Wheat Background Research Articles

Development and characterisation of novel durum wheat-H. chilense 4Hch chromosome lines as a source for resistance to Septoria tritici blotch.

The use of wild species as a source of genetic variability is a valued tool in the framework of crop breeding. Hordeum chilense Roem. et Schult is a wild barley species that can be a useful genetic donor for sustainable wheat breeding which carries genes conferring resistance to some diseases or increasing grain quality, among others. Septoria tritici blotch (STB), caused by the Zymoseptoria tritici fungus, is one of the most important wheat diseases worldwide, affecting both bread and durum wheat and having a high economic impact. Resistance to STB has been previously described in H. chilense chromosome 4Hch. In this study, we have developed introgression lines for H. chilense chromosome 4Hch in durum wheat using interspecific crosses, advanced backcrosses, and consecutive selfing strategies. Alien H. chilense chromosome segments have been reduced in size by genetic crosses between H. chilense disomic substitution lines in durum wheat and durum wheat lines carrying the Ph1 deletion. Hordeum chilense genetic introgressions were identified in the wheat background through several plant generations by fluorescence in situ hybridisation (FISH) and simple sequence repeat (SSR) markers. An STB infection analysis has also been developed to assess STB resistance to a specific H. chilense chromosome region. The development of these H. chilense introgression lines with moderate to high resistance to STB represents an important advance in the framework of durum breeding and can be a valuable tool for plant breeders.

The addition of Psathyrostachys Huashanica Keng 6Ns large segment chromosomes has positive impact on stripe rust resistance and plant spikelet number of common wheat

BackgroundDeveloping novel germplasm by using wheat wild related species is an effective way to rebuild the wheat resource bank. The Psathyrostachys huashanica Keng (P. huashanica, 2n = 2x = 14, NsNs) is regarded as a superior species to improve wheat breeding because of its multi-resistance, early maturation and numerous tiller traits. Introducing genetic components of P. huashanica into the common wheat background is the most important step in achieving the effective use. Therefore, the cytogenetic characterization and influence of the introgressed P. huashanica large segment chromosomes in the wheat background is necessary to be explored.ResultsIn this study, we characterized a novel derived line, named D88-2a, a progeny of the former characterized wheat-P. huashanica partial amphiploid line H8911 (2n = 7x = 49, AABBDDNs). Cytological identification showed that the chromosomal composition of D88-2a was 2n = 44 = 22II, indicating the addition of exogenous chromosomes. Genomic in situ hybridization demonstrated that the supernumerary chromosomes were a pair of homologues from the P. huashanica and could be stably inherited in the common wheat background. Molecular markers and 15 K SNP array indicated that the additional chromosomes were derived from the sixth homoeologous group (i.e., 6Ns) of P. huashanica. Based on the distribution of the heterozygous single-nucleotide polymorphism sites and fluorescence in situ hybridization karyotype of each chromosome, this pair of additional chromosomes was confirmed as P. huashanica 6Ns large segment chromosomes, which contained the entire short arm and the proximal centromere portion of the long arm. In terms of the agronomic traits, the addition line D88-2a exhibited enhanced stripe rust resistance, improved spike characteristics and increased protein content than its wheat parent line 7182.ConclusionsThe new wheat germplasm D88-2a is a novel cytogenetically stable wheat-P. huashanica 6Ns large segment addition line, and the introgressed large segment alien chromosome has positive impact on plant spikelet number and stripe rust resistance. Thus, this germplasm can be used for genetic improvement of cultivated wheat and the study of functional alien chromosome segment.

The 4T and 7T introgressions from Amblyopyrum muticum and the 5Au introgression from Triticum urartu increases grain zinc and iron concentrations in Malawian wheat backgrounds.

Micronutrient deficiencies (MNDs) particularly zinc (Zn) and iron (Fe) remain widespread in sub-Saharan Africa (SSA) due to low dietary intake. Wheat is an important source of energy globally, although cultivated wheat is inherently low in grain micronutrient concentrations. Malawian wheat/Am. muticum and Malawian wheat/T. urartu BC1F3 introgression lines, developed by crossing three Malawian wheat varieties (Kenya nyati, Nduna and Kadzibonga) with DH-348 (wheat/Am. muticum) and DH-254 (wheat/T. urartu), were phenotyped for grain Zn and Fe, and associated agronomic traits in Zn-deficient soils, in Malawi. 98% (47) of the BC1F3 introgression lines showed higher Zn above the checks Paragon, Chinese Spring, Kadzibonga, Kenya Nyati and Nduna. 23% (11) of the introgression lines showed a combination of high yields and an increase in grain Zn by 16-30 mg kg -1 above Nduna and Kadzibonga, and 11-25 mg kg -1 above Kenya nyati, Paragon and Chinese Spring. Among the 23%, 64% (7) also showed 8-12 mg kg -1 improvement in grain Fe compared to Nduna and Kenya nyati. Grain Zn concentrations showed a significant positive correlation with grain Fe, whilst grain Zn and Fe negatively and significantly correlated with TKW and grain yield. This work will contribute to the efforts of increasing mineral nutrient density in wheat, specifically targeting countries in the SSA.

Introgression of chromosome 5P from Agropyron cristatum enhances grain weight in a wheat background.

A grain weight locus from Agropyron cristatum chromosome 5P increases grain weight in different wheat backgrounds and is localized to 5PL (bin 7-12). Thousand-grain weight is an important trait in wheat breeding, with a narrow genetic basis being the main factor limiting improvement. Agropyron cristatum, a wild relative of wheat, harbors many desirable genes for wheat improvement. Here, we found that the introduction of the 5P chromosome from A. cristatum into wheat significantly increased the thousand-grain weight by 2.55-7.10g, and grain length was the main contributor to grain weight. An increase in grain weight was demonstrated in two commercial wheat varieties, indicating that the grain weight locus was not affected by the wheat background. To identify the chromosome segment harboring the grain weight locus, three A. cristatum 5P deletion lines, two wheat-A. cristatum 5P translocation lines and genetic populations of these lines were used to evaluate agronomic traits. We found that the translocation lines harboring the long arm of A. cristatum chromosome 5P (5PL) exhibited high grain weight and grain length, and the genetic locus associated with increased grain weight was mapped to 5PL (bin 7-12). An increase in grain weight did not adversely affect other agronomic traits in translocation line 5PT2, which is a valuable germplasm resource. Overall, we identified a grain weight locus from chromosome 5PL and provided valuable germplasm for improving wheat grain weight.

The effects of Lr34 and Lr67 on Fusarium head blight resistance and deoxynivalenol accumulation in wheat

AbstractThe resistance gene Lr34 conditions durable disease resistance to many biotrophic wheat pathogens and has been incorporated into many wheat cultivars throughout the world. Lr67 is a similar adult plant resistance gene that also conditions resistance to multiple wheat diseases. Both genes significantly reduce disease severity and work in an additive manner with other rust resistance genes. To determine the effect of Lr34 and Lr67 on Fusarium head blight (FHB), two doubled haploid populations, segregating for each of these genes, were developed in the Thatcher wheat background by crossing near‐isogenic lines. Progeny from these populations were tested in five Fusarium graminearum‐inoculated disease nurseries and assessed for FHB symptoms, using a visual rating index (VRI), and deoxynivalenol (DON) accumulation. Both Lr34 and Lr67 significantly reduced visual symptoms of FHB and DON overall, though those effects were not significant in all environments. The overall reduction in the group of progeny with the resistant allele compared to the group with the susceptible allele for VRI was 9.4% for Lr34 and 6.8% for Lr67, while for DON it was 16.4% for Lr34 and 14.9% for Lr67. These genes represent important tools for improving resistance to FHB and many other diseases in wheat.

Cytokinin: An invisible warrior to spot blotch disease: A new proposal to way forward

Background of Abstract: Wheat is threatened by spot blotch disease causing considerable yield loss, with existing genotypes lacking resistance and the necessary nutrients. Cytokinins (CKs) are key phytohormones that not only regulate plant development but also play an important role during spot blotch disease and in the nutrient metabolic pathway of crop plants. Body of Abstract: Spot blotch disease, caused by Bipolaris sorokiniana syn. Helminthosporium sativum syn. Cochliobolus sativus is one of the dangerous diseases of wheat (Triticum aestivum L.) in Asia. Previous study identified the significant impact of zinc (Zn), sulfur(S), iron (Fe), nitrogen(N), potassium(P), and chlorine (Cl) fertilization on dipping the spot blotch acuteness in two wheat varieties Bhrikuti and Sonalika in Nepal. Cytokinins (CKs) are crucial phytohormones that not only control plant growth but also show a significant function during the nutrient metabolic pathway and in the stressed condition of the cereal crop plants. Lack of vital nutrients like Zn, S and Fe initiates severe injury of the body which is pleading the urgent requirement to improve the increase of these micronutrients in the cereal crop plant. Crop bio-fortification is one of the promising methods through which these nutrients could be boosted to a desirable volume. Cytokinin has a crucial role in controlling environmental stress and defense methods of plants. It is also discovered that it has an effect over Zn growth in cereal crop plants. Many studies identified that an augmentation of Zn, S and Fe in the seeds of the cereal crop plants ensuing the improvement of the root elongation which is also helpful for foraging nutrients to the innate ends of the soil and supports in the water absorbance in the drought area. Traveling micronutrients from the lithosphere through the root supports in the uptake of the micronutrients and transferring them to the cereal crop plants. Short Conclusion: This review is exploring a crop bio- fortification method containing CRISPR-Cas9 through breeding methods could be a significant job for spot blotch stress management and developing the desirable traits to boost the nutritional rate of wheat which would be beneficial for mankind.

Identification and transfer of resistance to Fusarium head blight from Elymus repens chromosome arm 7StL into wheat

Fusarium head blight (FHB), mainly caused by Fusarium graminearum (Fg), is one of the most devastating fungal diseases in wheat production worldwide. Elymus repens (2n=6x=42, StStStStHH) is a wild relative of wheat with many biotic and abiotic stress resistance traits. To transfer and apply the wild germplasm's resistance gene (s) for wheat breeding, we identified a new translocation line K140-7 with high resistance to FHB, developed from the derivative progenies of E. repens crossed with common wheat cultivars. Cytogenetic analyses based on genomic in situ hybridization (GISH), non-denaturing fluorescence in situ hybridization (ND-FISH), oligonucleotide-FISH painting (Oligo-FISH painting), and single-gene FISH revealed that K140-7 had 40 wheat chromosomes and two 7DS·7StL translocated chromosomes. Wheat 55K SNP array analysis confirmed that the translocated breakpoint (340.8~342.5 Mb) was close to the centromere region of chromosome 7D (336.3~341.7 Mb), supporting the 7DS·7StL translocation event. Based on the diploid reference St genome of Pseudoroegneria libanotica, we developed 21 simple sequence repeats (SSR) markers, specific for chromosome arm 7StL. Genotyping and phenotyping analysis of the 7DS·7StL translocation in different wheat backgrounds demonstrated that the chromosome arm 7StL confers FHB resistance and possesses the dominant FHB resistance locus (s) named QFhb.Er-7StL. We further transferred QFhb.Er-7StL into three different wheat cultivars, their second 7DS·7StL translocation line-generations showed improved agronomic traits, representing new germplasms that could be used in wheat FHB-resistant breeding programs.

GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1.

Precise regulation of flowering time is critical for cereal crops to synchronize reproductive development with optimum environmental conditions, thereby maximizing grain yield. The plant-specific gene GIGANTEA (GI) plays an important role in the control of flowering time, with additional functions on the circadian clock and plant stress responses. In this study, we show that GI loss-of-function mutants in a photoperiod-sensitive tetraploid wheat background exhibit significant delays in heading time under both long-day (LD) and short-day photoperiods, with stronger effects under LD. However, this interaction between GI and photoperiod is no longer observed in isogenic lines carrying either a photoperiod-insensitive allele in the PHOTOPERIOD1 (PPD1) gene or a loss-of-function allele in EARLY FLOWERING 3 (ELF3), a known repressor of PPD1. These results suggest that the normal circadian regulation of PPD1 is required for the differential effect of GI on heading time in different photoperiods. Using crosses between mutant or transgenic plants of GI and those of critical genes in the flowering regulation pathway, we show that GI accelerates wheat heading time by promoting FLOWERING LOCUS T1 (FT1) expression via interactions with ELF3, VERNALIZATION 2 (VRN2), CONSTANS (CO), and the age-dependent microRNA172-APETALA2 (AP2) pathway, at both transcriptional and protein levels. Our study reveals conserved GI mechanisms between wheat and Arabidopsis but also identifies specific interactions of GI with the distinctive photoperiod and vernalization pathways of the temperate grasses. These results provide valuable knowledge for modulating wheat heading time and engineering new varieties better adapted to a changing environment.

Cytogenetic and agro-morphological study of Wheat addition lines possessing Thinopyrum elongatum and Aegilops triuncialis chromosomes

Novel genetic variation can be induced by introgression of alien chromosomes in wheat for which wheat-alien addition lines carrying 45 chromosomes are instrumental. In the course of developing wheat addition lines with 45 chromosomes, two different parental lines Wheat-Thinopyrum elongatum disomic addition lines (Wheat-Th. DALs; 2n=44)) and Wheat-Th. elongatum- Aegilops triuncialis 3CSAT double monosomic addition lines (Wheat-Th. DMALs; 2n=44) need to cross. The present study mainly focuses on the effects of chromosomal additions in wheat background by comparing the morphological and agronomic traits of the parental lines. Both the parental lines were reconfirmed 2n=44 cytologically by using squash technique. Pollen fertility was highest (75%) in Wheat-3CSAT-6E DMAL and lowest (44.73%) in Wheat-5E DAL, whereas, spike length was longest (8.71 cm) in Wheat-3CSAT-3E DMAL and shortest (5.92 cm) in Wheat-1E DAL. Plant height was highest (97.6 cm) in Wheat-3CSAT-5E DMAL and lowest (55.33 cm) in Wheat-7E DAL. The plant height of DMALs always exceeded that of DALs. Furthermore, seed set was highest (31 seeds per spike) in Wheat-7E DALs and lowest (13 seeds per spike) in addition lines disomic for 4E chromosomes. The effect of different alien chromosomes in wheat is discussed in this paper.

Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy.

Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.

A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops.

Breeding new and sustainable crop cultivars of high yields and desirable traits has been a major challenge for ensuring food security for the growing global human population. For polyploid crops such as wheat, introducing genetic variation from wild relatives of its subgenomes is a key strategy to improve the quality of their breeding pools. Over the past decades, considerable progress has been made in speed breeding, genome sequencing, high-throughput phenotyping and genomics-assisted breeding, which now allows us to realize whole-genome introgression from wild relatives to modern crops. Here, we present a standardized protocol to rapidly introgress the entire genome of Aegilops tauschii, the progenitor of the D subgenome of bread wheat, into elite wheat backgrounds. This protocol integrates multiple modern high-throughput technologies and includes three major phases: development of synthetic octaploid wheat, generation of hexaploid A. tauschii-wheat introgression lines (A-WIs) and homozygosis of the generated A-WIs. Our approach readily generates stable introgression lines in 2 y, thus greatly accelerating the generation of A-WIs and the introduction of desirable genes from A. tauschii to wheat cultivars. These A-WIs are valuable for wheat-breeding programs and functional gene discovery. The current protocol can be easily modified and used for introgressing the genomes of wild relatives to other polyploid crops.

MCSNet+: Enhanced Convolutional Neural Network for Detection and Classification of Tribolium and Sitophilus Sibling Species in Actual Wheat Storage Environments.

Insect pests like Tribolium and Sitophilus siblings are major threats to grain storage and processing, causing quality and quantity losses that endanger food security. These closely related species, having very similar morphological and biological characteristics, often exhibit variations in biology and pesticide resistance, complicating control efforts. Accurate pest species identification is essential for effective control, but workplace safety in the grain bin associated with grain deterioration, clumping, fumigator hazards, and air quality create challenges. Therefore, there is a pressing need for an online automated detection system. In this work, we enriched the stored-grain pest sibling image dataset, which includes 25,032 annotated Tribolium samples of two species and five geographical strains from real warehouse and another 1774 from the lab. As previously demonstrated on the Sitophilus family, Convolutional Neural Networks demonstrate distinct advantages over other model architectures in detecting Tribolium. Our CNN model, MCSNet+, integrates Soft-NMS for better recall in dense object detection, a Position-Sensitive Prediction Model to handle translation issues, and anchor parameter fine-tuning for improved matching and speed. This approach significantly enhances mean Average Precision (mAP) for Sitophilus and Tribolium, reaching a minimum of 92.67 ± 1.74% and 94.27 ± 1.02%, respectively. Moreover, MCSNet+ exhibits significant improvements in prediction speed, advancing from 0.055 s/img to 0.133 s/img, and elevates the recognition rates of moving insect sibling species in real wheat storage and visible light, rising from 2.32% to 2.53%. The detection performance of the model on laboratory-captured images surpasses that of real storage facilities, with better results for Tribolium compared to Sitophilus. Although inter-strain variances are less pronounced, the model achieves acceptable detection results across different Tribolium geographical strains, with a minimum recognition rate of 82.64 ± 1.27%. In real-time monitoring videos of grain storage facilities with wheat backgrounds, the enhanced deep learning model based on Convolutional Neural Networks successfully detects and identifies closely related stored-grain pest images. This achievement provides a viable solution for establishing an online pest management system in real storage facilities.

Development and molecular cytogenetic identification of a new wheat-rye 6RL ditelosomic addition and 1R (1B) substitution line with powdery mildew resistance

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious disease that critically threatens the yield and quality of wheat (Triticum aestivum L.). Using effective powdery mildew resistance genes is considered to be the optimal choice for controlling this disease. Against the background of high homogeneity among the modern commercial cultivars that are mainly derived from conventional interbreeding, the resistance genes from wheat relatives have especially prominent advantages. Octoploid triticale, produced by common wheat and rye (Secale cereale L.) through distant hybridization, is a new synthetic species and valuable gene donor for wheat improvement. In this study, we developed a wheat-rye line YT5 through the hybridization of octoploid triticale and two wheat lines. YT5 was confirmed to be a 6RL ditelosomic addition and 1R (1B) substitution line using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), multicolor GISH (mc-GISH) and molecular marker analysis. Genetic analysis showed that the powdery mildew resistance in YT5 was derived from the rye chromosome arm 6RL. After inoculation with different Bgt isolates at the seedling stage, YT5 had compound reaction patterns with both obvious spores and hypersensitivity and gradually became highly resistant until the adult-plant stage, thus showing a resistance response significantly different from the reported Pm genes from rye chromosome 6RL. Meanwhile, YT5 showed promising agronomic performance and hence is expected to be an elite resistance donor for wheat improvement. To promote the transfer of the chromosome arm 6RL of YT5 in marker-assisted selection breeding, we selected and verified two 6RL-specific kompetitive allele-specific PCR markers that can be applied to efficiently detect this chromosome arm in different wheat backgrounds.

Pyramiding Fusarium head blight resistance QTL from T. aestivum, T. dicoccum and T. dicoccoides in durum wheat

Key messageFHB resistance of durum wheat was improved by introgression of Fhb1 and resistance genes from emmer wheat and by selection against adverse alleles of elite durum wheat.Durum wheat is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is impeded by the low genetic variation within the elite gene pool. To extend the genetic basis for FHB resistance in durum wheat, we analyzed 603 durum wheat lines from crosses of elite durum wheat with resistance donors carrying resistance alleles derived from Triticum aestivum, T. dicoccum and T. dicoccoides. The lines were phenotyped for FHB resistance, anthesis date, and plant height in artificially inoculated disease nurseries over 5 years. A broad variation was found for all traits, while anthesis date and plant height strongly influenced FHB severities. To correct for spurious associations, we adjusted FHB scorings for temperature fluctuations during the anthesis period and included plant height as a covariate in the analysis. This resulted in the detection of seven quantitative trait loci (QTL) affecting FHB severities. The hexaploid wheat-derived Fhb1 QTL was most significant on reducing FHB severities, highlighting its successful introgression into several durum wheat backgrounds. For two QTL on chromosomes 1B and 2B, the resistance alleles originated from the T. dicoccum line Td161 and T. dicoccoides accessions Mt. Hermon#22 and Mt. Gerizim#36, respectively. The other four QTL featured unfavorable alleles derived from elite durum wheat that increased FHB severities, with a particularly negative effect on chromosome 6A that simultaneously affected plant height and anthesis date. Therefore, in addition to pyramiding resistance genes, selecting against adverse alleles present in elite durum wheat could be a promising avenue in breeding FHB-resistant durum wheat.

Chromosome-specific painting in Thinopyrum species using bulked oligonucleotides.

Chromosome-specific painting probes were developed to identify the individual chromosomes from 1 to 7E in Thinopyrum species and detect alien genetic material of the E genome in a wheat background. The E genome of Thinopyrum is closely related to the ABD genome of wheat (Triticum aestivum L.) and harbors genes conferring beneficial traits to wheat, including high yield, disease resistance, and unique end-use quality. Species of Thinopyrum vary from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70), and chromosome structural variation and differentiation have arisen during polyploidization. To investigate the variation and evolution of the E genome, we developed a complete set of E genome-specific painting probes for identification of the individual chromosomes 1E to 7E based on the genome sequences of Th. elongatum (Host) D. R. Dewey and wheat. By using these new probes in oligonucleotide-based chromosome painting, we showed that Th. bessarabicum (PI 531711, EbEb) has a close genetic relationship with diploid Th. elongatum (EeEe), with five chromosomes (1E, 2E, 3E, 6E, and 7E) maintaining complete synteny in the two species except for a reciprocal translocation between 4 and 5Eb. All 14 pairs of chromosomes of tetraploid Th. elongatum have maintained complete synteny with those of diploid Th. elongatum (Thy14), but the two sets of E genomes have diverged. This study also demonstrated that the E genome-specific painting probes are useful for rapid and effective detection of the alien genetic material of E genome in wheat-Thinopyrum derived lines.

Introgression of sharp eyespot resistance from Dasypyrum villosum chromosome 2VL into bread wheat

Wheat sharp eyespot, a stem disease caused by the soilborne fungus Rhizoctonia cerealis van der Hoeven, has become a threat to wheat production worldwide. Exploiting resistance resources from wild relatives of wheat is a promising strategy for controlling this disease. In this study, a new wheat–Dasypyrum villosum T2DS·2V#4L translocation line in the background of Chinese Spring (CS) showed stable resistance to R. cerealis. Introgression of the T2DS·2V#4L chromosome into wheat cultivar Aikang 58 by backcrossing produced a marked increase in sharp eyespot resistance in NIL-T2DS·2V#4L in comparison with NIL-T2DS·2DL, and no detrimental effects of 2V#4L on agronomic traits were observed in the BC2F2, BC2F2:3, and BC2F2:4 generations. Flow-sorted sequencing of 2V#4L yielded 384.3 Mb of assembled sequence, and 8836 genes were predicted of which 6154 had orthologs in at least one of the 2AL, 2BL, and 2DL arms of CS, whereas 1549 genes were unique to 2V#4L. About 100,000 SNPs were detected in genes of 2V#4L and 2DL in 10 sequenced bread wheat cultivars. A Kompetitive Allele Specific Polymerase chain reaction and 30 conserved ortholog sequence markers were developed to trace the 2V#4L chromatin in wheat backgrounds. T2DS·2V#4L compensating translocation lines represent novel germplasm with sharp eyespot resistance and the markers will allow rapid detection in breeding programs.

RNA-seq analysis revealed considerable genetic diversity and enabled the development of specific KASP markers for Psathyrostachys huashanica.

Psathyrostachys huashanica, which grows exclusively in Huashan, China, is an important wild relative of common wheat that has many desirable traits relevant for wheat breeding. However, the poorly characterized interspecific phylogeny and genomic variations and the relative lack of species-specific molecular markers have limited the utility of P. huashanica as a genetic resource for enhancing wheat germplasm. In this study, we sequenced the P. huashanica transcriptome, resulting in 50,337,570 clean reads that were assembled into 65,617 unigenes, of which 38,428 (58.56%) matched at least one sequence in public databases. The phylogenetic analysis of P. huashanica, Triticeae species, and Poaceae species was conducted using 68 putative orthologous gene clusters. The data revealed the distant evolutionary relationship between P. huashanica and common wheat as well as the substantial diversity between the P. huashanica genome and the wheat D genome. By comparing the transcriptomes of P. huashanica and Chinese Spring, 750,759 candidate SNPs between P. huashanica Ns genes and their common wheat orthologs were identified. Among the 90 SNPs in the exon regions with different functional annotations, 58 (64.4%) were validated as Ns genome-specific SNPs in the common wheat background by KASP genotyping assays. Marker validation analyses indicated that six specific markers can discriminate between P. huashanica and the other wheat-related species. In addition, five markers are unique to P. huashanica, P. juncea, and Leymus species, which carry the Ns genome. The Ns genome-specific markers in a wheat background were also validated regarding their specificity and stability for detecting P. huashanica chromosomes in four wheat-P. huashanica addition lines. Four and eight SNP markers were detected in wheat-P. huashanica 2Ns and 7Ns addition lines, respectively, and one marker was specific to both wheat-P. huashanica 3Ns, 4Ns, and 7Ns addition lines. These markers developed using transcriptome data may be used to elucidate the genetic relationships among Psathyrostachys, Leymus, and other closely-related species. They may also facilitate precise introgressions and the high-throughput monitoring of P. huashanica exogenous chromosomes or segments in future crop breeding programs.

Rapid identification of Psathyrostachys huashanica Keng chromosomes in wheat background based on ND-FISH and SNP array methods

Psathyrostachys huashanica Keng (2n=2x=14, NsNs) is regarded as a valuable wild relative species for common wheat cultivar improvement because of its abundant beneficial agronomic traits. However, although the development of many wheat–P. huashanica-derived lines provides a germplasm base for the transfer of excellent traits, the lag in the identification of P. huashanica chromosomes in the wheat background has limited the study of these lines. In this study, three novel nondenaturing fluorescence in situ hybridization (ND-FISH)-positive oligo probes were developed. Among them, HS-TZ3 and HS-TZ4 could specifically hybridize with P. huashanica chromosomes, mainly in the telomere area, and HS-CHTZ5 could hybridize with the chromosomal centromere area. We sequentially constructed a P. huashanica FISH karyotype and idiogram that helped identify the homologous groups of introduced P. huashanica chromosomes. In detail, 1Ns and 2Ns had opposite signals on the short and long arms, 3Ns, 4Ns, and 7Ns had superposed two-color signals, 5Ns and 6Ns had fluorescent signals only on their short arms, and 7Ns had signals on the intercalary of the long arm. In addition, we evaluated different ways to identify alien introgression lines by using low-density single nucleotide polymorphism (SNP) arrays and recommended the SNP homozygosity rate in each chromosome as a statistical pattern. The 15K SNP array is widely applicable for addition, substitution, and translocation lines, and the 40K SNP array is the most accurate for recognizing transposed intervals between wheat and alien chromosomes. Our research provided convenient methods to distinguish the homologous group of P. huashanica chromosomes in a common wheat background based on ND-FISH and SNP arrays, which is of great significance for efficiently identifying wheat–P. huashanica-derived lines and the further application of Ns chromosomes.

Identification of a Wheat Powdery Mildew Dominant Resistance Gene in the Pm5 Locus for High-Throughput Marker-Assisted Selection.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), poses a severe threat to wheat yield and quality worldwide. Rapid identification and the accurate transference of effective resistance genes are important to the development of resistant cultivars and the sustainable control of this disease. In the present study, the wheat line AL11 exhibited high levels of resistance to powdery mildew at both the seedling and adult plant stages. Genetic analysis of the AL11 × 'Shixin 733' mapping population revealed that its resistance was controlled by a single dominant gene, tentatively designated PmAL11. Using bulked segregant RNA-Seq and molecular marker analysis, PmAL11 was mapped to the Pm5 locus on chromosome 7B where it cosegregated with the functional marker Pm5e-KASP. Sequence alignment analysis revealed that the Pm5e-homologous sequence in AL11 was identical to the reported recessive gene Pm5e in wheat landrace 'Fuzhuang 30'. It appears that PmAL11 was most probably Pm5e, but it was mediated by a dominant inheritance pattern, so it should provide a valuable resistance resource for both genetic study and wheat breeding. To efficiently use and trace PmAL11 in breeding, a new kompetitive allele-specific PCR marker AL11-K2488 that cosegregated with this gene was developed and confirmed to be applicable in the different wheat backgrounds, thus promoting its use in the marker-assisted selection of PmAL11.

Evaluation of wheat stem sawfly‐resistant solid stem Qss.msub‐3BL alleles in hard red winter wheat

AbstractHost plant resistance provided by solid stems has been the most effective means for mitigating wheat stem sawfly (WSS) (Cephus cinctus Norton) damage in spring and winter wheat (Triticum aestivum L.). The solid stem trait originates from the spring wheat cultivar “Rescue” and is associated with a quantitative trait locus allele Qss.msub‐3BL.b that explains the majority of the variation for stem solidness. Recently, a new Qss.msub‐3BL solid stem allele, designated Qss.msub‐3BL.c, was identified in the spring wheat cultivar “Conan”. It produces a solid stem phenotype early in plant development but dissipates during plant growth. The Qss.msub‐3BL.c allele provides effective WSS resistance in spring wheat but has not been tested in winter wheat. To examine if the Qss.msub‐3BL.c allele provides adequate WSS resistance in winter wheat, near‐isogenic lines (NILs) were developed using marker‐assisted backcrossing. This enabled comparisons between the hollow stem Qss.msub‐3BL.a, solid stem Qss.msub‐3BL.b and solid stem Qss.msub‐3BL.c alleles for stem solidness, WSS resistance, and agronomic traits in Montana growing environments. Compared to the hollow stem allele, the NILs with the Qss.msub‐3BL.c allele increased stem solidness and reduced WSS stem cutting. However, the Qss.msub‐3BL.c allele resulted in lower solid stem scores and greater WSS stem cutting compared to the Qss.msub‐3BL.b allele. Overall, these findings indicate that the Qss.msub‐3BL.c allele failed to provide sufficient WSS resistance in the winter wheat backgrounds tested in this study.