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

High-density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat

KEY MESSAGE

The durable stripe rust resistance gene Yr30 was fine-mapped to a 610-kb region in which five candidate genes were identified by expression analysis and sequence polymorphisms. The emergence of genetically diverse and more aggressive races of Puccinia striiformis f. sp. tritici (Pst) in the past twenty years has resulted in global stripe rust outbreaks and the rapid breakdown of resistance genes. Yr30 is an adult plant resistance (APR) gene with broad-spectrum effectiveness and its durability. Here, we fine-mapped the YR30 locus to a 0.52-cM interval using 1629 individuals derived from residual heterozygous F5:6 plants in a Yaco"S"/Mingxian169 recombinant inbred line population. This interval corresponded to a 610-kb region in the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 2.1 on chromosome arm 3BS harboring 30 high-confidence genes. Five genes were identified as candidate genes based on functional annotation, expression analysis by RNA-seq and sequence polymorphisms between cultivars with and without Yr30 based on resequencing. Haplotype analysis of the target region identified six haplotypes (YR30_h1-YR30_h6) in a panel of 1215 wheat accessions based on the 660K feature genotyping array. Lines with YR30_h6 displayed more resistance to stripe rust than the other five haplotypes. Near-isogenic lines (NILs) with Yr30 showed a 32.94% higher grain yield than susceptible counterparts when grown in a stripe rust nursery, whereas there was no difference in grain yield under rust-free conditions. These results lay a foundation for map-based cloning Yr30.

Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat

The current study focuses on identifying the candidate genes of a grain yield QTL from a double haploid population, Westonia × Kauz. The QTL region spans 20 Mbp on the IWGSC whole-genome sequence flank with 90K SNP markers. The IWGSC gene annotation revealed 16 high-confidence genes and 41 low-confidence genes. Bioinformatic approaches, including functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available gene expression data, enabled the short-listing of four genes for further confirmation. Complete sequencing of those four genes demonstrated that only two genes are polymorphic between the parental cultivars, which are the ferredoxin-like protein gene and the tetratricopeptide-repeat (TPR) protein gene. The two genes were selected for downstream investigation. Two SNP variations were observed in the exon for both genes, with one SNP resulting in changes in amino acid sequence. qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines along with the parental cultivar Westonia. In contrast, their expression was significantly lower in the low-yielding lines in the other parent. It can be concluded that these two genes are the contributing genes to the grain yield QTL.

Genetic architecture of adult-plant resistance to stripe rust in bread wheat (Triticum aestivum L.) association panel

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.

Genome-wide QTL mapping for stripe rust resistance in spring wheat line PI 660122 using the Wheat 15K SNP array

Introduction

Stripe rust is a global disease of wheat. Identification of new resistance genes is key to developing and growing resistant varieties for control of the disease. Wheat line PI 660122 has exhibited a high level of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 239 recombinant inbred lines (RILs) was developed from a cross between PI 660122 and an elite Chinese cultivar Zhengmai 9023.

Methods

The RIL population was phenotyped for stripe rust response in three field environments and genotyped with the Wheat 15K single-nucleotide polymorphism (SNP) array.

Results

A total of nine quantitative trait loci (QTLs) for stripe rust resistance were mapped to chromosomes 1B (one QTL), 2B (one QTL), 4B (two QTLs), 4D (two QTLs), 6A (one QTL), 6D (one QTL), and 7D (one QTL), of which seven QTLs were stable and designated as QYrPI660122.swust-4BS, QYrPI660122.swust-4BL, QYrPI660122.swust-4DS, QYrPI660122.swust-4DL, QYrZM9023.swust-6AS, QYrZM9023.swust-6DS, and QYrPI660122.swust-7DS. QYrPI660122.swust-4DS was a major all-stage resistance QTL explaining the highest percentage (10.67%-20.97%) of the total phenotypic variation and was mapped to a 12.15-cM interval flanked by SNP markers AX-110046962 and AX-111093894 on chromosome 4DS.

Discussion

The QTL and their linked SNP markers in this study can be used in wheat breeding to improve resistance to stripe rust. In addition, 26 lines were selected based on stripe rust resistance and agronomic traits in the field for further selection and release of new cultivars.

Development and Characterization of a Novel Wheat-Tetraploid Thinopyrum elongatum 6E (6D) Disomic Substitution Line with Stripe Rust Resistance at the Adult Stage

Stripe rust, which is caused by Puccinia striiformis f. sp. tritici, is one of the most devastating foliar diseases of common wheat worldwide. Breeding new wheat varieties with durable resistance is the most effective way of controlling the disease. Tetraploid Thinopyrum elongatum (2n = 4x = 28, EEEE) carries a variety of genes conferring resistance to multiple diseases, including stripe rust, Fusarium head blight, and powdery mildew, which makes it a valuable tertiary genetic resource for enhancing wheat cultivar improvement. Here, a novel wheat-tetraploid Th. elongatum 6E (6D) disomic substitution line (K17-1065-4) was characterized using genomic in situ hybridization and fluorescence in situ hybridization chromosome painting analyses. The evaluation of disease responses revealed that K17-1065-4 is highly resistant to stripe rust at the adult stage. By analyzing the whole-genome sequence of diploid Th. elongatum, we detected 3382 specific SSR sequences on chromosome 6E. Sixty SSR markers were developed, and thirty-three of them can accurately trace chromosome 6E of tetraploid Th. elongatum, which were linked to the disease resistance gene(s) in the wheat genetic background. The molecular marker analysis indicated that 10 markers may be used to distinguish Th. elongatum from other wheat-related species. Thus, K17-1065-4 carrying the stripe rust resistance gene(s) is a novel germplasm useful for breeding disease-resistant wheat cultivars. The molecular markers developed in this study may facilitate the mapping of the stripe rust resistance gene on chromosome 6E of tetraploid Th. elongatum.

In-Depth Understanding of the Genetic Control of Stripe Rust Resistance (Puccinia striiformis f. sp. tritici) Induced in Wheat (Triticum aestivum) by Trichoderma asperellum T34

Wheat stripe rust (caused by Puccinia striiformis f. tritici Erikss.) causes severe yield losses worldwide. Due to the continuous appearance of new stripe rust races, resistance has been broken in most of the highly resistant genotypes in Egypt and worldwide. Therefore, looking for new ways to resist such a severe disease is urgently needed. Trichoderma asperellum strain T34 has been known as an effective bioagent against many crop diseases. It exists naturally in Egyptian fields. Therefore, in our study, the effectiveness of strain T34 was tested as a bioagent against wheat stripe rust. For this purpose, 198 spring wheat genotypes were tested for their resistance against two different P. striiformis f. tritici populations collected from the Egyptian fields. The most highly aggressive P. striiformis f. tritici population was used to test the effectiveness of strain T34. Highly significant differences were found between strain T34 and stripe rust, suggesting the effectiveness of strain T34 in stripe rust resistance. A genome-wide association study identified 48 gene models controlling resistance under normal conditions and 46 gene models controlling strain T34-induced resistance. Of these gene models, only one common gene model was found, suggesting the presence of two different genetic systems controlling resistance under each condition. The pathways of the biological processes were investigated under both conditions. This study provided in-depth understanding of genetic control and, hence, will accelerate the future of wheat breeding programs for stripe rust resistance.

Mapping QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Landrace

Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0–21.2%, 10.1–22.7%, and 11.6–18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.

Stripe rust and leaf rust resistance in CIMMYT wheat line "Mucuy" is conferred by combinations of race-specific and adult-plant resistance loci

Developing wheat varieties with durable resistance is a core objective of the International Maize and Wheat Improvement Center (CIMMYT) and many other breeding programs worldwide. The CIMMYT advanced wheat line "Mucuy" displayed high levels of resistance to stripe rust (YR) and leaf rust (LR) in field evaluations in Mexico and several other countries. To determine the genetic basis of YR and LR resistance, 138 F₅ recombinant inbred lines (RILs) derived from the cross of Apav#1× Mucuy were phenotyped for YR responses from 2015 to 2020 at field sites in India, Kenya, and Mexico, and LR in Mexico. Seedling phenotyping for YR and LR responses was conducted in the greenhouse in Mexico using the same predominant races as in field trials. Using 12,681 polymorphic molecular markers from the DArT, SNP, and SSR genotyping platforms, we constructed genetic linkage maps and QTL analyses that detected seven YR and four LR resistance loci. Among these, a co-located YR/LR resistance loci was identified as Yr29/Lr46, and a seedling stripe rust resistance gene YrMu was mapped on the 2AS/2NS translocation. This fragment also conferred moderate adult plant resistance (APR) under all Mexican field environments and in one season in Kenya. Field trial phenotyping with Lr37-virulent Puccinia triticina races indicated the presence of an APR QTL accounting for 18.3-25.5% of the LR severity variation, in addition to a novel YR resistance QTL, QYr.cim-3DS, derived from Mucuy. We developed breeder-friendly KASP and indel molecular markers respectively for Yr29/Lr46 and YrMu. The current study validated the presence of known genes and identified new resistance loci, a QTL combination effect, and flanking markers to facilitate accelerated breeding for genetically complex, durable rust resistance.

Identification of Three Novel QTLs Associated with Yellow Rust Resistance in Wheat (Triticum aestivum L.) Anong-179/Khaista-17 F2 Population

Wheat yellow rust (YR) caused by Puccinia striiformis is lethal for the leaf photosynthetic process, which substantially affects yield components and ultimately causes drastic yield reduction. The current study aimed to identify all-stage YR resistance linked QTLs in the best cross-combination. Experimental materials were phenotyped for disease severity in YR-hot spot area at Cereal Crops Research Institute, Pirsabak Pakistan in Khyber Pakhtunkhwa province in 2019 and 2020 and 2020 and 2021 Rabi seasons. The AN179 × KS17 was found to be the best cross combination, which showed high resistance to YR, whereas crosses AN179 × PK15 and PR129 × PK15 demonstrated susceptibility to YR with high disease severity. The recombinant inbred lines (RIL) F2 wheat population Annong-179/Khaista-17 demonstrated highly desirable YR resistance and yield component traits. Simple sequence repeat (SSR) markers were used to genotype the RIL population and their parents. Three novel QTLs linked to all-stage YR resistance were found on chromosomes 2BS, 3BS and 6BS, which explained 1.24, 0.54, and 0.75 phenotypic variance, respectively. Incorporation of the newly identified novel YR-resistance associated QTLs into hybridization wheat breeding program could be effective for marker-assisted selection of the improved and sustainable resistance.

Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL

YrFDC12 and PbcFDC, co-segregated in chromosome 4BL, and significantly interacted with Yr30/Pbc1 to enhance stripe rust resistance and to promote pseudo-black chaff development. Cultivars with durable resistance are the most popular means to control wheat stripe rust. Durable resistance can be achieved by stacking multiple adult plant resistance (APR) genes that individually have relatively small effect. Chinese wheat cultivars Ruihua 520 (RH520) and Fengdecun 12 (FDC12) confer partial APR to stripe rust across environments. One hundred and seventy recombinant inbred lines from the cross RH520 × FDC12 were used to determine the genetic basis of resistance and identify genomic regions associated with stripe rust resistance. Genotyping was carried out using 55 K SNP array, and eight quantitative trait loci (QTL) were detected on chromosome arms 2AL, 2DS, 3BS, 4BL, 5BL (2), and 7BL (2) by inclusive composite interval mapping. Only QYr.nwafu-3BS from RH520 and QYr.nwafu-4BL.2 (named YrFDC12 for convenience) from FDC12 were consistent across the four testing environments. QYr.nwafu-3BS is likely the pleiotropic resistance gene Sr2/Yr30. YrFDC12 was mapped in a 2.1-cM interval corresponding to 12 Mb and flanked by SNP markers AX-111121224 and AX-89518393. Lines harboring both Yr30 and YrFDC12 displayed higher resistance than the parents and expressed pseudo-black chaff (PBC) controlled by loci Pbc1 and PbcFDC12, which co-segregated with Yr30 and YrFDC12, respectively. Both marker-based and pedigree-based kinship analyses revealed that YrFDC12 was inherited from founder parent Zhou 8425B. Fifty-four other wheat cultivars shared the YrFDC12 haplotype. These results suggest an effective pyramiding strategy to acquire highly effective, durable stripe rust resistance in breeding.

A Stable Quantitative Trait Locus on Chromosome 5BL Combined with Yr18 Conferring High-Level Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Anyuehong

Chinese wheat landrace Anyuehong (AYH) has displayed high levels of stable adult plant resistance (APR) to stripe rust for >15 years. To identify quantitative trait loci (QTLs) for stripe rust resistance in AYH, a set of 110 recombinant inbred lines (RILs) was developed from a cross between AYH and susceptible cultivar Taichung 29. The parents and RILs were evaluated for final disease severity (FDS) in six field tests with a mixture of predominant Puccinia striiformis f. sp. tritici races at the adult plant stage and genotyped via the wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,143 SNP markers. Three QTLs, designated as QYr.AYH-1AS, QYr.AYH-5BL, and QYr.AYH-7DS, were mapped on chromosome 1AS, 5BL, and 7DS, respectively. RILs combining three QTLs showed significantly lower FDS compared with the lines in other combinations. Of them, QYr.AYH-5BL and QYr.AYH-7DS were stably detected in all environments, explaining 13.6 to 21.4% and 17.6 to 33.6% of phenotypic variation, respectively. Compared with previous studies, QYr.AYH-5BL may be a new QTL, whereas QYr.AYH-7DS may be Yr18. Haplotype analysis revealed that QYr.AYH-5BL is probably present in 6.2% of the 323 surveyed Chinese wheat landraces. The kompetitive allele specific PCR (KASP) markers for QYr.AYH-5BL were developed by the linked SNP markers to successfully confirm the effects of the QTL in a validation population derived from a residual heterozygous line and were further assessed in 38 Chinese wheat landraces and 92 cultivars. Our results indicated that QYr.AYH-5BL with linked KASP markers has potential value for marker-assisted selection to improve stripe rust resistance in breeding programs.

Genomic regions associated with stripe rust resistance against the Egyptian race revealed by genome-wide association study

BACKGROUND

Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs.

RESULTS

In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected.

CONCLUSION

the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.

Genome-wide association analysis of stripe rust resistance in modern Chinese wheat

BACKGROUND

Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm.

RESULTS

Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation.

CONCLUSION

The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.

Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS

Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.

Role of Fungicide Applications on the Integrated Management of Wheat Stripe Rust

First described in Europe in 1777, stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss (Pst) is one of the most important and destructive diseases of wheat worldwide. Until 2000, SR was mainly endemic to cooler regions, but since then, new aggressive strains have emerged, spread intercontinentally, and caused severe epidemics in warmer regions across the world. This has put SR as a disease that poses a threat to the world food security. At present, the preferred strategy for control of SR is the access to wheat cultivars with adequate levels of SR resistance. However, wheat breeding programs are not sufficiently advanced to cope with the recently emerged Pst strains. Under this scenario, foliar fungicide applications have become an important component of SR management, but information on the effects of fungicide applications on SR control and wheat cultivar yield response is scarce. This review seeks to provide an overview of the impact and role of fungicides on SR management. With focus on wheat management in the major wheat-growing regions of the world, the review addresses: (a) the efficacy of different fungicide active ingredients, optimal fungicide timing and number of applications in controlling SR, and (b) the impact of fungicide on wheat grain yield response. Inclusion of fungicides in an integrated crop management approach is discussed.

Molecular cytogenetic characterization of a novel wheat-Psathyrostachys huashanica Keng T3DS-5NsL•5NsS and T5DL-3DS•3DL dual translocation line with powdery mildew resistance

BACKGROUND

Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) carries many outstanding agronomic traits, therefore is a valuable resource for wheat genetic improvement. Wheat-P. huashanica translocation lines are important intermediate materials for wheat breeding and studying the functions of alien chromosomes. However, powdery mildew resistance in these translocation lines has not been reported previously.

RESULTS

This study developed a novel wheat-P. huashanica translocation line TR77 by selecting a F₇ progeny from the cross between heptaploid hybrid H8911 (2n = 7x = 49, AABBDDNs) and durum wheat line Trs-372. Chromosome karyotype of 2n = 42 = 21II was observed in both mitotic and meiotic stages of TR77. Genomic in situ hybridization analysis identified two translocated chromosomes that paired normally at meiosis stage in TR77. Molecular marker analysis showed that part of chromosome 5D was replaced by part of alien chromosome fragment 5Ns. It meant replacement made part 5DL and part 5NsL·5NsS existed in wheat background, and then translocation happened between these chromosomes and wheat 3D chromosome. Fluorescence in situ hybridization demonstrated that TR77 carries dual translocations: T3DS-5NsL·5NsS and T5DL-3DS·3DL. Analysis using a 15 K-wheat-SNP chip confirmed that SNP genotypes on the 5D chromosome of TR77 matched well with these of P. huashanica, but poorly with common wheat line 7182. The translocation was physically located between 202.3 and 213.1 Mb in 5D. TR77 showed longer spikes, more kernels per spike, and much better powdery mildew resistance than its wheat parents: common wheat line 7182 and durum wheat line Trs-372.

CONCLUSIONS

TR77 is a novel stable wheat-P. huashanica T3DS-5NsL·5NsS and T5DL-3DS·3DL dual translocation line and showed significant improved spike traits and resistance to powdery mildew compared to its parents, thus, it can be an useful germplasm for breeding disease resistance and studying the genetic mechanism of dual translocations.

Molecular dissection of Secale africanum chromosome 6Rafr in wheat enabled localization of genes for resistance to powdery mildew and stripe rust

BACKGROUND

Introgression of chromatin from Secale species into common wheat has for decades been a successful strategy for controlling the wheat diseases. The wild Secale species, Secale africanum Stapf., is a valuable source for resistance to foliar disease of wheat. A wheat-S. africanum chromosome 6R^afr substitution line displayed resistance to both powdery mildew and stripe rust at the adult-plant stage.

RESULTS

Wheat-S. africanum chromosome 6R^afr deletion and translocation lines were produced and identified by sequential non-denaturing fluorescence in situ hybridization (ND-FISH) using multiple Oligo-based probes. Different ND-FISH patterns were observed between S. cereale 6R and S. africanum 6R^afr. With reference to the physical map of the draft genome sequence of rye inbred line Lo7, a comprehensive PCR marker analysis indicated that insertions and deletions had occurred by random exchange between chromosomes 6R and 6R^afr. A survey of the wheat- S. africanum 6R^afr lines for disease resistance indicated that a powdery mildew resistance gene(s) was present on the long arm of 6R^afr at FL0.85-1.00, and that a stripe rust resistance gene(s) was located in the terminal region of 6R^afrS at FL0.95-1.00. The wheat-S. africanum 6R^afr introgression lines also displayed superior agronomic traits, indicating that the chromosome 6R^afr may have little linkage drag in the wheat background.

CONCLUSIONS

The combination of molecular and cytogenetic methods allowed to precisely identify the chromosome rearrangements in wheat- S. africanum 6R^afr substitution, deletion and translocation lines, and compare the structural difference between chromosomes 6R and 6R^afr. The wheat- S. africanum 6R^afr lines containing gene(s) for powdery mildew and stripe rust resistance could be used as novel germplasm for wheat breeding by chromosome engineering.

Evaluation of a global spring wheat panel for stripe rust: Resistance loci validation and novel resources identification

Stripe rust (incited by Puccinia striiformis f. sp. tritici) is airborne wheat (Triticum aestivum L.) disease with dynamic virulence evolution. Thus, anticipatory and continued screening in hotspot regions is crucial to identify new pathotypes and integrate new resistance resources to prevent potential disease epidemics. A global wheat panel consisting of 882 landraces and 912 improved accessions was evaluated in two locations in Egypt during 2016 and 2017. Five prevalent and aggressive pathotypes of stripe rust were used to inoculate the accessions during the two growing seasons and two locations under field conditions. The objectives were to evaluate the panel for stripe rust resistance at the adult plant stage, identify potentially novel QTLs associated with stripe rust resistance, and validate previously reported stripe rust QTLs under the Egyptian conditions. The results indicated that 42 landraces and 140 improved accessions were resistant to stripe rust. Moreover, 24 SNPs were associated with stripe rust resistance and were within 18 wheat functional genes. Four of these genes were involved in several plant defense mechanisms. The number of favorable alleles, based upon the associated SNPs, was significant and negatively correlated with stripe rust resistance score, i.e., as the number of resistances alleles increased the observed resistance increased. In conclusion, generating new stripe rust phenotypic information on this panel while using the publicly available molecular marker data, contributed to identifying potentially novel QTLs associated with stripe rust and validated 17 of the previously reported QTLs in one of the global hotspots for stripe rust.

Utilization of the Genomewide Wheat 55K SNP Array for Genetic Analysis of Stripe Rust Resistance in Common Wheat Line P9936

Breeding for resistance to stripe rust (caused by Puccinia striiformis f. tritici) is essential for reducing losses in yield and quality in wheat. To identify genes for use in breeding, a biparental population of 186 recombinant inbred lines (RILs) from a cross of the Chinese landrace Mingxian 169 and CIMMYT-derived line P9936 was evaluated in field nurseries either artificially or naturally inoculated in two crop seasons. Each of the RILs and parents was genotyped with the wheat 55K single-nucleotide polymorphism (SNP) 'Breeders' array and a genetic linkage map with 8,225 polymorphic SNP markers spanning 3,593.37 centimorgans was constructed. Two major quantitative trait loci (QTL) and two minor QTL were identified. The major QTL QYr.nwafu-3BS.2 and QYr.nwafu-7BL on chromosomes arms 3BS and 7BL were detected in all field locations and explained an average 20.4 and 38.9% of phenotypic variation stripe rust severity, respectively. QYr.nwafu-3BS.2 likely corresponds to the locus Yr30/Sr2 and QYr.nwafu-7BL may be a resistance allele identified previously in CIMMYT germplasm. The other minor QTL had limited individual effects but increased resistance when in combinations with other QTL. Markers linked to QYr.nwafu-7BL were converted to kompetitive allele-specific polymerase chain reaction markers and validated in a panel of wheat accessions. Wheat accessions carrying the same haplotype as P9936 at the identified SNP loci had lower average stripe rust severity than the average severity of all other haplotypes.

Characterization of Chromosomal Rearrangement in New Wheat—Thinopyrum intermedium Addition Lines Carrying Thinopyrum—Specific Grain Hardness Genes

The wild species, Thinopyrum intermedium. (Genome StStJSJSJJ), serves as a valuable germplasm resource providing novel genes for wheat improvement. In the current study, non-denaturing fluorescence in situ hybridization (ND-FISH) with multiple probes and comparative molecular markers were applied to characterize two wheat-Th. intermedium chromosome additions. Sequential ND-FISH with new labeled Th. intermedium specific oligo-probes were used to precisely determine the chromosomal constitution of Th. intermedium, wheat—Th. intermedium partial amphiploids and addition lines Hy36 and Hy37. The ND-FISH results showed that the added JS-St translocated chromosomes in Hy36 had minor Oligo-5S ribosomal DNA (rDNA) signals at the short arm, while a pair of J-St chromosomes in Hy37 had major Oligo-pTa71 and minor Oligo-5S rDNA signals. The 90K SNP array and PCR-based molecular markers that mapped on wheat linkage group 5 and 3 facilitated the identification of Thinopyrum chromosome introgressions in the addition lines, and confirmed that added chromosomes in Hy36 and Hy37 were 5JSS.3StS and 5JS.3StS, respectively. Complete coding sequences at the paralogous puroindoline-a (Pina) loci from Th. intermedium were cloned and localized on the short arm of chromosome 5JS of Hy36. Line Hy36 showed a reduction in the hardness index, which suggested that Th. intermedium-specific Pina gene sequences may be associated with the softness trait in wheat background. The molecular cytogenetic identification of novel wheat—Th. intermedium derivatives indicated that the frequent chromosome rearrangement occurred in the progenies of wheat-Thinopyrum hybridization. The new wheat-Thinopyrum derived lines may increase the genetic diversity for wheat breeding.

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

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