Grain quality traits within the wheat (Triticum spp.) genepool: prospects for improved nutrition through de novo domestication.

BACKGROUND: Wild relatives of wheat (Triticum spp.) harbor beneficial alleles for potential improvement and de novo domestication of selected genotypes with advantageous traits. We analyzed the nutrient composition in wild diploid and tetraploid wheats and their domesticated diploid, tetraploid and hexaploid relatives under field conditions in Germany and compared them with modern Triticum aestivum and Triticum durum cultivars. Grain iron (Fe) and zinc (Zn) concentrations, phytate:mineral molar ratios, grain protein content (GPC) and antioxidant activity were analyzed across 125 genotypes. RESULTS: Grain Fe and Zn concentrations in wild wheats were 72 mg kg-1 and 59 mg kg-1, respectively, with improved bioavailability indicated by Phytate:Fe and Phytate:Zn molar ratios (11.7 and 16.9, respectively) and GPC (231 g kg-1). By comparison, grain Fe and Zn concentrations in landrace taxa were 54 mg kg-1 and 55 mg kg-1, respectively, with lower Phytate:Fe and Phytate:Zn molar ratios (15.1 and 17.5, respectively) and GPC (178 g kg-1). Average grain Fe accumulation in Triticum araraticum was 73 mg kg-1, reaching 116 mg kg-1, with high Fe bioavailability (Phyt:Fe: 11.7; minimum: 7.2). Wild wheats, landraces and modern cultivars showed no differences in antioxidant activity. Triticum zhukovskyi stood out with high grain micronutrient concentrations and favorable molar ratios. It was also the only taxon with elevated antioxidant activity. CONCLUSION: Our results indicate alteration of grain quality during domestication. T. araraticum has promising genotypes with advantageous grain quality characteristics that could be selected for de novo domestication. Favorable nutritional traits in the GGAA wheat lineage (T. araraticum and T. zhukovskyi) hold promise for improving grain quality traits. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data.

Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, we provide information about predicted introgressions at 1-Mb resolution for 9,172 wheat samples as a resource for breeders and scientists. We recommend that all plant genetic resources, including genebank collections, be characterized using a combination of variant calling and introgression prediction. This is necessary to identify potential duplicates in collections efficiently and reliably, and to select promising germplasms with potentially beneficial introgressions for further characterization and prospective breeding application.

Genomics and biochemical analyses reveal a metabolon key to ß-L-ODAP biosynthesis in Lathyrus sativus.

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, ß-L-oxalyl-2,3-diaminopropionic acid (ß-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce ß-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.

Insights into breeding history, hotspot regions of selection, and untapped allelic diversity for bread wheat breeding.

Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools.

Capturing Wheat Phenotypes at the Genome Level.

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Reaping the Potential of Wild Cajanus Species through Pre-Breeding for Improving Resistance to Pod Borer, Helicoverpa armigera, in Cultivated Pigeonpea (Cajanus cajan (L.) Millsp.).

Pod borer (Helicoverpa armigera) causes the highest yield losses in pigeonpea, followed by pod fly (Melanagromyza obtusa). High levels of resistance to pod borer are not available in the cultivated genepool. Several accessions of wild Cajanus species with strong resistance, and different resistance mechanisms (antixenosis and antibiosis) to pod borer have been identified. These accessions can be utilized to improve the pod borer resistance of cultivated pigeonpea. Using pod borer resistant Cajanus scarabaeoides and Cajanus acutifolius as pollen donors and popular pigeonpea varieties as recipients, pre-breeding populations were developed following simple- and complex-cross approaches. Preliminary evaluation of four backcross populations consisting of >2300 introgression lines (ILs) under un-sprayed field conditions resulted in identifying 156 ILs with low visual damage rating scores (5.0−6.0) and low pod borer damage (<50%). Precise re-screening of these ILs over different locations and years resulted in the identification of 21 ILs having improved resistance to pod borer. Because these ILs were derived from wild Cajanus species, they may contain different alleles for different resistance components to pod borer. Hence, these ILs are ready-to-use novel and diverse sources of pod borer resistance that can be utilized for improving the pod borer resistance of cultivated pigeonpea.

Detecting major introgressions in wheat and their putative origins using coverage analysis.

Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.

Reap the crop wild relatives for breeding future crops.

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.

Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat.

KEY MESSAGE: We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

The grain quality of wheat wild relatives in the evolutionary context.

KEY MESSAGE: We evaluated the potential of wheat wild relatives for the improvement in grain quality characteristics including micronutrients (Fe, Zn) and gluten and identified diploid wheats and the timopheevii lineage as the most promising resources. Domestication enabled the advancement of civilization through modification of plants according to human requirements. Continuous selection and cultivation of domesticated plants induced genetic bottlenecks. However, ancient diversity has been conserved in crop wild relatives. Wheat (Triticum aestivum L.; Triticum durum Desf.) is one of the most important staple foods and was among the first domesticated crop species. Its evolutionary diversity includes diploid, tetraploid and hexaploid species from the Triticum and Aegilops taxa and different genomes, generating an AA, BBAA/GGAA and BBAADD/GGAAAmAm genepool, respectively. Breeding and improvement in wheat altered its grain quality. In this review, we identified evolutionary patterns and the potential of wheat wild relatives for quality improvement regarding the micronutrients Iron (Fe) and Zinc (Zn), the gluten storage proteins α-gliadins and high molecular weight glutenin subunits (HMW-GS), and the secondary metabolite phenolics. Generally, the timopheevii lineage has been neglected to date regarding grain quality studies. Thus, the timopheevii lineage should be subject to grain quality research to explore the full diversity of the wheat gene pool.

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm.

Wheat (Triticum sp.) is one of the world's most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.

Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel-Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.).

The harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. The mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit-pedicel junction. The natural propensity for pedicel-fruit abscission zone (PFAZ) activation varies by cultivar, and the general molecular basis for PFAZ activation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time-course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In 'Skeena', mean PFRF for both control and treatment fruit dropped below the 0.40 kg-force (3.92 N) threshold for mechanical harvesting, indicating the activation of a discrete PFAZ. In 'Bing', mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in 'Chelan' the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ region followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts, as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for the induction or inhibition of PFAZ activation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.

Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints.

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.

Segmental duplications are hot spots of copy number variants affecting barley gene content.

Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and for identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16 605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. The present study delivers a comprehensive genome-wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs.

Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer.

Enhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. 'Oregon Spring' grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.

Genome-wide sequence information reveals recurrent hybridization among diploid wheat wild relatives.

Many conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome-wide sequence information, independent data were obtained from genotyping-by-sequencing and a target-enrichment experiment that returned 244 low-copy nuclear loci. The data were analyzed using Bayesian, likelihood and coalescent-based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat-group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species except Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa except Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat-group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case for tetraploid and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.

Non-Invasive Phenotyping Reveals Genomic Regions Involved in Pre-Anthesis Drought Tolerance and Recovery in Spring Barley.

With ongoing climate change, drought events are becoming more frequent and will affect biomass formation when occurring during pre-flowering stages. We explored growth over time under such a drought scenario, via non-invasive imaging and revealed the underlying key genetic factors in spring barley. By comparing with well-watered conditions investigated in an earlier study and including information on timing, QTL could be classified as constitutive, drought or recovery-adaptive. Drought-adaptive QTL were found in the vicinity of genes involved in dehydration tolerance such as dehydrins (Dhn4, Dhn7, Dhn8, and Dhn9) and aquaporins (e.g. HvPIP1;5, HvPIP2;7, and HvTIP2;1). The influence of phenology on biomass formation increased under drought. Accordingly, the main QTL during recovery was the region of HvPPD-H1. The most important constitutive QTL for late biomass was located in the vicinity of HvDIM, while the main locus for seedling biomass was the HvWAXY region. The disappearance of QTL marked the genetic architecture of tiller number. The most important constitutive QTL was located on 6HS in the region of 1-FEH. Stage and tolerance specific QTL might provide opportunities for genetic manipulation to stabilize biomass and tiller number under drought conditions and thereby also grain yield.

Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing.

Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.