A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat

Colored wheat and derived products: key to global nutritional security

Ensuring food and nutritional security of fast-growing population will pose a huge challenge in future. An estimated one-half population who does not go hungry, nonetheless suffers the debilitating effects of unhealthy diets. In view of the nutritional awareness, when the major wheat breeding programs have started shifting to quality, instead of quantity in wheat, the colored wheats give a novel twist of targeting the malnutrition by enhancing the antioxidants such as anthocyanin, carotenoids, flavonoids, polyphenols etc. Moreover, changing consumer demands have picked the trend to prefer a nutritionally balanced diet over the conventional high energy diets and thus, colored wheat has opened up a hidden avenue for providing additional value to the wheat-based products. Besides providing nutrition, these pigments have the potential to replace the synthetic dyes and food colorants prevalent in the market. The review summarizes the genetics and biochemistry of the pigments of colored wheat along with their product development, nutritional status and consumer preference. The review also sheds light on the environmental effect on color accumulation and the effect of increased colorants on other quality traits of wheat.

Resistance mechanisms involved in complex immunity of wheat against rust diseases

The review is devoted to the disclosure of the modern concept of plant immunity as a hierarchical system of plant host protection, controlled by combinations of major and minor resistance genes (loci). The “zigzag” model is described in detail for discussing the molecular bases of plant immunity with key concepts: pathogen-associated molecular patterns triggering innate immunity, ambivalent effectors causing susceptibility, but when interacting with resistance genes, a hypersensitive reaction or alternative defense mechanisms. There are three types of resistance in cereals: (1) basal resistance provided by plasma membrane-localized receptors proteins; (2) racespecific resistance provided by intracellular immune R-receptors; (3) partial resistance conferred by quantitative gene loci. The system ‘wheat (Triticum aestivum) – the fungus causing leaf rust (Puccinia triticina)’ is an interesting model for observing all the resistance mechanisms listed above, since the strategy of this pathogen is aimed at the constitutive use of host resources. The review focuses on known wheat genes responsible for various types of resistance to leaf rust: race-specific genes Lr1, Lr10, Lr19, and Lr21; adult resistance genes which are hypersensitive Lr12, Lr13, Lr22a, Lr22b, Lr35, Lr48, and Lr49; nonhypersensitive genes conferring partial resistance Lr34, Lr46, Lr67, and Lr77. The involvement of some wheat R-genes in pre-haustorial resistance to leaf rust has been discovered recently: Lr1, Lr3a, Lr9, LrB, Lr19, Lr21, Lr38. The presence of these genes in the genotype ensures the interruption of early pathogenesis through the following mechanisms: disorientation and branching of the germ tube; formation of aberrant fungal penetration structures (appressorium, substomatal vesicle); accumulation of callose in mesophyll cell walls. Breeding for immunity is accelerated by implementation of data on various mechanisms of wheat resistance to rust diseases, which are summarized in this review.

Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities

Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat (T. durum, 4x), widening the genetic base is a priority and primary target to cope with the many challenges that the crop has to face. These include recent climate changes, as well as actual and projected demographic growth, contrasting with reduction of arable land and water reserves. All of these environmental and societal modifications pose major constraints to the required production increase in the wheat crop. A sustainable approach to address this task implies resorting to non-conventional breeding strategies, such as “chromosome engineering”. This is based on cytogenetic methodologies, which ultimately allow for the incorporation into wheat chromosomes of targeted, and ideally small, chromosomal segments from the genome of wild relatives, containing the gene(s) of interest. Chromosome engineering has been successfully applied to introduce into wheat genes/QTL for resistance to biotic and abiotic stresses, quality attributes, and even yield-related traits. In recent years, a substantial upsurge in effective alien gene exploitation for wheat improvement has come from modern technologies, including use of molecular markers, molecular cytogenetic techniques, and sequencing, which have greatly expanded our knowledge and ability to finely manipulate wheat and alien genomes. Examples will be provided of various types of stable introgressions, including pyramiding of different alien genes/QTL, into the background of bread and durum wheat genotypes, representing valuable materials for both species to respond to the needed novelty in current and future breeding programs. Challenging contexts, such as that inherent to the 4x nature of durum wheat when compared to 6x bread wheat, or created by presence of alien genes affecting segregation of wheat-alien recombinant chromosomes, will also be illustrated.

Cytogenetic mapping of a major locus for resistance to Fusarium head blight and crown rot of wheat on Thinopyrum elongatum 7EL and its pyramiding with valuable genes from a Th. ponticum homoeologous arm onto bread wheat 7DL

A major locus for resistance to different Fusarium diseases was mapped to the most distal end of Th. elongatum 7EL and pyramided with Th. ponticum beneficial genes onto wheat 7DL. Perennial Triticeae species of the Thinopyrum genus are among the richest sources of valuable genes/QTL for wheat improvement. One notable and yet unexploited attribute is the exceptionally effective resistance to a major wheat disease worldwide, Fusarium head blight, associated with the long arm of Thinopyrum elongatum chromosome 7E (7EL). We targeted the transfer of the temporarily designated Fhb-7EL locus into bread wheat, pyramiding it with a Th. ponticum 7el₁L segment stably inserted into the 7DL arm of wheat line T4. Desirable genes/QTL mapped along the T4 7el₁L segment determine resistance to wheat rusts (Lr19, Sr25) and enhancement of yield-related traits. Mapping of the Fhb-7EL QTL, prerequisite for successful pyramiding, was established here on the basis of a bioassay with Fusarium graminearum of different 7EL-7el₁L bread wheat recombinant lines. These were obtained without resorting to any genetic pairing promotion, but relying on the close 7EL-7el₁L homoeology, resulting in 20% pairing frequency between the two arms. Fhb-7EL resided in the telomeric portion and resistant recombinants could be isolated with useful combinations of more proximally located 7el₁L genes/QTL. The transferred Fhb-7EL locus was shown to reduce disease severity and fungal biomass in grains of infected recombinants by over 95%. The same Fhb-7EL was, for the first time, proved to be effective also against F. culmorum and F. pseudograminearum, predominant agents of crown rot. Prebreeding lines possessing a suitable 7EL-7el₁L gene/QTL assembly showed very promising yield performance in preliminary field tests.

A wheat NBS-LRR gene TaRGA19 participates in Lr19-mediated resistance to Puccinia triticina

Wheat leaf rust, caused by Puccinia triticina (Pt), is one of the most severe fungal diseases on wheat globally. Rational utilization of wheat leaf rust resistance (Lr) genes is still the best choice for control this disease. Wheat seedlings carrying Lr19 showed a high resistance phenotype to all Pt races in China. So far, all the cloned seedling Lr genes including Lr1, Lr10 and Lr21, encode protein with NBS-LRR domain. In this study, a wheat gene with NBS-LRR domain from previously established Lr19-resistance-related cDNA library was cloned and designated as TaRGA19. Full length of this gene was amplified by rapid amplification of cDNA ends (RACE). By blast against IWGSC wheat genome database, we have noticed that TaRGA19 was located on chromosome 2DS, which was different from Lr19 located on chromosome 7DL. Compared with susceptible Thatcher line, expression level of TaRGA19 was upregulated in wheat isogenic lines carrying Lr19 (TcLr19) after inoculation of Pt race THTS. By particle bombardment, TaRGA19-GFP fused protein was localized on plasma membrane of epidermal cells. Using virus-induced gene silencing (VIGS), TaRGA19-knockdown plants of TcLr19 showed reduced resistance and few sporulation phenotype upon Pt challenge. Further histological observation indicated that Pt hyphal growth at the infection sites was less suppressed in the TaRGA19-knockdown plants. In conclusion, we speculate this TaRGA19 gene was involved in the Lr19-mediated resistance to wheat leaf rust along with other components.

Microscopic and Molecular Characterization of the Prehaustorial Resistance against Wheat Leaf Rust (Puccinia triticina) in Einkorn (Triticum monococcum)

Puccinia triticina f. sp. tritici (Eriks.), the causal agent of leaf rust, causes substantial yield losses in wheat production. In wheat many major leaf rust resistance genes have been overcome by virulent races. In contrast, the prehaustorial resistance (phr) against wheat leaf rust detected in the diploid wheat Einkorn (Triticum monoccocum var. monococcum) accession PI272560 confers race-independent resistance against isolates virulent on accessions harboring resistance genes located on the A-genome of Triticum aestivum. Phr in PI272560 leads to abortion of fungal development during the formation of haustorial mother cells and to increased hydrogen peroxide concentration in comparison to the susceptible accession 36554 (Triticum boeoticum ssp. thaoudar var. reuteri). Increased peroxidase and endochitinase activity was detected in PI272560 within 6 h after inoculation (hai). Comparative transcriptome profiling using Massive Analysis of cDNA Ends (MACE) in infected and non-infected leaves detected 14220 differentially expressed tags in PI272560 and 15472 in accession 36554. Of these 2908 and 3004, respectively, could be assigned to Gene Ontology (GO) categories of which 463 were detected in both accessions and 311 were differentially expressed between the accessions. In accordance with the concept of non-host resistance in PI272560, genes with similarity to peroxidases, chitinases, β-1,3-glucanases and other pathogenesis-related genes were up-regulated within the first 8 hai, whereas up-regulation of such genes was delayed in 36554. Moreover, a Phosphoribulokinase gene contributing to non-host resistance in rice against stripe rust was exclusively expressed in the resistant accession PI272560. Gene expression underpinned physiological and phenotypic observations at the site of infection and are in accordance with the concept of non-host resistance.

The wheat homolog of putative nucleotide-binding site-leucine-rich repeat resistance gene TaRGA contributes to resistance against powdery mildew

Powdery mildew, one of the most destructive wheat diseases worldwide, is caused by Blumeria graminis f. sp. tritici (Bgt), a fungal species with a consistently high mutation rate that makes individual resistance (R) genes ineffective. Therefore, effective resistance-related gene cloning is vital for breeding and studying the resistance mechanisms of the disease. In this study, a putative nucleotide-binding site-leucine-rich repeat (NBS-LRR) R gene (TaRGA) was cloned using a homology-based cloning strategy and analyzed for its effect on powdery mildew disease and wheat defense responses. Real-time reverse transcription-PCR (RT-PCR) analyses revealed that a Bgt isolate 15 and salicylic acid stimulation significantly induced TaRGA in the resistant variety. Furthermore, the silencing of TaRGA in powdery mildew-resistant plants increased susceptibility to Bgt15 and prompted conidia propagation at the infection site. However, the expression of TaRGA in leaf segments after single-cell transient expression assay highly increased the defense responses to Bgt15 by enhancing callose deposition and phenolic autofluorogen accumulation at the pathogen invading sites. Meanwhile, the expression of pathogenesis-related genes decreased in the TaRGA-silenced plants and increased in the TaRGA-transient-overexpressing leaf segments. These results implied that the TaRGA gene positively regulates the defense response to powdery mildew disease in wheat.

TEF-7A, a transcript elongation factor gene, influences yield-related traits in bread wheat (Triticum aestivum L.)

In this study, TaTEF-7A, a member of the transcript elongation factor gene family, and its flanking sequences were isolated. TaTEF-7A was located on chromosome 7A and was flanked by markers Xwmc83 and XP3156.3. Subcellular localization revealed that TaTEF-7A protein was localized in the nucleus. This gene was expressed in all organs, but the highest expression occurred in young spikes and developing seeds. Overexpression of TaTEF-7A in Arabidopsis thaliana produced pleiotropic effects on vegetative and reproductive development that enhanced grain length, silique number, and silique length. No diversity was found in the coding region of TaTEF-7A, but 16 single nucleotide polymorphisms and Indels were detected in the promoter regions of different cultivars. Markers based on sequence variations in the promoter regions (InDel-629 and InDel-604) were developed, and three haplotypes were identified based on those markers. Haplotype-trait association analysis of the Chinese wheat mini core collection revealed that TaTEF-7A was significantly associated with grain number per spike. Phenotyping of near-isogenic lines (NILs) confirmed that TaTEF-7A increases potential grain yield and yield-related traits. Frequency changes in favoured haplotypes gradually increased in cultivars released in China from the 1940s. Geographic distributions of favoured haplotypes were characterized in six major wheat production regions worldwide. The presence of Hap-7A-3, the favoured haplotype, showed a positive correlation with yield in a global set of breeding lines. These results suggest that TaTEF-7A is a functional regulatory factor for grain number per spike and provide a basis for marker-assisted selection.

Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining

In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, 'Salambo 80.' Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance.

Development and characterization of a Psathyrostachys huashanica Keng 7Ns chromosome addition line with leaf rust resistance

The aim of this study was to characterize a Triticum aestivum-Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) disomic addition line 2-1-6-3. Individual line 2-1-6-3 plants were analyzed using cytological, genomic in situ hybridization (GISH), EST-SSR, and EST-STS techniques. The alien addition line 2-1-6-3 was shown to have two P. huashanica chromosomes, with a meiotic configuration of 2n = 44 = 22 II. We tested 55 EST-SSR and 336 EST-STS primer pairs that mapped onto seven different wheat chromosomes using DNA from parents and the P. huashanica addition line. One EST-SSR and nine EST-STS primer pairs indicated that the additional chromosome of P. huashanica belonged to homoeologous group 7, the diagnostic fragments of five EST-STS markers (BE404955, BE591127, BE637663, BF482781 and CD452422) were cloned, sequenced and compared. The results showed that the amplified polymorphic bands of P. huashanica and disomic addition line 2-1-6-3 shared 100% sequence identity, which was designated as the 7Ns disomic addition line. Disomic addition line 2-1-6-3 was evaluated to test the leaf rust resistance of adult stages in the field. We found that one pair of the 7Ns genome chromosomes carried new leaf rust resistance gene(s). Moreover, wheat line 2-1-6-3 had a superior numbers of florets and grains per spike, which were associated with the introgression of the paired P. huashanica chromosomes. These high levels of disease resistance and stable, excellent agronomic traits suggest that this line could be utilized as a novel donor in wheat breeding programs.

The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology

Thinopyrum elongatum is an important relative of wheat, it is favored by many researchers for the disease resistant genes that exist in its E genome. Some studies have showed that the 7E chromosome of Th. elongatum contains resistance genes related to Fusarium head blight and wheat rust. Therefore, developing 7E chromosome-specific molecular markers linked to resistance genes will provide an important tool for exploring and using the resistant genes of Th. elongatum. In addition, it would greatly contribute in the effort to cultivate disease-resistant wheat varieties. Featured in high throughput, high-accuracy and low-cost, SLAF-seq technology has been widely used in molecular breeding, system evolution, and germplasm resource detection. Based on SLAF-seq, 518 specific fragments on the 7E chromosome of Th. elongatum were successfully amplified. A total of 135 primers were designed according to 135 randomly selected fragments, and 89 specific molecular markers of Th. elongatum were developed, with efficiencies up to 65.9%. These markers were all detected in a variety of materials, and they are all proved to be specific and stable. These markers can be used not only for detecting the 7E chromosome of Th. elongatum but also for providing an important theoretical and practical basis for wheat breeding by marker-assisted selection (MAS). This paper reports the first application of SLAF-seq technology with a high success rate in developing specific molecular markers for Th. elongatum, providing a strong case for the application of this new technology.

Functional markers in wheat: current status and future prospects

Functional markers (FM) are developed from sequence polymorphisms present in allelic variants of a functional gene at a locus. FMs accurately discriminate alleles of a targeted gene, and are ideal molecular markers for marker-assisted selection in wheat breeding. In this paper, we summarize FMs developed and used in common wheat. To date, more than 30 wheat loci associated with processing quality, agronomic traits, and disease resistance, have been cloned, and 97 FMs were developed to identify 93 alleles based on the sequences of those genes. A general approach is described for isolation of wheat genes and development of FMs based on in silico cloning and comparative genomics. The divergence of DNA sequences of different alleles that affect gene function is summarized. In addition, 14 molecular markers specific for alien genes introduced from common wheat relatives were also described. This paper provides updated information on all FMs and gene-specific STS markers developed so far in wheat and should facilitate their application in wheat breeding programs.

Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding

Chinese wheat mini core collection (262 accessions) was genotyped at 531 microsatellite loci representing a mean marker density of 5.1 cM. One-thousand-kernel weights (TKW) of lines were measured in five trials (three environments in four growing seasons). Structure analysis based on 42 unlinked SSR loci indicated that the materials formed two sub-populations, viz., landraces and modern varieties. A large difference in TKW (7.08 g, P<0.001) was found between the two sub-groups. Therefore, TKW is a major yield component that was improved in the past 6 decades; it increased from a mean 31.5 g in the 1940s to 44.64 g in the 2000s, representing a 2.19 g increase in each decade. Analyses based on a mixed linear model (MLM), population structure (Q) and relative kinship (K) revealed 22 SSR loci that were significantly associated with mean TKW (MTKW) of the five trials estimated by the best linear unbiased predictor (BLUP) method. They were mainly distributed on chromosomes of homoeologous groups 1, 2, 3, 5 and 7. Six loci, cfa2234-3A, gwm156-3B, barc56-5A, gwm234-5B, wmc17-7A and cfa2257-7A individually explained more than 11.84% of the total phenotypic variation. Favored alleles for breeding at the 22 loci were inferred according to their estimated effects on MTKW based on mean difference of varieties grouped by genotypes. Statistical simulation showed that these favored alleles have additive genetic effects. Frequency changes of alleles at loci associated with TKW are much more dramatic than those at neutral loci between the sub-groups. The numbers of favored alleles in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of TKW in wheat breeding. Alleles that can be used globally to increase TKW were inferred according to their distribution by latitude and frequency of changes between landraces and the modern varieties.

Genetic and correlation analysis of silique-traits in Brassica napus L. by quantitative trait locus mapping

Rapeseed yield is directly and indirectly influenced by the silique-traits, such as silique length (SL), seeds per silique (SS), seed weight (SW), because the silique is an organ which produced yield and a major photosynthesis organ as well. In this study, a linkage map comprising 150 simple sequence repeat and 195 amplified fragment length polymorphism markers covering 1,759.6 cM was constructed in a doubled haploid population from a cross between two genotypes of 'HZ396' and 'Y106'. In field experiments across three seasons and two locations in China 140 doubled haploid lines and their corresponding parents were evaluated for silique-traits. In total, 26 quantitative trait loci (QTL) were detected, of which 15 were clustered and integrated into 5 pleiotropic unique QTL by meta-analysis. These unique QTL, which in a certain sense reflected the significant positive correlation between SS and SL and the significant negative correlation between SW and SS by the genomic location and effects of QTL detected, were mapped on linkage groups N7, N8 and N13. A trait-by-trait meta-analysis revealed 5, 2 and 3 consensus QTL for SL, SS and SW, respectively. Epistatic effects varied according to the specific traits performed. All the epistatic interactions showed significant additive by additive effects while no significant epistasis by environment effect was identified. These findings provided a better understanding of the genetic factors controlling silique-traits and gained insights into the gene networks affecting silique-traits at QTL level in rapeseed.