Transfer of stripe rust resistance from Aegilops variabilis to bread wheat

In terms of area, the bread wheat producing regions of China comprise the largest area in the world that is constantly threatened by stripe rust epidemics. Consequently, it is important to exploit new adultplant resistance genes in breeding. This study reports the transfer of stripe rust resistance from Aegilops variabilis to bread wheat resulting in resistant line, TKL2(R). Genetic analysis of the segregating populations derived from a cross between TKL2(R) and a susceptible sister line, TKL2(S), indicated that the adult-plant resistance to Puccinia striiformis f. sp. tritici in TKL2(R) is conferred by a single dominant gene. This gene provided resistance to physiological races currently endemic to China, thus indicating its potential usefulness in wheat breeding.Keywords: Aegilops variabilis, gene transfer, Puccinia striiformis f. sp. tritici, Triticum aestivum, wide hybridizatio

Empirical verification of heterogeneous DNA fragments generated from wheat genome-specific SSR primers

Publisher's version/PDFDue to the high polymorphisms between synthetic hexaploid wheat (SHW) and common wheat, SHW has been widely used in genetic studies. The transferability of simple sequence repeats (SSR) among common wheat and its donor species, Triticum turgidum and Aegilops tauschii, and their SHW suggested the possibility that some SSRs, specific for a single locus in common wheat, might appear in two or more loci in SHWs. This is an important genetic issue when using synthetic hexaploid wheat population and SSR for mapping. However, it is largely ignored and never empirically well verified. The present study addressed this issue by using the well-studied SSR marker Xgwm261 as an example. The Xgwm261 produced a 192 bp fragment specific to chromosome 2D in common wheat Chinese Spring, but generated a 176 bp fragment in the D genome of Ae. tauschii AS60. Chromosomal location and DNA sequence data revealed that the 176 bp fragment also donated by 2B chromosome of durum wheat Langdon. These results indicated that although a single 176 bp fragment was appeared in synthetic hexaploid wheat Syn-SAU-5 between Langdon and AS60, the fragment contained two different loci, one from chromosome 2D of AS60 and the other from 2B of Langdon which were confirmed by the segregating analysis of SSR Xgwm261 in 185 plants from a F2 population between Syn-SAU-5 and Chinese Spring. If Xgwm261 in Syn-SAU-5 was considered as a single locus in genetic analysis, distorted segregation or incorrect conclusions would be yielded. A proposed strategy to avoid this problem is to include SHW’s parental T. turgidum and Ae. tauschii in SSR analysis as control for polymorphism detection

Genome-Wide Association Study Reveals Novel Genomic Regions Associated With High Grain Protein Content in Wheat Lines Derived From Wild Emmer Wheat

Grain protein content (GPC) and yield are of two important traits in wheat, but their negative correlation has hampered their simultaneous improvement in conventional breeding. Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is an important genetic resource for wheat quality improvement. In this study, we report a genome-wide association study (GWAS) using 13116 DArT-seq markers to characterize GPC in 161 wheat lines derived from wild emmer. Using a general linear model, we identified 141 markers that were significantly associated with GPC, and grouped into 48 QTL regions. Using both general linear model and mixed linear model, we identified four significant markers that were grouped into two novel QTL regions on chromosomes 2BS (QGpc.cd1-2B.1) and 7BL (QGpc.cd1-7B.2). The two QTLs have no negative effects on thousand kernel weight (TKW) and should be useful for simultaneous improvement of GPC and TKW in wheat breeding. Searches of public databases revealed 61 putative candidate/flanking genes related to GPC. The putative proteins of interest were grouped in four main categories: enzymes, kinase proteins, metal transport-related proteins, and disease resistance proteins. The linked markers and associated candidate genes provide essential information for cloning genes related to high GPC and performing marker-assisted breeding in wheat

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

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

Uncovering the dispersion history, adaptive evolution and selection of wheat in China

Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27,933 DArTseq (for 717 landraces) and 312,831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes, such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to south China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas

The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat

Dataset S7. List of nonadditively expressed genes in F1 hybrids derived from AS2255 × AS60. (XLSX 72 kb

An ancestral NB-LRR with duplicated 3'UTRs confers stripe rust resistance in wheat and barley.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a global threat to wheat production. Aegilops tauschii, one of the wheat progenitors, carries the YrAS2388 locus for resistance to Pst on chromosome 4DS. We reveal that YrAS2388 encodes a typical nucleotide oligomerization domain-like receptor (NLR). The Pst-resistant allele YrAS2388R has duplicated 3' untranslated regions and is characterized by alternative splicing in the nucleotide-binding domain. Mutation of the YrAS2388R allele disrupts its resistance to Pst in synthetic hexaploid wheat; transgenic plants with YrAS2388R show resistance to eleven Pst races in common wheat and one race of P. striiformis f. sp. hordei in barley. The YrAS2388R allele occurs only in Ae. tauschii and the Ae. tauschii-derived synthetic wheat; it is absent in 100% (n = 461) of common wheat lines tested. The cloning of YrAS2388R will facilitate breeding for stripe rust resistance in wheat and other Triticeae species

Mitotic Illegitimate Recombination Is a Mechanism for Novel Changes in High-Molecular-Weight Glutenin Subunits in Wheat-Rye Hybrids

Wide hybrids can have novel traits or changed expression of a quantitative trait that their parents do not have. These phenomena have long been noticed, yet the mechanisms are poorly understood. High-molecular-weight glutenin subunits (HMW-GS) are seed storage proteins encoded by Glu-1 genes that only express in endosperm in wheat and its related species. Novel HMW-GS compositions have been observed in their hybrids. This research elucidated the molecular mechanisms by investigating the causative factors of novel HMW-GS changes in wheat-rye hybrids. HMW-GS compositions in the endosperm and their coding sequences in the leaves of F1 and F2 hybrids between wheat landrace Shinchunaga and rye landrace Qinling were investigated. Missing and/or additional novel HMW-GSs were observed in the endosperm of 0.5% of the 2078 F1 and 22% of 36 F2 hybrid seeds. The wildtype Glu-1Ax null allele was found to have 42 types of short repeat sequences of 3-60 bp long that appeared 2 to 100 times. It also has an in-frame stop codon in the central repetitive region. Analyzing cloned allele sequences of HMW-GS coding gene Glu-1 revealed that deletions involving the in-frame stop codon had happened, resulting in novel ∼1.8-kb Glu-1Ax alleles in some F1 and F2 plants. The cloned mutant Glu-1Ax alleles were expressed in Escherichia coli, and the HMW-GSs produced matched the novel HMW-GSs found in the hybrids. The differential changes between the endosperm and the plant of the same hybrids and the data of E. coli expression of the cloned deletion alleles both suggested that mitotic illegitimate recombination between two copies of a short repeat sequence had resulted in the deletions and thus the changed HMW-GS compositions. Our experiments have provided the first direct evidence to show that mitotic illegitimate recombination is a mechanism that produces novel phenotypes in wide hybrids

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Towards cultivar-oriented gene discovery for better crops

The continued expansion of the world population, increasingly inconsistent climate and shrinking agricultural resources present major challenges to crop breeding. Fortunately, the increasing ability to discover and manipulate genes creates new opportunities to develop more productive and resilient cultivars. Many genes have been described in papers as being beneficial for yield increase. However, few of them have been translated into increased yield on farms. In contrast, commercial breeders are facing gene decidophobia, i.e., puzzled about which gene to choose for breeding among the many identified, a huge chasm between gene discovery and cultivar innovation. The purpose of this paper is to draw attention to the shortfalls in current gene discovery research and to emphasise the need to align with cultivar innovation. The methodology dictates that genetic studies not only focus on gene discovery but also pay good attention to the genetic backgrounds, experimental validation in relevant environments, appropriate crop management, and data reusability. The close of the gaps should accelerate the application of molecular study in breeding and contribute to future global food security