Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Am. muticum introgression lines

Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is limited by poor genomic resolution and limited understanding of the genomic impact of introgression breeding. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that introgressed genes tend to be downregulated, shifting the expression balance of triads towards suppression of the introgressed region, with no discernible compensation in the expression of the homoeologous copies. This analysis explores the genomic impact of introgression breeding and provides an affordable way for breeders to better characterise introgression lines and more effectively deploy wild relative variation.

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Exploiting the ZIP4 homologue within the wheat Ph1 locus has identified two lines exhibiting homoeologous crossover in wheat-wild relative hybrids

10.1101/142596 ◽

2017 ◽

Author(s):

María-Dolores Rey ◽

Azahara C Martín ◽

Janet Higgins ◽

David Swarbreck ◽

Cristobal Uauy ◽

...

Keyword(s):

Hexaploid Wheat ◽

Wild Relatives ◽

Deletion Mutants ◽

Wild Relative ◽

Homologous Chromosomes ◽

Chromosome Translocations ◽

Ph1 Locus ◽

Mutant Lines ◽

Chromosome Segments ◽

Selection Of

AbstractDespite possessing related ancestral genomes, hexaploid wheat behaves as a diploid during meiosis. The wheat Ph1 locus promotes accurate synapsis and crossover of homologous chromosomes. Interspecific hybrids between wheat and wild relatives are exploited by breeders to introgress important traits from wild relatives into wheat, although in hybrids between hexaploid wheat and wild relatives, which possess only homoeologues, crossovers do not take place during meiosis at metaphase I. However, in hybrids between Ph1 deletion mutants and wild relatives, crossovers do take place. A single Ph1 deletion (ph1b) mutant has been exploited for the last 40 years for this activity. We show here that selection of chemical induced mutant lines possessing mutations in TaZIP4-B2 exhibit high levels of homoeologous crossovers when crossed with a wild relative. Exploitation of Tazip4-B2 mutants rather than mutants with whole Ph1 locus deletions may improve introgression of wild relative chromosome segments into wheat. Such mutant lines may be more stable over multiple generations, as multivalents causing accumulation of chromosome translocations are less frequent.Key messageExploiting the ZIP4 homologue within the wheat Ph1 locus has identified two wheat mutants through a non-GM route, which can be exploited as an alternative to the Chinese Spring ph1b mutant in wheat introgression strategies.

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Evaluation of a Novel Molecular Marker Associated with the Tan Spot Disease Response in Wheat

Agriculture ◽

10.3390/agriculture11060513 ◽

2021 ◽

Vol 11 (6) ◽

pp. 513

Author(s):

Pao Theen See ◽

Caroline S. Moffat

Keyword(s):

Molecular Marker ◽

Hexaploid Wheat ◽

Wheat Breeding ◽

Tan Spot ◽

Growth Stages ◽

Disease Score ◽

Wheat Varieties ◽

Disease Response ◽

Spot Disease ◽

Tan Spot Disease

After nearly 40 years of DNA molecular marker development in plant breeding, the wheat research community has amassed an extensive collection of molecular markers which have been widely and successfully used for selection of agronomic, physiological and disease resistance traits in wheat breeding programs. Tan spot is a major fungal disease of wheat and a significant global economic challenge and is caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr). Here, the potential for using a PCR-based marker (Ta1AS3422) present on the short arm of wheat chromosome 1A, was evaluated for effectiveness in distinguishing tan spot disease susceptibility. The marker was initially screened against 40 commercial Australian hexaploid wheat varieties, and those that amplified the marker had an overall lower disease score (2.8 ± 0.7 for seedlings and 2.4 ± 0.4 for plants at the tillering stage), compared to those lacking the marker which exhibited a higher disease score (3.6 ± 0.8 for both growth stages). The potential of Ta1AS3422 as a marker for the tan spot disease response was further assessed against a panel of 100 commercial Australian hexaploid wheat varieties. A significant association was observed between marker absence/presence and tan spot disease rating (Pearson’s chi-squared test, χ2 (6) = 20.53, p = 0.002), with absence of Ta1AS3422 associated with susceptibility. This simple and cost-effective PCR-based marker may be useful for varietal improvement against tan spot, although further work is required to validate its effectiveness.

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Stem Rust Resistance in A-Genome Diploid Relatives of Wheat

Plant Disease ◽

10.1094/pdis-04-10-0260 ◽

2011 ◽

Vol 95 (8) ◽

pp. 941-944 ◽

Cited By ~ 39

Author(s):

M. N. Rouse ◽

Y. Jin

Keyword(s):

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Infection Type ◽

Genetic Resistance ◽

Wheat Breeding ◽

Stem Rust Resistance ◽

Wheat Stem Rust ◽

A Genome ◽

Stem Rust Resistance Genes

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, has been effectively controlled through the use of genetic resistance. P. graminis f. sp. tritici race TTKSK (Ug99) possesses virulence to many resistance genes that have been used in wheat breeding worldwide. One strategy to aid breeders in developing resistant cultivars is to utilize resistance genes transferred from wild relatives to wheat. Stem rust resistance genes have previously been introgressed from Triticum monococcum to wheat. In order to identify additional resistance genes, we screened 1,061 accessions of T. monococcum and 205 accessions of T. urartu against race TTKSK and four additional P. graminis f. sp. tritici races: TTTTF, TRTTF, QFCSC, and MCCFC. A high frequency of the accessions (78.7% of T. monococcum and 93.0% of T. urartu) were resistant to P. graminis f. sp. tritici race TTKSK, with infection types ranging from 0 to 2+. Among these resistant accessions, 55 T. monococcum accessions (6.4% of the total) were also resistant to the other four races. Associations of resistance in T. monococcum germplasm to different races indicated the presence of genes conferring resistance to multiple races. Comparing the observed infection type patterns to the expected patterns of known genes indicated that previously uncharacterized genes for resistance to race TTKSK exist in both T. monococcum and T. urartu.

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Identification of a Novel Genomic Region Associated With Resistance to Fusarium Head Blight in Chinese Winter Wheat

10.21203/rs.3.rs-149839/v1 ◽

2021 ◽

Author(s):

Yunzhe Zhao ◽

Xinying Zhao ◽

Mengqi Ji ◽

Wenqi Fang ◽

Hong Guo ◽

...

Keyword(s):

Winter Wheat ◽

Fusarium Head Blight ◽

Genome Wide Association Study ◽

Wheat Breeding ◽

Scab Resistance ◽

Yield Reduction ◽

Transferase Activity ◽

Head Blight ◽

A Genome ◽

Fhb Resistance

Abstract Background: Fusarium head blight (FHB) is a disease affecting wheat spikes caused by Fusarium species, which leads to cases of severe yield reduction and seed contamination. Therefore, identifying resistance genes from various sources is always of importance to wheat breeders. In this study, a genome-wide association study (GWAS) focusing on FHB using a high-density genetic map constructed with 90K single nucleotide polymorphism (SNP) arrays in a panel of 205 elite winter wheat accessions, was conducted in 3 environments. Results: Sixty-six significant marker–trait associations (MTAs) were identified (P<0.001) on fifteen chromosomes explaining 5.4–11.2% of the phenotypic variation therein. Some important new genomic regions involving FHB resistance were found on chromosomes 2A, 3B, 5B, 6A, and 7B. On chromosome 7B, 6 MTAs at 92 genetic positions were found in 2 environments. Moreover, there were 11 MTAs consistently associated with diseased spikelet rate and diseased rachis rate as pleiotropic effect loci. Eight new candidate genes of FHB resistance were predicated in wheat. Of which, three genes: TraesCS5D01G006700, TraesCS6A02G013600, and TraesCS7B02G370700 on chromosome 5DS, 6AS, and 7BL, respectively, were important in defending against FHB by regulating chitinase activity, calcium ion binding, intramolecular transferase activity, and UDP-glycosyltransferase activity in wheat. In addition, a total of six excellent alleles associated with wheat scab resistance were discovered. Conclusion: These results provide important genes/loci for enhancing FHB resistance in wheat breeding populations by marker-assisted selection.

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Applicability of chromosome-specific SSR wheat markers for the introgression of Triticum urartu in durum wheat breeding programmes

Plant Genetic Resources ◽

10.1017/s147926211100061x ◽

2011 ◽

Vol 9 (3) ◽

pp. 439-444 ◽

Cited By ~ 8

Author(s):

C. Rodríguez-Suárez ◽

M. C. Ramírez ◽

A. Martín ◽

S. G. Atienza

Keyword(s):

Durum Wheat ◽

Triticum Turgidum ◽

Crop Improvement ◽

Wheat Chromosome ◽

Wheat Breeding ◽

Triticum Urartu ◽

Founder Line ◽

A Genome ◽

Breeding Programmes ◽

Novel Alleles

Triticum urartu, the A-genome donor of tetraploid and hexaploid wheats, is a potential source of novel alleles for crop improvement. A fertile amphiploid between T. urartu (2n = 2x = 14; AuAu) and durum wheat cv ‘Yavaros’ (Triticum turgidum ssp. durum; 2n = 4x = 28, AABB) was obtained as a first step to making the genetic variability of the wild ancestor available to durum wheat breeding. The amphiploid was backcrossed with ‘Yavaros’ and the offspring from this cross was selfed. A plant from this progeny (founder line) with 28 chromosomes and active x and y subunits of the Glu-A1 locus of T. urartu was selfed, which resulted in the obtaining of 98 pre-introgression lines (pre-ILs). In this work, a set of 78 wheat chromosome-specific microsatellite markers (simple sequence repeats, SSR), uniformly distributed over the A genome, was used for marker-assisted selection of T. urartu in a durum wheat background. A total of 57 SSRs allowed a clear discrimination between T. urartu and ‘Yavaros’. This set of markers was further used for characterizing the pre-ILs, identifying and defining the T. urartu introgressed regions. The applicability of these markers is discussed.

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Genome-wide Survey of the Dehydrin Genes in Bread Wheat (Triticum Aestivum L.) and its Relatives: Identification, Evolution and Expression Profiling Under Various Abiotic Stresses

10.21203/rs.3.rs-709007/v1 ◽

2021 ◽

Author(s):

Yongchao Hao ◽

Ming Hao ◽

Hongwei Wang

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Abiotic Stresses ◽

Aegilops Tauschii ◽

Protein Structures ◽

Interaction Network ◽

Wheat Breeding ◽

Functional Study ◽

Genome Wide ◽

A Genome

Abstract Background: Bread wheat (Triticum aestivum) is an important and fundamental cereal worldwide. With increasingly severe environmental stress, it is very important to mine stress-resistant genes for wheat breeding. Dehydrin (DHN) genes are primary candidates because they are involved in the response to many stressors. Results: Here, a genome-wide analysis of this gene family was performed on the genomes of wheat and its three relatives. A total of 55 DHN genes in Triticum aestivum, 31 in Triticum dicoccoides, 15 in Triticum urartu, and 16 in Aegilops tauschii were identified. The phylogenetic, synteny, sequence and protein structure analyses showed that the DHN genes were divided into five groups, Genes in the same group share similar conserved motifs, protein structures, and potential functions. The tandem TaDHN genes responded strongly to drought, cold and high salinity stresses, while the non-tandem genes were responded weakly to all stress conditions. Further, multiple DHN proteins cooperation maybe an important way to prevent plants from abiotic stress according to the interaction network analysis. Conclusions: Conserved, duplicated DHN genes may have played an important role in the adaptation of wheat to a variety of conditions, hence, contributing to the distribution of bread wheat as a global staple food. This research illuminates the contributions of DHN genes to abiotic stresses in Triticeae species and offers helpful information for further functional study of DHN genes in these crops.

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A genome-wide survey of DNA methylation in hexaploid wheat

Genome Biology ◽

10.1186/s13059-015-0838-3 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 44

Author(s):

Laura-Jayne Gardiner ◽

Mark Quinton-Tulloch ◽

Lisa Olohan ◽

Jonathan Price ◽

Neil Hall ◽

...

Keyword(s):

Dna Methylation ◽

Hexaploid Wheat ◽

Genome Wide ◽

A Genome ◽

Genome Wide Survey

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Hybrid necrosis as a problem in handling hexaploid × tetraploid wheat crosses

The Journal of Agricultural Science ◽

10.1017/s0021859600028987 ◽

1980 ◽

Vol 94 (2) ◽

pp. 377-382 ◽

Cited By ~ 6

Author(s):

R. S. Gregory

Keyword(s):

Hexaploid Wheat ◽

Tetraploid Wheat ◽

Wheat Breeding ◽

Small Scale ◽

Hybrid Necrosis ◽

Agronomic Characters ◽

Wheat Varieties ◽

Hybrid Plants ◽

Plant Breeding Institute ◽

Selection For

SummaryA tetraploid wheat breeding programme was initiated at the Plant Breeding Institute in 1970. Hexaploid × tetraploid wheat crosses were expected to contribute to the improvement of the tetraploid wheats but severe hybrid necrosis caused the death of the pentaploid Fxhybrid plants in most crosses. The genotypes of tetraploid wheat selections derived from crosses involving Rampton Rivet, a non-carrier of Neu were determined by test crossing to hexaploid wheat varieties which were known to carry the Neim allele. Similarly, hexaploid wheat selections which did not carry Ne2 were identified from crosses involving Maris Ranger by test crossing to durum selections which carried the Nef allele. By the careful choice of one parent, hexaploid x tetraploid wheat crosses were then made which avoided the hybrid necrosis problem. Segregation of the Ne% gene was as expected but selection for agronomic characters appeared to favour the retention of the dominant allele of the Ne1gene. Nevertheless, test crossing on a relatively small scale still identified many non-carriers.

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Fine Mapping of the Wheat Leaf Rust Resistance Gene Lr42

International Journal of Molecular Sciences ◽

10.3390/ijms20102445 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2445 ◽

Cited By ~ 8

Author(s):

Harsimardeep S. Gill ◽

Chunxin Li ◽

Jagdeep S. Sidhu ◽

Wenxuan Liu ◽

Duane Wilson ◽

...

Keyword(s):

Leaf Rust ◽

Hexaploid Wheat ◽

Rust Resistance ◽

Reference Genome ◽

Aegilops Tauschii ◽

Leaf Rust Resistance ◽

Wheat Breeding ◽

Chromosome 1 ◽

Adult Plant ◽

Leaf Rust Resistance Gene

Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both recessive and dominant in hexaploid wheat; however, in diploid Aegilops tauschii (TA2450), we found Lr42 to be dominant by studying segregation in two independent F2 and their F2:3 populations. We further fine-mapped Lr42 in hexaploid wheat using a KS93U50/Morocco F5 recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers TC387992 and WMC432. The 3.7 cM Lr42 region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the Ae. tauschii reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in Ae. tauschii, respectively, and these are the likely candidates for Lr42. Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers (SNP113325 and TC387992) flanking Lr42 to facilitate marker-assisted selection for rust resistance in wheat breeding programs.

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Genomic Selection—Considerations for Successful Implementation in Wheat Breeding Programs

Agronomy ◽

10.3390/agronomy9090479 ◽

2019 ◽

Vol 9 (9) ◽

pp. 479 ◽

Cited By ~ 7

Author(s):

Larkin ◽

Lozada ◽

Mason

Keyword(s):

Genomic Selection ◽

Wheat Yield ◽

Wheat Breeding ◽

Breeding Value ◽

Selection Marker ◽

Successful Implementation ◽

Head Blight ◽

Phenotypic Data ◽

Breeding Programs ◽

A Genome

In order to meet the goal of doubling wheat yield by 2050, breeders must work to improve breeding program efficiency while also implementing new and improved technologies in order to increase genetic gain. Genomic selection (GS) is an expansion of marker assisted selection which uses a statistical model to estimate all marker effects for an individual simultaneously to determine a genome estimated breeding value (GEBV). Breeders are thus able to select for performance based on GEBVs in the absence of phenotypic data. In wheat, genomic selection has been successfully implemented for a number of key traits including grain yield, grain quality and quantitative disease resistance, such as that for Fusarium head blight. For this review, we focused on the ways to modify genomic selection to maximize prediction accuracy, including prediction model selection, marker density, trait heritability, linkage disequilibrium, the relationship between training and validation sets, population structure, and training set optimization methods. Altogether, the effects of these different factors on the accuracy of predictions should be thoroughly considered for the successful implementation of GS strategies in wheat breeding programs.

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