity stress leading to an improvement of shoot growth parameters could be determined. The two accessions, Aegilops biuncialis accession TGB 026219 and Aegilops columnaris accession TGB 000107, were identified as the potential genotypes with B toxicity stress tolerance and can be utilized for developing a pre-breeding material in B tolerance-based breeding programs.

Characterization of synthetic wheat line Largo for resistance to stem rust

Resistance breeding is an effective approach against wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The synthetic hexaploid wheat line Largo (pedigree: durum wheat “Langdon” × Aegilops tauschii PI 268210) was found to have resistance to a broad spectrum of Pgt races including the Ug99 race group. To identify the stem rust resistance (Sr) genes, we genotyped a population of 188 recombinant inbred lines developed from a cross between the susceptible wheat line ND495 and Largo using the wheat Infinium 90 K SNP iSelect array and evaluated the population for seedling resistance to the Pgt races TTKSK, TRTTF, and TTTTF in the greenhouse conditions. Based on genetic linkage analysis using the marker and rust data, we identified six quantitative trait loci (QTL) with effectiveness against different races. Three QTL on chromosome arms 6AL, 2BL, and 2BS corresponded to Sr genes Sr13c, Sr9e, and a likely new gene from Langdon, respectively. Two other QTL from PI 268210 on 2DS and 1DS were associated with a potentially new allele of Sr46 and a likely new Sr gene, respectively. In addition, Sr7a was identified as the underlying gene for the 4AL QTL from ND495. Knowledge of the Sr genes in Largo will help to design breeding experiments aimed to develop new stem rust-resistant wheat varieties. Largo and its derived lines are particularly useful for introducing two Ug99-effective genes Sr13c and Sr46 into modern bread wheat varieties. The 90 K SNP-based high-density map will be useful for identifying the other important genes in Largo.

Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions

We utilized 2300 wheat accessions including worldwide landraces, cultivars and primary synthetic-derived germplasm with three Australian cultivars: Annuello, Yitpi and Correll, to investigate field-based resistance to leaf (Lr) rust, stem (Sr) rust and stripe (Yr) rust diseases across a range of Australian wheat agri-production zones. Generally, the resistance in the modern Australian cultivars, synthetic derivatives, South and North American materials outperformed other geographical subpopulations. Different environments for each trait showed significant correlations, with average r values of 0.53, 0.23 and 0.66 for Lr, Sr and Yr, respectively. Single-trait genome-wide association studies (GWAS) revealed several environment-specific and multi-environment quantitative trait loci (QTL). Multi-trait GWAS confirmed a cluster of Yr QTL on chromosome 3B within a 4.4-cM region. Linkage disequilibrium and comparative mapping showed that at least three Yr QTL exist within the 3B cluster including the durable rust resistance gene Yr30. An Sr/Lr QTL on chromosome 3D was found mainly in the synthetic-derived germplasm from Annuello background which is known to carry the Agropyron elongatum 3D translocation involving the Sr24/Lr24 resistance locus. Interestingly, estimating the SNP effects using a BayesR method showed that the correlation among the highest 1% of QTL effects across environments (excluding GWAS QTL) had significant correlations, with average r values of 0.26, 0.16 and 0.55 for Lr, Sr and Yr, respectively. These results indicate the importance of small effect QTL in achieving durable rust resistance which can be captured using genomic selection.

An Update of Recent Use of Aegilops Species in Wheat Breeding

Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.

Inheritance and Bulked Segregant Analysis of Leaf Rust and Stem Rust Resistance in Durum Wheat Genotypes

Leaf rust, caused by Puccinia triticina, and stem rust, caused by P. graminis f. sp. tritici, are important diseases of durum wheat. This study determined the inheritance and genomic locations of leaf rust resistance (Lr) genes to P. triticina race BBBQJ and stem rust resistance (Sr) genes to P. graminis f. sp. tritici race TTKSK in durum accessions. Eight leaf-rust-resistant genotypes were used to develop biparental populations. Accessions PI 192051 and PI 534304 were also resistant to P. graminis f. sp. tritici race TTKSK. The resulting progenies were phenotyped for leaf rust and stem rust response at seedling stage. The Lr and Sr genes were mapped in five populations using single-nucleotide polymorphisms and bulked segregant analysis. Five leaf-rust-resistant genotypes carried single dominant Lr genes whereas, in the remaining accessions, there was deviation from the expected segregation ratio of a single dominant Lr gene. Seven genotypes carried Lr genes different from those previously characterized in durum. The single dominant Lr genes in PI 209274, PI 244061, PI387263, and PI 313096 were mapped to chromosome arms 6BS, 2BS, 6BL, and 6BS, respectively. The Sr gene in PI 534304 mapped to 6AL and is most likely Sr13, while the Sr gene in PI 192051 could be uncharacterized in durum.

Fine mapping of the stem rust resistance gene SrTA10187

SrTA10187 was fine-mapped to a 1.1 cM interval, candidate genes were identified in the region of interest, and molecular markers were developed for marker-assisted selection and Sr gene pyramiding. Stem rust (Puccinia graminis f. sp. tritici, Pgt) races belonging to the Ug99 (TTKSK) race group pose a serious threat to global wheat (Triticum aestivum L.) production. To improve Pgt host resistance, the Ug99-effective resistance gene SrTA10187 previously identified in Aegilops tauschii Coss. was introgressed into wheat, and mapped to the short arm of wheat chromosome 6D. In this study, high-resolution mapping of SrTA10187 was done using a population of 1,060 plants. Pgt resistance was screened using race QFCSC. PCR-based SNP and STS markers were developed from genotyping-by-sequencing tags and SNP sequences available in online databases. SrTA10187 segregated as expected in a 3:1 ratio of resistant to susceptible individuals in three out of six BC₃F₂ families, and was fine-mapped to a 1.1 cM region on wheat chromosome 6DS. Marker context sequence was aligned to the reference Ae. tauschii genome to identify the physical region encompassing SrTA10187. Due to the size of the corresponding region, candidate disease resistance genes could not be identified with confidence. Comparisons with the Ae. tauschii genetic map developed by Luo et al. (PNAS 110(19):7940-7945, 2013) enabled identification of a discrete genetic locus and a BAC minimum tiling path of the region spanning SrTA10187. Annotation of pooled BAC library sequences led to the identification of candidate genes in the region of interest-including a single NB-ARC-LRR gene. The shorter genetic interval and flanking KASP™ and STS markers developed in this study will facilitate marker-assisted selection, gene pyramiding, and positional cloning of SrTA10187.

Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat

A robust and diagnostic STS marker for stem rust resistance gene Sr47 was developed and validated for marker-assisted selection. Stem rust (caused by Puccinia graminis f. sp. tritici, Pgt) resistance gene Sr47, originally transferred from Aegilops speltoides to durum wheat (Triticum turgidum subsp. durum) line DAS15, confers a high level of resistance to Pgt race TTKSK (Ug99). Recently, the durum Rusty 5D(5B) substitution line was used to reduce the Ae. speltoides segment, and the resulting lines had Sr47 on small Ae. speltoides segments on wheat chromosome arm 2BL. The objective of this study was to develop a robust marker for marker-assisted selection of Sr47. A 200-kb segment of the Brachypodium distachyon genome syntenic with the Sr47 region was used to identify wheat expressed sequence tags (ESTs) homologous to the B. distachyon genes. The wheat EST sequences were then used to develop sequence-tagged site (STS) markers. By analyzing the markers for polymorphism between Rusty and DAS15, we identified a co-dominant STS marker, designated as Xrwgs38, which amplified 175 and 187 bp fragments from wheat chromosome 2B and Ae. speltoides chromosome 2S segments, respectively. The marker co-segregated with the Ae. speltoides segments carrying Sr47 in the families from four BC2F1 plants, including the parent plants for durum lines RWG35 and RWG36 with the pedigree of Rusty/3/Rusty 5D(5B)/DAS15//47-1 5D(5B). Analysis of 62 durum and common wheat cultivars/lines lacking the Sr47 segment indicated that they all possessed the 175-bp allele of Xrwgs38, indicating that it was diagnostic for the small Ae. speltoides segment carrying Sr47. This study demonstrated that Xrwgs38 will facilitate the selection of Sr47 in durum and common wheat breeding.

Recent trends and perspectives of molecular markers against fungal diseases in wheat

Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40-60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases.