Delineating the structural, functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses

<p>Abstract</p> <p>Background</p> <p>Sucrose phosphate synthase (SPS) is an important component of the plant sucrose biosynthesis pathway. In the monocotyledonous Poaceae, five <it>SPS </it>genes have been identified. Here we present a detailed analysis of the wheat <it>SPSII </it>family in wheat. A set of homoeologue-specific primers was developed in order to permit both the detection of sequence variation, and the dissection of the individual contribution of each homoeologue to the global expression of <it>SPSII</it>.</p> <p>Results</p> <p>The expression in bread wheat over the course of development of various sucrose biosynthesis genes monitored on an Affymetrix array showed that the <it>SPS </it>genes were regulated over time and space. <it>SPSII </it>homoeologue-specific assays were used to show that the three homoeologues contributed differentially to the global expression of <it>SPSII</it>. Genetic mapping placed the set of homoeoloci on the short arms of the homoeologous group 3 chromosomes. A resequencing of the A and B genome copies allowed the detection of four haplotypes at each locus. The 3B copy includes an unspliced intron. A comparison of the sequences of the wheat <it>SPSII </it>orthologues present in the diploid progenitors einkorn, goatgrass and <it>Triticum speltoides</it>, as well as in the more distantly related species barley, rice, sorghum and purple false brome demonstrated that intronic sequence was less well conserved than exonic. Comparative sequence and phylogenetic analysis of <it>SPSII </it>gene showed that false purple brome was more similar to <it>Triticeae </it>than to rice. Wheat - rice synteny was found to be perturbed at the SPS region.</p> <p>Conclusion</p> <p>The homoeologue-specific assays will be suitable to derive associations between SPS functionality and key phenotypic traits. The amplicon sequences derived from the homoeologue-specific primers are informative regarding the evolution of <it>SPSII </it>in a polyploid context.</p

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Insights into Tan Spot and Stem Rust Resistance and Susceptibility by Studying the Pre-Green Revolution Global Collection of Wheat

Tan spot (TS), caused by the fungus Pyrenophora tritici-repentis (Died) Drechs, is an important foliar disease of wheat and has become a threat to world wheat production since the 1970s. In this study a globally diverse pre-1940s collection of 247 wheat genotypes was evaluated against Ptr ToxA, P. tritici-repentis race 1, and stem rust to determine if; (i) acquisition of Ptr ToxA by the P. tritici-repentis from Stagonospora nodorum led to increased pathogen virulence or (ii) incorporation of TS susceptibility during development stem rust resistant cultivars led to an increase in TS epidemics globally. Most genotypes were susceptible to stem rust; however, a range of reactions to TS and Ptr ToxA were observed. Four combinations of disease-toxin reactions were observed among the genotypes; TS susceptible-Ptr ToxA sensitive, TS susceptible-Ptr ToxA insensitive, TS resistant-Ptr ToxA insensitive, and TS resistant-Ptr ToxA toxin sensitive. A weak correlation (r = 0.14 for bread wheat and −0.082 for durum) was observed between stem rust susceptibility and TS resistance. Even though there were no reported epidemics in the pre-1940s, TS sensitive genotypes were widely grown in that period, suggesting that Ptr ToxA may not be an important factor responsible for enhanced prevalence of TS

Characterization of Pyrenophora tritici-repentis (Tan Spot of Wheat) Races in Baltic States and Romania

Tan spot, caused by the fungus Pyrenophora triticirepentis, is economically important foliar disease in Latvia, Lithuania, and Romania; however, race structure from Baltic States and Romania is not known. In this study, we performed genotypic and phenotypic race characterization of a large collection of P. triticirepentis isolates from these countries to determine race structure and utilize this information for better disease management and breeding wheat for tan spot resistance. We characterized 231 single spore isolates from Latvia (n = 15), Lithuania (n = 107), and Romania (n = 109) for Ptr ToxA and Ptr ToxB genes using two genes specific primers. A subset (139) of 231 isolates were further characterized for their race structure by inoculating them individually on tan spot wheat differentials set. Majority (83%) of the 231 isolates amplified Ptr ToxA gene suggesting prevalence of race 1 and 2. Further, phenotypic characterization of 139 isolates also showed wide prevalence of races 1 (68%), 2 (8%), 3 (11%), and 4 (5%) were also identified from Baltic States as well as Romania. Eighteen of the isolates (13%) did not seem to be of any of the eight known races as they lacked Ptr ToxA gene but they behaved like either race 1 or race 2, suggesting possibility of novel toxins in these isolates as their virulence tools

Deciphering the Role of Stay-Green Trait to Mitigate Terminal Heat Stress in Bread Wheat

The present study aimed to reveal the impact of the stay-green trait in bread wheat under terminal heat stress. Field experiments (early and late sowing; for two consecutive years) were conducted to investigate the influence of terminal heat stress on the morpho-physiological traits in different stay-green types i.e., non-stay-green, moderately non-stay-green, moderately stay-green, and stay-green. In addition, the greenhouse experiment was performed to dissect the stay-green trait in functional stay-green, non-functional stay-green, and non-stay-green genotypes. The results of the field experiments confirmed that genotypes exhibiting the stay-green trait have a significantly high chlorophyll content, normalized difference vegetative index, grain yield, biological yield, kernel weight, and low canopy temperature under control and heat stress conditions. In the greenhouse experiment, functional stay-green and non-functional stay-green genotypes showed a high chlorophyll content and photochemical efficiency, whereas biological yield and grain yield showed a significant relation with the functional stay-green genotype under control and terminal heat stress treatments. The sequencing and expression analysis of chlorophyllide a oxygenase (CaO), light-harvesting complex (Cab), stay-green (SGR), and red chlorophyll catabolite reductase (RCCR) in functional stay-green, non-functional stay-green, and non-stay-green genotypes revealed variations in the exons of CaO and RCCR; and significant difference in the regulation of CaO and Cab at 7 days after anthesis under terminal heat stress. This study confirms that genotypes displaying the stay-green trait can aid wheat breeders to cope with increasing temperature in the impending decades

Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat.

Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops