Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene

Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.

Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding

Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource. However, relatively little is known about the origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide wheat accessions, including representative spelt wheat, we demonstrate that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt's primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We propose a haplotype-based "spelt index" to identify spelt-type wheat varieties and to quantify utilization of the spelt gene pool in modern wheat cultivars. This study reveals the genetic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.

Molecular Mapping of Yr85 and Comparison with Other Genes for Resistance to Stripe Rust on Wheat Chromosome 1B

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most serious plant diseases worldwide. Resistant cultivars are the most effective way to control the disease. YrTr1 is an important stripe rust resistance gene that has been used in wheat breeding programs and is represented in the host differential set to identify P. striiformis f. sp. tritici races in the United States. To map YrTr1, AvSYrTr1NIL was backcrossed to its recurrent parent Avocet S (AvS). Seedlings of BC7F2, BC7F3, and BC8F1 populations were tested with YrTr1-avirulent races under controlled conditions, and BC7F2 plants were genotyped using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. YrTr1 was mapped to the short arm of chromosome 1B using four SSR and seven SNP markers. The genetic distances of YrTr1 from the nearest flanking markers IWA2583 and IWA7480 were 1.8 and 1.3 centimorgans (cM), respectively. DNA amplification of a set of 21 Chinese Spring (CS) nulli-tetrasomic lines and seven CS 1B deletion lines with three SSR markers confirmed the chromosome arm location and further placed the gene in chromosomal bin region 1BS18 (0.5). The gene was determined to be about 7.4 cM proximal to Yr10. Based on multirace response array and chromosomal location, YrTr1 was determined to be different from other permanently named stripe rust resistance genes in chromosome arm 1BS and was named Yr85.

Updated guidelines for gene nomenclature in wheat

KEY MESSAGE

Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

Development of Non-Targeted Mass Spectrometry Method for Distinguishing Spelt and Wheat

Food fraud, even when not in the news, is ubiquitous and demands the development of innovative strategies to combat it. A new non-targeted method (NTM) for distinguishing spelt and wheat is described, which aids in food fraud detection and authenticity testing. A highly resolved fingerprint in the form of spectra is obtained for several cultivars of spelt and wheat using liquid chromatography coupled high-resolution mass spectrometry (LC-HRMS). Convolutional neural network (CNN) models are built using a nested cross validation (NCV) approach by appropriately training them using a calibration set comprising duplicate measurements of eleven cultivars of wheat and spelt, each. The results reveal that the CNNs automatically learn patterns and representations to best discriminate tested samples into spelt or wheat. This is further investigated using an external validation set comprising artificially mixed spectra, samples for processed goods (spelt bread and flour), eleven untypical spelt, and six old wheat cultivars. These cultivars were not part of model building. We introduce a metric called the D score to quantitatively evaluate and compare the classification decisions. Our results demonstrate that NTMs based on NCV and CNNs trained using appropriately chosen spectral data can be reliable enough to be used on a wider range of cultivars and their mixes.

Population Genomics and Haplotype Analysis in Bread Wheat Identify a Gene Regulating Glume Pubescence

Glume hairiness or pubescence is an important morphological trait with high heritability to distinguish/characterize wheat and is related to the resistance to biotic and abiotic stresses. Hg1 (formerly named Hg) on chromosome arm 1AS controlled glume hairiness in wheat. Its genetic analysis and mapping have been widely studied, yet more useful and accurate information for fine mapping of Hg1 and identification of its candidate gene is lacking. The cloning of this gene has not yet been reported for the large complex wheat genome. Here, we performed a GWAS between SNP markers and glume pubescence (Gp) in a wheat population with 352 lines and further demonstrated the gene expression and haplotype analysis approach for isolating the Hg1 gene. One gene, TraesCSU02G143200 (TaELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was identified as the most promising candidate gene of Hg1. The gene annotation, expression pattern, function SNP variation, haplotype analysis, and co-expression analysis in floral organ (spike) development indicated that it is likely to be involved in the regulation of glume pubescence. Our study demonstrates the importance of high-quality reference genomes and annotation information, as well as bioinformatics analysis, for gene cloning in wheat.

A Combinatorial Q-locus and Tubulin-Based Polymorphism (TBP) Approach Helps in Discriminating Triticum Species

The simple and straightforward recognition of Triticum species is not an easy task due to their complex genetic origins. To provide a recommendation, we have compared the performance of different PCR-based methods relying on the discrimination ability of the Q- and γ-gliadin (GAG56D) genes, as well as TBP (Tubulin-Based Polymorphism), a method based on the multiple amplification of genes of the β-tubulin family. Among these approaches, the PCR-RFLP (Restriction Fragment Length Polymorphism) assay based on a single-nucleotide polymorphism (SNP) present in the Q gene is the only one capable of fully discerning hexaploid spelt and common wheat species, while both γ-gliadin and TBP fail with similar error frequencies. The Q-locus assay results in the attainment of either a single fragment or a doublet, depending on the presence of a suitable restriction site, which is affected by the mutation. This dual pattern of resolution limits both the diagnostic effectiveness, when additional Triticum species are assayed and compared to each other, and its usefulness, when commercially available flours are analyzed. These limitations are overtaken by flanking the Q-locus assay with the TBP analysis. In this way, almost all of the Triticum species can be accurately identified.

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease¹. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity^2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future.

Chromosome-scale genome assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega facilitates the cloning of the stripe rust resistance gene Yr27.

Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes

The seed protein α-gliadin is a major component of wheat flour and causes gluten-related diseases. However, due to the complexity of this multigene family with a genome structure composed of dozens of copies derived from tandem and genome duplications, little was known about the variation between accessions, and thus little effort has been made to explicitly target α-gliadin for bread wheat breeding. Here, we analyzed genomic variation in α-gliadins across 11 recently published chromosome-scale assemblies of hexaploid wheat, with validation using long-read data. We unexpectedly found that the Gli-B2 locus is not a single contiguous locus but is composed of two subloci, suggesting the possibility of recombination between the two during breeding. We confirmed that the number of immunogenic epitopes among 11 accessions varied. The D subgenome of a European spelt line also contained epitopes, in agreement with its hybridization history. Evolutionary analysis identified amino acid sites under diversifying selection, suggesting their functional importance. The analysis opens the way for improved grain quality and safety through wheat breeding.

Induction of useful mutations in Triticum aestivum in the conditions of the radionuclide-contaminated alienation zone of the Chornobyl Power Plant

Induced mutagenesis opens great perspectives for radical genetic improvement of cultivated plants. Scientists seeking new sources and methodological approaches to improve the frequency and extend the range of mutations have drawn attention to the Zone of Alienation around the Chornobyl Nuclear Power Plant, where unique conditions of the influence of mutagenic factors have developed, and therefore needs to be studied for possible use of its territory in propagating parent material for selective breeding of wheat. Plants of winter wheat of Albatros Odesky and Zymoiarka varieties were grown within 10 km of the Chernobyl Plant, inside the Alienation Zone, in Chystohalivka, Kopachi and Yaniv villages of Chornobyl district of Kyiv Oblast. The exposure occurred in the dose of 7.2 ∙ 10–12– 50.0 ∙ 10–12 A/kg. As the control, we used the territory of the Research Institute of Physiology of Plants and Genetics of the Academy of Sciences of Ukraine (Hlevaha urbanized settlement of Vasylkivsky District of Kyiv Oblast), where the power of the exposure dose equaled 0.93 ∙ 10–12 A/kg. Frequency and spectrum of mutant forms were determined in M2–M3 generations according to the ratio of the number of families with mutagenic plants to studied M2 families. Among the observed mutations, we determined the share of the ones important for selective breeding. Chronic ionizing radiation throughout the vegetation period of winter wheat increased the level of noticeable mutations, the frequency of which exceeded the control parameters by 8.0–14.9 times. In the conditions of cultivation of winter wheat in the territory of Kopachi village, where the dose was the lowest, we recorded a high level of mutation variability which exceeded the control parameters by 8.0–9.2 times and was notably different from the frequency of mutations induced by radionuclide contamination of soil in the territories of Chystohalivka and Yaniv villages. The mutation range contained 12–20 types and depended on the density of soil contamination with radio nuclides, magnitude of exposure dose and genotype of plants. The predominant mutations were the ones related to the duration of vegetation period, length of the stem, morphology and awns of the ear. Among the detected mutations, the important selective ones accounted for 24.3–49.3%, predominant being low height, intense growth and long cylindrical ear. Because beneficial agronomic traits are highly likely to be inherited in complex with mutations that reduce the productivity of winter wheat, efficiency of direct selection of mutant forms that are valuable for selective breeding is limited. Enlargement of genetic diversity of the initial selection material using the radionuclide-induced mutagenesis resulting from contamination creates the possibility of using it in cross breeding for the purpose of implementing selective breeding genetic programs of improving wheat varieties.