A new 2DS·2RL Robertsonian translocation transfers stem rust resistance gene Sr59 into wheat

Genome-wide simple sequence repeat analysis and specific molecular marker development of rye

BACKGROUND

Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics.

RESULTS

In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes.

CONCLUSION

These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.

Molecular Cytogenetic Characterization of Novel Wheat-Rye T1RS.1AL Translocation Lines with Resistance to Powdery Mildew and Stripe Rust Derived from the Chinese Rye Landrace Qinling

Stripe rust and powdery mildew are serious diseases that severely decrease the yield of wheat. Planting wheat cultivars with powdery mildew and stripe rust resistance genes is the most effective way to control these two diseases. Introducing disease resistance genes from related species into the wheat genome via chromosome translocation is an important way to improve wheat disease resistance. In this study, nine novel T1RS.1AL translocation lines were developed from the cross of wheat cultivar Chuannong25 (CN25) and a Chinese rye Qinling. The results of non-denaturing fluorescence in situ hybridization and PCR showed that all new lines were homozygous for the T1RS.1AL translocation. These new T1RS.1AL translocation lines exhibited strong resistance to stripe rust and powdery mildew. The cytogenetics results indicated that the resistance of the new lines was conferred by the 1RS chromosome arms, which came from Qinling rye. The genetic analysis indicated that there were new dominant resistance genes on the 1RS chromosome arm resistant to stripe rust and powdery mildew, and their resistance patterns were different from those of Yr9, Pm8, and Pm17 genes. In addition, the T1RS.1AL translocation lines generally exhibited better agronomic traits in the field relative to CN25. These T1RS.1AL translocations have great potential in wheat-breeding programs in the future.

Alien introgression to wheat for food security: functional and nutritional quality for novel products under climate change

Crop yield and quality has increased globally during recent decades due to plant breeding, resulting in improved food security. However, climate change and shifts in human dietary habits and preferences display novel pressure on crop production to deliver enough quantity and quality to secure food for future generations. This review paper describes the current state-of-the-art and presents innovative approaches related to alien introgressions into wheat, focusing on aspects related to quality, functional characteristics, nutritional attributes, and development of novel food products. The benefits and opportunities that the novel and traditional plant breeding methods contribute to using alien germplasm in plant breeding are also discussed. In principle, gene introgressions from rye have been the most widely utilized alien gene source for wheat. Furthermore, the incorporation of novel resistance genes toward diseases and pests have been the most transferred type of genes into the wheat genome. The incorporation of novel resistance genes toward diseases and pests into the wheat genome is important in breeding for increased food security. Alien introgressions to wheat from e.g. rye and Aegilops spp. have also contributed to improved nutritional and functional quality. Recent studies have shown that introgressions to wheat of genes from chromosome 3 in rye have an impact on both yield, nutritional and functional quality, and quality stability during drought treatment, another character of high importance for food security under climate change scenarios. Additionally, the introgression of alien genes into wheat has the potential to improve the nutritional profiles of future food products, by contributing higher minerals levels or lower levels of anti-nutritional compounds into e.g., plant-based products substituting animal-based food alternatives. To conclude, the present review paper highlights great opportunities and shows a few examples of how food security and functional-nutritional quality in traditional and novel wheat products can be improved by the use of genes from alien sources, such as rye and other relatives to wheat. Novel and upcoming plant breeding methods such as genome-wide association studies, gene editing, genomic selection and speed breeding, have the potential to complement traditional technologies to keep pace with climate change and consumer eating habits.

Pre-breeding of spontaneous Robertsonian translocations for density planting architecture by transferring Agropyron cristatum chromosome 1P into wheat

KEY MESSAGE

We developed T1AL·1PS and T1AS·1PL Robertsonian translocations by breakage-fusion mechanism based on wheat-A. cristatum 1P(1A) substitution line with smaller leaf area, shorter plant height, and other excellent agronomic traits Agropyron cristatum, a wild relative of wheat, is a valuable germplasm resource for improving wheat genetic diversity and yield. Our previous study confirmed that the A. cristatum chromosome 1P carries alien genes that reduce plant height and leaf size in wheat. Here, we developed T1AL·1PS and T1AS·1PL Robertsonian translocations (RobTs) by breakage-fusion mechanism based on wheat-A. cristatum 1P (1A) substitution line II-3-1c. Combining molecular markers and cytological analysis, we identified 16 spontaneous RobTs from 911 F2 individuals derived from the cross of Jimai22 and II-3-1c. Fluorescence in situ hybridization (FISH) was applied to detect the fusion structures of the centromeres in wheat and A. cristatum chromosomes. Resequencing results indicated that the chromosomal junction point was located at the physical position of Triticum aestivum chromosome 1A (212.5 Mb) and A. cristatum chromosome 1P (230 Mb). Genomic in situ hybridization (GISH) in pollen mother cells showed that the produced translocation lines could form stable ring bivalent. Introducing chromosome 1PS translocation fragment into wheat significantly increased the number of fertile tillers, grain number per spike, and grain weight and reduced the flag leaf area. However, introducing chromosome 1PL translocation fragment into wheat significantly reduced flag leaf area and plant height with a negative effect on yield components. The pre-breeding of two spontaneous RobTs T1AL·1PS and T1AS·1PL was important for wheat architecture improvement.

Two functional CC-NBS-LRR proteins from rye chromosome 6RS confer differential age-related powdery mildew resistance to wheat

Rye (Secale cereale), a valuable relative of wheat, contains abundant powdery mildew resistance (Pm) genes. Using physical mapping, transcriptome sequencing, barley stripe mosaic virus-induced gene silencing, ethyl methane sulfonate mutagenesis, and stable transformation, we isolated and validated two coiled-coil, nucleotide-binding site and leucine-rich repeat (CC-NBS-LRR) alleles, PmTR1 and PmTR3, located on rye chromosome 6RS from different triticale lines. PmTR1 confers age-related resistance starting from the three-leaf stage, whereas its allele, PmTR3, confers typical all-stage resistance, which may be associated with their differential gene expression patterns. Overexpression in Nicotiana benthamiana showed that the CC, CC-NBS, and CC-LRR fragments of PMTR1 induce cell death, whereas in PMTR3 the CC and full-length fragments perform this function. Luciferase complementation imaging and pull-down assays revealed distinct interaction activities between the CC and NBS fragments. Our study elucidates two novel rye-derived Pm genes and their derivative germplasm resources and provides novel insights into the mechanism of age-related resistance, which can aid the improvement of resistance against wheat powdery mildew.

Construction of a high-density genetic map and mapping of a spike length locus for rye

Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.

Identification and introgression of a novel leaf rust resistance gene from Thinopyrum intermedium chromosome 7Js into wheat

KEY MESSAGE

A novel leaf rust resistance locus located on a terminal segment (0-69.29 Mb) of Thinopyrum intermedium chromosome arm 7JsS has been introduced into wheat genome for disease resistance breeding. Xiaoyan 78829, a wheat-Thinopyrum intermedium partial amphiploid, exhibits excellent resistance to fungal diseases in wheat. To transfer its disease resistance to common wheat (Triticum aestivum), we previously developed a translocation line WTT26 using chromosome engineering. Disease evaluation showed that WTT26 was nearly immune to 14 common races of leaf rust pathogen (Puccinia triticina) and highly resistant to Ug99 race PTKST of stem rust pathogen (P. graminis f. sp. tritici) at the seedling stage. It also displayed high adult plant resistance to powdery mildew (caused by Blumeria graminis f. sp. tritici). Cytogenetic and molecular marker analysis revealed that WTT26 carried a T4BS·7JsS chromosome translocation. Once transferred into the susceptible wheat genetic background, chromosome 7JsS exhibited its resistance to leaf rust, indicating that the resistance locus was located on this alien chromosome. To enhance the usefulness of this locus in wheat breeding, we further developed several new translocation lines with small Th. intermedium segments using irradiation and developed 124 specific markers using specific-locus amplified fragment sequencing, which increased the marker density of chromosome 7JsS. Furthermore, a refined physical map of chromosome 7JsS was constructed with 74 specific markers, and six bins were thus arranged according to the co-occurrence of markers and alien chromosome segments. Combining data from specific marker amplification and resistance evaluation, we mapped a new leaf rust resistance locus in the 0-69.29 Mb region on chromosome 7JsS. The translocation lines carrying the new leaf rust resistance locus and its linked markers will contribute to wheat disease-resistance breeding.

Developing adapted wheat lines with broad-spectrum resistance to stem rust: Introgression of Sr59 through backcrossing and selections based on genotyping-by-sequencing data

Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum resistance genes could impart durable stem rust resistance. This study attempted transfer of Sr59 resistance gene from line TA5094 (developed through CSph1bM-induced T2DS·2RL Robertsonian translocation conferring broad-spectrum resistance). Poor agronomic performance of line TA5094 necessitates Sr59 transfer to adapted genetic backgrounds and utility evaluations for wheat improvement. Based on combined stem rust seedling and molecular analyses, 2070 BC1F1 and 1230 BC2F1 plants were derived from backcrossing BAJ#1, KACHU#1, and REEDLING#1 with TA5094. Genotyping-by-sequencing (GBS) results revealed the physical positions of 15,116 SNPs on chromosome 2R. The adapted genotypes used for backcrossing were found not to possess broad-spectrum resistance to selected stem rust races, whereas Sr59-containing line TA5094 showed resistance to all races tested. Stem rust seedling assays combined with kompetitive allele-specific PCR (KASP) marker analysis successfully selected and generated the BC2F2 population, which contained the Sr59 gene, as confirmed by GBS. Early-generation data from backcrossing suggested deviations from the 3:1 segregation, suggesting that multiple genes may contribute to Sr59 resistance reactions. Using GBS marker data (40,584 SNPs in wheat chromosomes) to transfer the recurrent parent background to later-generation populations resulted in average genome recovery of 71.2% in BAJ#1*2/TA5094, 69.8% in KACHU#1*2/TA5094, and 70.5% in REEDLING#1*2/TA5094 populations. GBS data verified stable Sr59 introgression in BC2F2 populations, as evidenced by presence of the Ph1 locus and absence of the 50,936,209 bp deletion in CSph1bM. Combining phenotypic selections, stem rust seedling assays, KASP markers, and GBS data substantially accelerated transfer of broad-spectrum resistance into adapted genotypes. Thus, this study demonstrated that the Sr59 resistance gene can be introduced into elite genetic backgrounds to mitigate stem rust-related yield losses.

Identification of a Small Translocation from 6R Possessing Stripe Rust Resistance to Wheat

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici Eriks. & E. Henn, is the most devastating fungal disease of bread wheat. Here, a wheat-rye multiple disomic substitution line, SLU126 4R (4D), 5R (5D), and 6R (7D), possessing resistance against 25 races of P. striiformis f. sp. tritici, was used and crossed with Chinese Spring ph1b to induce homeologous recombination to produce introgressions with a reduced rye chromosome segment. Seedling assays confirmed that the stripe rust resistance from SLU126 was retained over multiple generations. Through genotyping-by-sequencing (GBS) platforms and aligning the putative GBS-single-nucleotide polymorphism (SNPs) to the full-length annotated rye nucleotide-binding leucine-rich repeat (NLR) genes in the parental lines (CS ph1b, SLU126, CSA, and SLU820), we identified the physical position of 26, 13, and 9 NLR genes on chromosomes 6R, 4R, and 5R, respectively. The physical positions of 25 NLR genes on chromosome 6R were identified from 568,460,437 bp to 879,958,268 bp in the 6RL chromosome segment. Based on these NLR positions on the 6RL chromosome segment, the three linked SNPs (868,123,650 to 873,285,112 bp) were validated through kompetitive allele-specific PCR (KASP) assays in SLU126 and resistance plants in the family 29-N3-5. Using these KASP markers, we identified a small piece of the rye translocation (i.e., as a possible 6DS.6DL.6RL.6DL) containing the stripe resistance gene, temporary designated YrSLU, within the 6RL segment. This new stripe rust resistance gene provides an additional asset for wheat improvement to mitigate yield losses caused by stripe rust.

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.

Transfer of the Resistance to Multiple Diseases from a Triticum-Secale-Thinopyrum Trigeneric Hybrid to Ningmai 13 and Yangmai 23 Wheat Using Specific Molecular Markers and GISH

The middle to lower reaches of the Yangtze River are China's second largest area for wheat production; wheat disease is more serious there than in other areas because of the high humidity and warm weather. However, most cultivated varieties are susceptible to Fusarium head blight (FHB), powdery mildew, and stripe rust, and the lack of disease-resistant germplasm is an obstacle in wheat breeding. Rye and Thinopyrum elongatum, related species of wheat, carry many genes involved in disease resistance. In this study, a trigeneric hybrid, YZU21, with resistance to FHB, powdery mildew, and stripe rust was used to improve two major wheat cultivars, Ningmai 13 (NM13) and Yangmai 23 (YM23). Specific molecular markers and GISH were used to identify hybrid progenies. Five addition or substitution lines and one translocation line of the Triticum-Secale-Thinopyrum trigeneric hybrid were obtained and evaluated for agronomic traits and the resistance to multiple diseases. The results showed that the six trigeneric hybrid lines had desirable agronomic traits and improved resistance to FHB, powdery mildew, and stripe rust; they might be used as parents in wheat breeding for the resistance to multiple disease.

Studying Stem Rust and Leaf Rust Resistances of Self-Fertile Rye Breeding Populations

Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseq^TM. In total, ten SR-QTLs were found that caused a reduction of 5-17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R, Pgs3.1, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only Pgs3.1 could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (Pr7 and Pr8) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction.

Wheat Genes Associated with Different Types of Resistance against Stem Rust (Puccinia graminis Pers.)

Stem rust is one wheat's most dangerous fungal diseases. Yield losses caused by stem rust have been significant enough to cause famine in the past. Some races of stem rust are considered to be a threat to food security even nowadays. Resistance genes are considered to be the most rational environment-friendly and widely used way to control the spread of stem rust and prevent yield losses. More than 60 genes conferring resistance against stem rust have been discovered so far (so-called Sr genes). The majority of the Sr genes discovered have lost their effectiveness due to the emergence of new races of stem rust. There are some known resistance genes that have been used for over 50 years and are still effective against most known races of stem rust. The goal of this article is to outline the different types of resistance against stem rust as well as the effective and noneffective genes, conferring each type of resistance with a brief overview of their origin and usage.

Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat

Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.

Development and Molecular Cytogenetic Characterization of a Novel Wheat-Rye T6RS.6AL Translocation Line from Secale cereale L. Qinling with Resistance to Stripe Rust and Powdery Mildew

In this study, a novel T6RS.6AL translocation line, 117-6, was selected from a cross between common Chuannong25 (CN25) wheat and Qinling rye. The results of nondenaturing fluorescence in situ hybridization (ND-FISH) and PCR showed that 117-6 contained two T6RS.6AL translocation chromosomes. The distal region of the 6RS chromosome in 117-6 was mutant and showed different FISH signal patterns. When inoculated with different stripe rust races and powdery mildew races in seedlings, 117-6 expressed high resistance to them. The 117-6 line also exhibited high resistance to stripe rust and powdery mildew in the field under natural Puccinia striiformis f. sp. tritici (Pst) and Blumeria graminis f. sp. tritici (Bgt) infection. The cytogenetic analysis indicated that the introduction of 6RS conferred resistance ability. Compared with wheat parent CN25, 117-6 exhibited excellent agronomic traits in the field. The present study indicated that Qinling rye may carry favorite genes as a potential source for wheat genetic improvement, and 117-6 could be a useful germplasm for wheat breeding programs in the future.

A Novel Wheat-Rye 2R (2D) Disomic Substitution Line Pyramids Two Types of Resistance to Powdery Mildew

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is a devastating disease of wheat that seriously affects yield and quality worldwide. Because of the extensive growth of wheat cultivars with homogeneous genetic background, exploring novel resistant resources from wheat relatives has become important for increasing the genetic diversity of wheat. Rye (Secale cereale) is a wheat relative possessing abundant resistance genes because of its high variation. Wheat line AL69, resistant to powdery mildew, was developed by crossing, backcrossing, and self-pollination for multiple generations between hexaploid triticale Zhongsi 237 and common wheat cultivar Zimai 17. Through genomic in situ hybridization (GISH) and multicolor fluorescence in situ hybridization (FISH), nondenaturing FISH, multicolor GISH, and selection with specific molecular markers, AL69 was determined to be a wheat-rye 2R (2D) disomic substitution line. Testing with different B. graminis f. sp. tritici isolates and genetic analysis showed that the all-stage resistance (also called seedling resistance) of AL69 was conferred by the cataloged powdery mildew resistance gene Pm4b derived from Zimai 17, and its adult-plant resistance was derived from the alien chromosome 2R of Zhongsi 237, which was found to be different from the previously reported rye-derived Pm genes, including Pm7 on 2RL. In addition, AL69 showed improved spike number per plant, spike length, fertile spikelet number per spike, kernel number per spike, and grain yield per plant compared with its wheat parent Zimai 17. An elite line S251 combining powdery mildew resistance with excellent agronomic performance was selected from the progenies of AL69 and wheat cultivar Jimai 22. Therefore, AL69 has two types of resistance genes to powdery mildew and improved agronomic traits through pyramiding and thus can be used as a promising genetic stock for wheat breeding.

Molecular cytogenetic identification of new wheat-rye 6R, 6RS, and 6RL addition lines with resistance to stripe rust and powdery mildew

Stripe rust and powdery mildew are devastating diseases that have severe effects on wheat production. Introducing resistant genes/loci from wheat-related species into the wheat genome is an important method to improve wheat resistance. Rye (Secale cereale L.) is a cross-pollinating plant and is the most important related species for wheat genetic improvement. In this study, we developed three 6RS ditelosomic addition lines, three 6RL ditelosomic addition lines, and two 6R disomic addition lines by crossing common wheat cultivar Chuannong 25 and rye inbred line QL2. The chromosome composition of all new lines was confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH) and molecular marker analyses. Disease responses to different Puccinia striiformis f. sp. tritici (Pst) races and Blumeria graminis f. sp. tritici (Bgt) isolates and cytogenetic analysis showed that the resistance of the new lines was derived from the rye chromosome 6R of QL2, and both arms (6RS and 6RL) may harbor resistance genes against Pst and Bgt. These new lines could be used as a promising bridging parent and valuable genetic resource for wheat disease resistance improvement.

Development and Molecular Cytogenetic Characterization of Novel Primary Wheat-Rye 1RS.1BL Translocation Lines from Multiple Rye Sources with Resistance to Stripe Rust

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases for wheat production. An important method to improve the stripe rust resistance of wheat is to introduce resistance genes from related species into the wheat genome. The 1RS.1BL wheat-rye translocation from Petkus rye has contributed substantially to wheat resistance breeding worldwide. However, given the breakdown of the stripe rust resistance gene Yr9 in 1RS, its importance for wheat improvement has decreased. In this study, we developed 166 new primary 1RS.1BL translocation lines by crossing rye varieties Weining, Baili, and Aigan with several wheat cultivars. Cytogenetic and molecular analyses indicated that all of these lines contained a pair of intact 1RS.1BL translocation chromosomes. The stripe rust resistance of these translocation lines and their wheat parents was evaluated in southwestern China during the severe stripe rust epidemics in 2015 and 2021. The results showed diverse effects of the 1RS.1BL translocations from different rye cultivars on resistance to stripe rust. The highest genetic diversity was observed in 1RS.1BL translocations derived from diverse rye varieties but in the same wheat background. The development of diverse 1RS.1BL translocation lines offers ample opportunities to introduce new variations into wheat for improving stripe rust resistance. Finally, 71 new translocation lines, including nine developed from the cross of MY11 × Aigan, four from MY11 × Baili, 40 from MY11 × Weining, 14 from A42912 × Baili, and four from A42912 × Weining. These lines showed consistent resistance to stripe rust in fields under frequent changes of the pathogen races and could be useful genetic stocks for breeding wheat cultivars with resistance to stripe rust.

Development of wheat-Dasypyrum villosum T6V#4S·6AL translocation lines with enhanced inheritance for powdery mildew resistance

New translocation lines with T6V#4S·6AL in the Ph1 and ph1b backgrounds were developed with improved inheritance of powdery mildew resistance. The wheat-Dasypyrum villosum T6V#4S·6DL translocation line Pm97033, which exhibits strong powdery mildew (PM) resistance, was developed many years ago, but has limited application in wheat breeding. One of the major reasons for this is that the translocation chromosome has low transmission rate, which makes it difficult to obtain ideal genotype through recombination with other elite agronomic traits in a limited segregating population. Further modifications are thus needed to make better use of this genetic resource. In this study, Pm97033 and the T6V#2S·6AL translocation line NY-W were hybridized with the CS ph1b mutant, and two F₁ hybrids were hybridized with each other. Then, plants homozygous for the ph1b deletion carrying the alien chromosome arm(s) 6V#2S and 6V#4S were identified from the segregating populations using molecular markers. New T6V#4S·6AL and T6V#2-6V#4S·6AL translocations were identified by molecular markers and confirmed by genomic in situ hybridization (GISH). Individuals that were heterozygous or homozygous for the translocation chromosome in Ph1 and ph1b backgrounds were obtained. The ratio of PM resistance vs. susceptibility in the self-pollinated heterozygous plants was 3:1, and the phenotype was completely consistent with the KASP genotyping. Thus, the new translocation chromosomes had higher transmission rate than the original T6V#4S·6DL, and so can be effectively applied in breeding programs.

Establishment of a set of wheat-rye addition lines with resistance to stem rust

Complete new wheat-rye disomic, telosomic addition lines and various chromosomal aberrations were developed and characterized by molecular cytogenetic method as novel chromosome engineering materials. A new stem rust resistance (Ug99) gene was located on 3RL. Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating fungal disease worldwide. A recently emerged great threat to global wheat production is Pgt strain Ug99 and its derivatives, which have overcome most of the commonly used resistance genes. Rye (Secale cereale L.), closely related to wheat (Triticum aestivum L.), is a significant and valuable resource of resistance genes for wheat germplasm improvement. It is of great importance and urgency to identify new resistance gene sources of rye and transfer them into wheat. In this study, two complete sets of wheat-rye addition lines were established through wide hybridization, chromosome doubling and backcrossing. A wheat-rye 3RL telosomic addition line was identified with high resistance to stem rust strain Ug99. PCR-based markers specific for the rye chromosome were developed. Furthermore, abundant chromosomal aberrations such as minichromosomes, ring chromosomes as well as centromere reduction and expansion were identified in the progeny of wheat-rye addition lines by multicolor GISH and FISH. The line carrying a novel resistance gene to stem rust can be utilized as a bridge material for wheat disease resistance breeding. The chromosomal and centromeric variation within the wheat-rye hybrids can further contribute to genetic diversity of their offspring.

Climate Change Impact on Wheat Performance—Effects on Vigour, Plant Traits and Yield from Early and Late Drought Stress in Diverse Lines

Global climate change is threatening wheat productivity; improved yield under drought conditions is urgent. Here, diverse spring-wheat lines (modern, old and wheat-rye introgressions) were examined in an image-based early-vigour assay and a controlled-conditions (Biotron) trial that evaluated 13 traits until maturity. Early root vigour was significantly higher in the old Swedish lines (root length 8.50 cm) and introgressed lines with 1R (11.78 cm) and 1RS (9.91 cm) than in the modern (4.20 cm) and 2R (4.67 cm) lines. No significant correlation was noted between early root and shoot vigour. A higher yield was obtained under early drought stress in the 3R genotypes than in the other genotype groups, while no clear patterns were noted under late drought. Evaluating the top 10% of genotypes in terms of the stress-tolerance index for yield showed that root biomass, grains and spikes per plant were accountable for tolerance to early drought, while 1000-grain weight and flag-leaf area were accountable for tolerance to late drought. Early root vigour was determined as an important focus trait of wheat breeding for tolerance to climate-change-induced drought. The responsible genes for the trait should be searched for in these diverse lines. Additional drought-tolerance traits determined here need further elaboration to identify the responsible genes.

Wheat speciation and adaptation: perspectives from reticulate evolution

Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.

Impact of the United States Department of Agriculture, Agricultural Research Service on Plant Pathology: 2015-2020

There is an increasing need to supply the world with more food as the population continues to grow. Research on mitigating the effects of plant diseases to improve crop yield and quality can help provide more food without increasing the land area devoted to farming. National Program 303 (NP 303) within the U.S. Department of Agriculture, Agricultural Research Service is dedicated to research across multiple fields in plant pathology. This review article highlights the research impact within NP 303 between 2015 and 2020, including case studies on wheat and citrus diseases and the National Plant Disease Recovery System, which provide specific examples of this impact.

Mapping and validating stem rust resistance genes directly in self-incompatible genetic resources of winter rye

Individual stem rust resistance genes could be directly mapped within self-incompatible rye populations. Genetic resources of rye (Secale cereale L.) are cross-pollinating populations that can be highly diverse and are naturally segregating. In this study, we show that this segregation could be used for mapping stem rust resistance. Populations of pre-selected donors from the Russian Federation, the USA and Austria were tested on a single-plant basis for stem rust resistance by a leaf-segment test with three rust isolates. Seventy-four plants per population were genotyped with a 10 K-SNP chip. Using cumulative logit models, significant associations between the ordinal infection score and the marker alleles could be found. Three different loci (Pgs1, Pgs2, Pgs3) in three populations were highly significant, and resistance-linked markers could be validated with field experiments of an independent seed sample from the original population and were used to fix two populations for resistance. We showed that it is possible to map monogenically inherited seedling resistance genes directly in genetic resources, thus providing a competitive alternative to linkage mapping approaches that require a tedious and time-consuming inbreeding over several generations.

Development and Molecular Cytogenetic Identification of a New Wheat-Psathyrostachys huashanica Keng Translocation Line Resistant to Powdery Mildew

Psathyrostachys huashanica Keng, a wild relative of common wheat with many desirable traits, is an invaluable source of genetic material for wheat improvement. Few wheat-P. huashanica translocation lines resistant to powdery mildew have been reported. In this study, a wheat-P. huashanica line, E24-3-1-6-2-1, was generated via distant hybridization, ethyl methanesulfonate (EMS) mutagenesis, and backcross breeding. A chromosome karyotype of 2n = 44 was observed at the mitotic stage in E24-3-1-6-2-1. Genomic in situ hybridization (GISH) analysis revealed four translocated chromosomes in E24-3-1-6-2-1, and P. huashanica chromosome-specific marker analysis showed that the alien chromosome fragment was from the P. huashanica 4Ns chromosome. Moreover, fluorescence in situ hybridization (FISH) analysis demonstrated that reciprocal translocation had occurred between the P. huashanica 4Ns chromosome and the wheat 3D chromosome; thus, E24-3-1-6-2-1 carried two translocations: T3DS·3DL-4NsL and T3DL-4NsS. Translocation also occurred between wheat chromosomes 2A and 4A. At the adult stage, E24-3-1-6-2-1 was highly resistant to powdery mildew, caused by prevalent pathotypes in China. Further, the spike length, numbers of fertile spikelets, kernels per spike, thousand-kernel weight, and grain yield of E24-3-1-6-2-1 were significantly higher than those of its wheat parent 7182 and addition line 24-6-3-1. Thus, this translocation line that is highly resistant to powdery mildew and has excellent agronomic traits can be used as a novel promising germplasm for breeding resistant and high-yielding cultivars.

Chromosomal composition analysis and molecular marker development for the novel Ug99-resistant wheat-Thinopyrum ponticum translocation line WTT34

A novel Ug99-resistant wheat-Thinopyrum ponticum translocation line was produced, its chromosomal composition was analyzed and specific markers were developed. Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn (Pgt) has seriously threatened global wheat production since Ug99 race TTKSK was first detected in Uganda in 1998. Thinopyrum ponticum is near immune to Ug99 races and may be useful for enhancing wheat disease resistance. Therefore, developing new wheat-Th. ponticum translocation lines that are resistant to Ug99 is crucial. In this study, a novel wheat-Th. ponticum translocation line, WTT34, was produced. Seedling and field evaluation revealed that WTT34 is resistant to Ug99 race PTKST. The resistance was derived from the alien parent Th. ponticum. Screening WTT34 with markers linked to Sr24, Sr25, Sr26, Sr43, and SrB resulted in the amplification of different DNA fragments from Th. ponticum, implying WTT34 carries at least one novel stem rust resistance gene. Genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and multi-color GISH (mc-GISH) analyses indicated that WTT34 carries a T5DS·5DL-Th translocation, which was consistent with wheat660K single-nucleotide polymorphism (SNP) array results. The SNP array also uncovered a deletion event in the terminal region of chromosome 1D. Additionally, the homeology between alien segments and the wheat chromosomes 2A and 5D was confirmed. Furthermore, 51 PCR-based markers derived from the alien segments of WTT34 were developed based on specific-locus amplified fragment sequencing (SLAF-seq). These markers may enable wheat breeders to rapidly trace Th. ponticum chromosomal segments carrying Ug99 resistance gene(s).

Identification of an Elite Wheat-Rye T1RS·1BL Translocation Line Conferring High Resistance to Powdery Mildew and Stripe Rust

Wheat-rye T1RS·1BL translocations have been widely used worldwide in wheat production for multiple disease resistance and superior yield traits. However, many T1RS·1BL translocations have successively lost their resistance to pathogens due to the coevolution of pathogen virulence with host resistance. Because of the extensive variation in rye (Secale cereale L.) as a naturally cross-pollinating relative of wheat, it still has promise to widen the variation of 1RS and to fully realize its application value in wheat improvement. In the present study, the wheat-rye breeding line R2207 was characterized by comprehensive analyses using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization with multiple probes, multicolor GISH, and molecular marker analysis, and then was proven to be a cytogenetically stable wheat-rye T1RS·1BL translocation line. Based on the disease responses to different isolates of powdery mildew and genetic analysis, R2207 appears to possess a novel variation for resistance, which was confirmed to be located on the rye chromosome arm 1RS. Line R2207 also exhibited high levels of resistance to stripe rust at both seedling and adult stages, as well as enhanced agronomic performance, so it has been transferred into a large number of commercial cultivars using an efficient 1RS-specific kompetitive allele specific PCR marker for marker-assisted selection.

Molecular and Cytogenetic Characterization of a Wheat-Rye 7BS.7RL Translocation Line with Resistance to Stripe Rust, Powdery Mildew, and Fusarium Head Blight

Secale cereale is used as a source of genes for disease resistance in wheat cultivation. In this study, a homozygous translocation line (RT14-245) that originated from a cross between a commercial wheat cultivar (Mianyang 11) and a local Chinese variety of rye (Baili) was developed. Multicolor fluorescence in situ hybridization and PCR analysis demonstrated that the translocation chromosome was 7BS.7RL. Resistance analysis showed that RT14-245 was resistant to prevalent pathotypes of stripe rust and powdery mildew. RT14-245 also exhibited high resistance to Fusarium head blight, which was similar to the resistance exhibited by the wheat cultivar Sumai 3. The results indicated that RT14-245 simultaneously exhibited high levels of resistance against stripe rust, powdery mildew, and Fusarium head blight. These results indicate that chromosome arm 7RL in the translocation line RT14-245 is an excellent new resource for wheat breeding programs.

Generation and molecular marker and cytological characterization of wheat - Secale strictum subsp. anatolicum derivatives

Cereal rye and its wild forms are important sources of genetic diversity for wheat breeding due to their resistances to biotic and abiotic stresses. Secale strictum subsp. anatolicum (Boiss.) K. Hammer (SSA) is a weedy relative of cultivated rye, S. cereale. Meiotic chromosome pairing in F₁ hybrids of SSA and S. cereale reveals strong genomic affinity between the two genomes. A study of the transferability of S. cereale sequence-based markers to SSA and hexaploid triticale demonstrated their applicability for tracing SSA chromatin in wheat. The transferability of the markers was over 80% from homoeologous groups 1, 2, and 3, and greater than 70% from groups 4 to 7. This study focused on the generation and molecular and cytogenetic characterization of wheat-SSA alien derivatives. Twelve were identified using combinations of non-denaturing fluorescence in situ hybridization (ND-FISH), genomic in situ hybridization (GISH), and molecular marker analysis. All SSA chromosomes, except 3R^a and 6R^a, were transferred to wheat either in the form of monosomic additions (MA), mono-telosomic additions (MtA), double-mono-telosomic additions (dMtA), or double-monosomic additions (dMA). The germplasm developed in this study will help to enhance the genetic base of wheat and facilitate molecular breeding of wheat and triticale.

Diverse Wheat-Alien Introgression Lines as a Basis for Durable Resistance and Quality Characteristics in Bread Wheat

Wheat productivity has been significantly improved worldwide through the incorporation of novel genes from various gene pools, not least from wild relatives of wheat, into the commonly cultivated bread and durum wheat. Here, we present and summarize results obtained from a diverse set of wheat-alien introgression lines with mainly introgressions of rye, but also of Leymus spp. and Thinopyrum junceiforme into bread-wheat (Triticum aestivum L.). From this material, lines carrying 2RL were found with good agronomic performance and multiple resistance not least towards several races of powdery mildew. A novel resistance gene, one of few showing resistance towards all today identified stem rust races, designated Sr59, was also found originating from 2RL. Lines with multiple introgressions from 4R, 5R, and 6R were found resistant towards the majority of the stripe rust races known today. Due to lack of agricultural adaptation in these lines, transfer of useful genes into more adapted wheat material is a necessity, work which is also in progress through crosses with the CSph1b mutant, to be able to only transfer small chromosome segments that carry the target gene. Furthermore, resistance towards Russian wheat aphid was found in lines having a substitution of 1R (1D) and translocations of 3DL.3RS and 5AL.5RS. The rye chromosomes 1R, 2R, and 6R were found responsible for resistance towards the Syrian Hessian fly. High levels of especially zinc was found in several lines obtained from crosses with Leymus racemosus and Leymus mollis, while also some lines with 1R, 2R, or 5R showed increased levels of minerals and in particular of iron and zinc. Moreover, lines with 1R, 2R, 3R, and Leymus spp. introgressions were also found to have a combination of high iron and zinc and low cadmium concentrations. High variation was found both in grain protein concentration and gluten strength, measured as %UPP, within the lines, indicating large variation in bread-making quality. Thus, our study emphasizes the impact that wheat-alien introgression lines can contribute to current wheat lines and shows large opportunities both to improve production, resistance, and quality. To obtain such improvements, novel plant breeding tools, as discussed in this paper, opens unique opportunities, to transfer suitable genes into the modern and adapted wheat cultivars.

Identification and characterization of a new stripe rust resistance gene Yr83 on rye chromosome 6R in wheat

A physical map of Secale cereale chromosome 6R was constructed using deletion mapping, and a new stripe rust resistance gene Yr83 was mapped to the deletion bin of FL 0.73-1.00 of 6RL. Rye (Secale cereale L., RR) possesses valuable genes for wheat improvement. In the current study, we report a resistance gene conferring stripe rust resistance effective from seedling to adult plant stages located on chromosome 6R. This chromosome was derived from triticale line T-701 and also carries highly effective resistance to the cereal cyst nematode species Heterodera avenae Woll. A wheat-rye 6R(6D) disomic substitution line exhibited high levels of seedling resistance to Australian pathotypes of the stripe rust (Puccinia striiformis f. sp. tritici; Pst) pathogen and showed an even greater resistance to the Chinese Pst pathotypes in the field. Ten chromosome 6R deletion lines and five wheat-rye 6R translocation lines were developed earlier in the attempt to transfer the nematode resistance gene to wheat and used herein to map the stripe rust resistance gene. These lines were subsequently characterized by sequential multicolor fluorescence in situ hybridization (mc-FISH), genomic in situ hybridization (GISH), mc-GISH, PCR-based landmark unique gene (PLUG), and chromosome 6R-specific length amplified fragment sequencing (SLAF-Seq) marker analyses to physically map the stripe rust resistance gene. The new stripe rust resistance locus was located in a chromosomal bin with fraction length (FL) 0.73-1.00 on 6RL and was named Yr83. A wheat-rye translocation line T6RL (#5) carrying the stripe rust resistance gene will be useful as a new germplasm in breeding for resistance.

The Resurgence of Introgression Breeding, as Exemplified in Wheat Improvement

Breeding progress in most crops has relied heavily on the exploitation of variation within the species' primary gene pool, a process which is destined to fail once the supply of novel variants has been exhausted. Accessing a crop's secondary gene pool, as represented by its wild relatives, has the potential to greatly expand the supply of usable genetic variation. The crop in which this approach has been most strongly championed is bread wheat (Triticum aestivum), a species which is particularly tolerant of the introduction of chromosomal segments of exotic origin thanks to the genetic buffering afforded by its polyploid status. While the process of introgression can be in itself cumbersome, a larger problem is that linkage drag and/or imperfect complementation frequently impose a yield and/or quality penalty, which explains the reluctance of breeders to introduce such materials into their breeding populations. Thanks to the development of novel strategies to induce introgression and of genomic tools to facilitate the selection of desirable genotypes, introgression breeding is returning as a mainstream activity, at least in wheat. Accessing variation present in progenitor species has even been able to drive genetic advance in grain yield. The current resurgence of interest in introgression breeding can be expected to result in an increased deployment of exotic genes in commercial wheat cultivars.

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

Background

Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will facilitate the transfer and utilization of elite genes derived from rye in wheat breeding.

Results

In the present study, five rye cultivars including Imperial, German White, Jingzhouheimai, Baili and Guyuan were sequenced by specific-locus amplified fragment sequencing (SLAF-seq) to develop large-scale rye-specific markers. Based on SLAF-seq and bioinformatics analyses, a total of 404 universal PCR-based and a whole set of Kompetitive allele-specific PCR (KASP) markers specific for the 14 individual rye chromosome arms were developed and validated. Additionally, two KASP markers specific for 1RS and 2RL were successfully applied in the detection of 1RS translocations in a natural population and 2RL chromosome arms in wheat-rye derived progenies that conferred adult resistance to powdery mildew.

Conclusion

The 404 PCR-based markers and 14 KASP markers specific for the 14 individual rye chromosome arms developed in this study can enrich the marker densities for gene mapping and accelerate the utilization of rye-derived genes in wheat improvement. Especially, the KASP markers achieved high-throughput and accurate detection of rye chromatin in wheat background, thus can be efficiently used in marker-assisted selection (MAS). Besides, the strategy of rye-specific PCR-based markers converting into KASP markers was high-efficient and low-cost, which will facilitate the tracing of alien genes, and can also be referred for other wheat relatives.

Development of Novel Wheat-Rye Chromosome 4R Translocations and Assignment of Their Powdery Mildew Resistance

Rye (Secale cereale L.) is an important gene donor for wheat improvement because of its many valuable traits, especially disease resistance. Development of novel wheat-rye translocations with disease resistance can contribute to transferring resistance into common wheat. In a previous study, a wheat-rye T4BL·4RL and T7AS·4RS translocation line (WR41-1) was developed by distant hybridization, and it was speculated that its resistance to powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), was derived from rye based on pedigree analysis. To make accurate use of chromosome 4R in wheat improvement, a set of new 4R translocations involving different arm translocations (e.g., 4RS monosomic, 4RL monosomic, 4RL disomic, 4RS monosomic plus 4RL monosomic, 4RS monosomic plus 4RL disomic, and 4RS disomic plus 4RL disomic translocations) was developed from crosses with common wheat. Those translocations were characterized by genomic in situ hybridization and expressed sequence tag simple sequence repeat marker analysis. To confirm the source of powdery mildew resistance, the translocation plants were tested against Bgt isolate E09. The results indicated that all translocations with 4RL were resistant at all tested growth stages, whereas those with only 4RS translocation or no alien translocation were susceptible. This further indicated that the powdery mildew resistance of WR41-1 was derived from the alien chromosome arm 4RL. To effectively use 4RL resistance in wheat improvement, two competitive allele-specific PCR markers specific for chromosome arm 4RL were developed to detect the alien chromosome in the wheat genome. These new translocation lines with diagnostic markers can efficiently serve as important bridges for wheat improvement.

Introgression of a Novel Ug99-Effective Stem Rust Resistance Gene into Wheat and Development of Dasypyrum villosum Chromosome-Specific Markers via Genotyping-by-Sequencing (GBS)

Dasypyrum villosum is a wild relative of common wheat (Triticum aestivum L.) with resistance to Puccinia graminis f. tritici, the causal agent of stem rust, including the highly virulent race TTKSK (Ug99). In order to transfer resistance, T. durum-D. villosum amphiploids were initially developed and used as a bridge to create wheat-D. villosum introgression lines. Conserved ortholog set (COS) markers were used to identify D. villosum chromosome introgression lines, which were then subjected to seedling P. graminis f. tritici resistance screening with race TTKSK. A COS marker-verified line carrying chromosome 2V with TTKSK resistance was further characterized by combined genomic in situ and fluorescent in situ analyses to confirm a monosomic substitution line MS2V(2D) (20″ + 1' 2V[2D]). This is the first report of stem rust resistance on 2V, which was temporarily designated as SrTA10276-2V. To facilitate the use of this gene in wheat improvement, a complete set of previously developed wheat-D. villosum disomic addition lines was subjected to genotyping-by-sequencing analysis to develop D. villosum chromosome-specific markers. On average, 350 markers per chromosome were identified. These markers can be used to develop diagnostic markers for D. villosum-derived genes of interest in wheat improvement.

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.

Development and molecular cytogenetic identification of a new wheat-rye 4R chromosome disomic addition line with resistances to powdery mildew, stripe rust and sharp eyespot

A wheat-rye 4R chromosome disomic addition line with resistances to powdery mildew, stripe rust, sharp eyespot and high kernel number per spike was developed and characterized by molecular cytogenetic method as novel resistant germplasm. Rye (Secale cereale L.), a close relative of common wheat, is an important and valuable gene donor with multiple disease resistance for wheat improvement. However, resistance genes derived from rye have successively lost resistance to pathogens due to the coevolution of pathogen virulence and host resistance. Development and identification of new effective resistance gene sources from rye therefore are of special importance and urgency. In the present study, a wheat-rye line WR35 was produced through distant hybridization, embryo rescue culture, chromosome doubling and backcrossing. WR35 was then proven to be a new wheat-rye 4R disomic addition line using sequential GISH (genomic in situ hybridization), mc-FISH (multicolor fluorescence in situ hybridization) and ND-FISH (non-denaturing FISH) with multiple probes, mc-GISH (multicolor GISH), rye chromosome arm-specific marker analysis and SLAF-seq (specific-locus amplified fragment sequencing) analysis. At the adult stage, WR35 exhibited high levels of resistance to the powdery mildew (Blumeria graminis f. sp. tritici, Bgt) and stripe rust (Puccinia striiformis f. sp. tritici, Pst) pathogens prevalent in China, and a highly virulent isolate of Rhizoctonia cerealis, the cause of wheat sharp eyespot. At the seedling stage, it was highly resistant to 22 of 23 Bgt isolates and four Pst races. Based on its disease responses to different pathogen isolates, WR35 may possess resistance gene(s) for powdery mildew, stripe rust and sharp eyespot, which differed from the known resistance genes from rye. In addition, WR35 was cytologically stable and produced high kernel number per spike. Therefore, WR35 with multi-disease resistances and desirable agronomic traits should serve as a promising bridging parent for wheat chromosome engineering breeding.

Identification and Validation of a Common Stem Rust Resistance Locus in Two Bi-parental Populations

Races belonging to Ug99 lineage of stem rust fungus Puccinia graminis f. sp. tritici (Pgt) continue to pose a threat to wheat (Triticum aestivum L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent 'Cacuke' with the resistant parents 'Huhwa' and 'Yaye' were phenotyped for resistance at the seedling stage to Pgt race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as SrH and SrY, were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations. SrH mapped between markers cim109 and cim114 at a distance of 0.9 cM proximal, and cim117 at 2.9 cM distal. SrY was flanked by markers cim109 and cim116 at 0.8 cM proximal, and IWB45932 at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat, Sr9h and Sr28, have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that Sr28 was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against Sr9h-virulent race TTKSF+ confirmed the presence of a common resistance locus Sr9h in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and Sr9h. Marker cim117 linked to SrH was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of Sr9h in breeding programs.

Development of a new 7BS.7HL winter wheat-winter barley Robertsonian translocation line conferring increased salt tolerance and (1,3;1,4)-β-D-glucan content

Interspecific hybridization between bread wheat (Triticum aestivum, 2n = 42) and related species allows the transfer of agronomic and quality traits, whereby subsequent generations comprise an improved genetic background and can be directly applied in wheat breeding programmes. While wild relatives are frequently used as sources of agronomically favourable traits, cultivated species can also improve wheat quality and stress resistance. A salt-tolerant 'Asakaze'/'Manas' 7H disomic addition line (2n = 44) with elevated β-glucan content, but with low fertility and an unstable genetic background was developed in an earlier wheat-barley prebreeding programme. The aim of the present study was to take this hybridization programme further and transfer the favourable barley traits into a more stable genetic background. Taking advantage of the breakage-fusion mechanism of univalent chromosomes, the 'Rannaya' winter wheat 7B monosomic line was used as female partner to the 7H addition line male, leading to the development of a compensating wheat/barley Robertsonian translocation line (7BS.7HL centric fusion, 2n = 42) exhibiting higher salt tolerance and elevated grain β-glucan content. Throughout the crossing programme, comprising the F1-F4 generations, genomic in situ hybridization, fluorescence in situ hybridization and chromosome-specific molecular markers were used to trace and identify the wheat and barley chromatin. Investigations on salt tolerance during germination and on the (1,3;1,4)-β-D-glucan (mixed-linkage glucan [MLG]) content of the seeds confirmed the salt tolerance and elevated grain MLG content of the translocation line, which can be directly applied in current wheat breeding programmes.

A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.

Introgression of Powdery Mildew Resistance Gene Pm56 on Rye Chromosome Arm 6RS Into Wheat

Powdery mildew, caused by the fungus Blumeria graminis f. sp. tritici, represents a yield constraint in many parts of the world. Here, the introduction of a resistance gene carried by the cereal rye cv. Qinling chromosome 6R was transferred into wheat in the form of spontaneous balanced translocation induced in plants doubly monosomic for chromosomes 6R and 6A. The translocation, along with other structural variants, was detected using in situ hybridization and genetic markers. The differential disease response of plants harboring various fragments of 6R indicated that a powdery mildew resistance gene(s) was present on both arms of rye chromosome 6R. Based on karyotyping, the short arm gene, designated Pm56, was mapped to the subtelomere region of the arm. The Robertsonian translocation 6AL⋅6RS can be exploited by wheat breeders as a novel resistance resource.

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.

A systematic review of rye (Secale cereale L.) as a source of resistance to pathogens and pests in wheat (Triticum aestivum L.)

Wheat is globally one of the most important crops. With the current human population growth rate, there is an increasing need to raise wheat productivity by means of plant breeding, along with development of more efficient and sustainable agricultural systems. Damage by pathogens and pests, in combination with adverse climate effects, need to be counteracted by incorporating new germplasm that makes wheat more resistant/tolerant to such stress factors. Rye has been used as a source for improved resistance to pathogens and pests in wheat during more than 50 years. With new devastating stem and yellow rust pathotypes invading wheat at large acreage globally, along with new biotypes of pest insects, there is renewed interest in using rye as a source of resistance. Currently the proportion of wheat cultivars with rye chromatin varies between countries, with examples of up to 34%. There is mainly one rye source, Petkus, that has been widely exploited and that has contributed considerably to raise yields and increase disease resistance in wheat. Successively, the multiple disease resistances conferred by this source has been overcome by new pathotypes of leaf rust, yellow rust, stem rust and powdery mildew. However, there are several other rye sources reported to make wheat more resistant to various biotic constraints when their rye chromatin has been transferred to wheat. There is also development of knowledge on how to produce new rye translocation, substitution and addition lines. Here we compile information that may facilitate decision making for wheat breeders aiming to transfer resistance to biotic constraints from rye to elite wheat germplasm.