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Aims Diversity of root systems among genetic resources can contribute to optimize water and nutrient uptake. Topsoil exploitation vs. deep soil exploration represent two contrasting ideotypes in relation to resource use. Our study reveals how rooting patterns changed between wheat wild progenitors and landraces in regard to these ideotypes. Methods Root (partitioning, morphology, distribution, elongation, anatomy) and shoot traits (dry-matter, leaf area, assimilation) of durum landraces, wild emmer and wild einkorn from Iran, Syria, Turkey and Lebanon were phenotyped using the GrowScreen-Rhizo platform. Distinctive rooting patterns were identified via principal component analysis and relations with collection site characteristics analyzed. Results Shoot trait differentiation was strongly driven by seed weight, leading to superior early vigor of landraces. Wild progenitors formed superficial root systems with a higher contribution of lateral and early-emerging nodal axes to total root length. Durum landraces had a root system dominated by seminal axes allocated evenly over depth. Xylem anatomy was the trait most affected by the environmental influence of the collection site. Conclusions The durum landrace root system approximated a deep soil exploration ideotype which would optimize subsoil water uptake, while monococcum -type wild einkorn was most similar to a topsoil exploiting strategy with potential competitive advantages for subsistence in natural vegetation.

Key messageA novel recessive gene YrZ15-1370 derived from Triticum boeoticum confers adult–plant resistance to wheat stripe rust.Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most damaging diseases of wheat globally and resistance is the effectively control strategy. Triticum boeoticum Boiss (T. monococcum L. ssp. aegilopoides, 2n = 2x = 14, AbAb) accession G52 confers a high level of adult–plant resistance against a mixture of the Chinese prevalent Pst races. To transfer the resistance to common wheat, a cross was made between G52 and susceptible common wheat genotype Crocus. A highly resistant wheat-T. boeoticum introgression line Z15-1370 (F5 generation) with 42 chromosomes was selected cytologically and by testing with Pst races. F1, F2, and F2:3 generations of the cross between Z15-1370 and stripe rust susceptible common wheat Mingxian169 were developed. Genetic analysis revealed that the resistance in Z15-1370 was controlled by a single recessive gene, tentatively designated YrZ15-1370. Using the bulked segregant RNA-Seq (BSR-Seq) analysis, YrZ15-1370 was mapped to chromosome 6AL and flanked by markers KASP1370-3 and KASP-1370-5 within a 4.3 cM genetic interval corresponding to 1.8 Mb physical region in the Chinese Spring genome, in which a number of disease resistance-related genes were annotated. YrZ15-1370 differed from previously Yr genes identified on chromosome 6A based on its position and/or origin. The YrZ15-1370 would be a valuable resource for wheat resistance improvement and the flanking markers developed here could be useful tools for marker-assisted selection (MAS) in breeding and further cloning the gene.

Prehistoric cultivation of wild wheat in the Fertile Crescent led to the selection of mutants with indehiscent (nonshattering) ears, which evolved into modern domestic wheat. Previous estimates suggested that this transformation was rapid, but our analyses of archaeological plant remains demonstrate that indehiscent domesticates were slow to appear, emerging approximately 9500 years before the present, and that dehiscent (shattering) forms were still common in cultivated fields approximately 7500 years before the present. Slow domestication implies that after cultivation began, wild cereals may have remained unchanged for a long period, supporting claims that agriculture originated in the Near East approximately 10,500 years before the present.

A survey of genome-wide polymorphisms between closely related species is required to understand the molecular basis of the evolutionary differentiation of their genomes. Two wild diploid wheat species, namely Triticum monococcum ssp. aegilopoides and T. urartu, are closely related and harbour the Am and A genomes, respectively. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat subspecies aegilopoides. Although subspecies aegilopoides has been a useful genetic resource in wheat breeding, genome-wide molecular markers for this subspecies have not been sufficiently developed. Here, we describe the detection of genome-wide polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The SNPs and indels, detected using the A genome of common wheat as the reference genome, covered the entire chromosomes of these species. The polymorphism information facilitated a comparison of the genetic diversity of einkorn wheat with that of two related diploid Aegilops species, namely, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the addition of aegilopoides subspecies chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genomes. In addition, the CAPS markers permitted linkage map construction in mapping populations of aegilopoides subspecies accessions. Therefore, these RNA-seq data provide information for further breeding of closely related species with no reference genome sequence data.

Crop Wild Relatives (CWR) are wild plants that are genetically related to cultivated crops. Conserving the genetic diversity of CWR is essential for maintaining the sustainability of agriculture and food production in the face of various anthropogenic and environmental pressures. In this study we aim to contribute to the conservation planning of CWR taxa in Lebanon, in particular, to document ecogeographic survey and collection missions, carried out in 2022 and 2023, to assess the presence and conservation status of CWR taxa populations belonging to Poaceae and Fabaceae families and eventually propose sites for in situ conservation based on collected data. Ecogeographic and botanical surveys were carried out using the transect method and targeting priority CWR taxa. Agrobiodiversity trends, based on distribution data available in public databases, were compared with the current occurrence of the priority CWR taxa. Preliminary observations of disturbances (e.g. grazing, urbanization) were also documented to serve as a baseline for future monitoring of agrobiodiversity. Additional survey and collection missions were specifically targeted on wild Triticum populations. Forty-seven sites were surveyed, in which 500 new records for target CWR taxa (Aegilops L., Triticum L., Avena L., Hordeum L., Cicer L., Lens Mill. and Pisum L. genera) were documented. A total of 17 new collections were performed and the material stored in ICARDA genebank. Two sites (Yanta/Kfarqouq and Ham) were recommended for the in situ conservation of wild Triticum as well as two other sites for conservation of wild Lens culinaris Medik. Several concerns were raised, mainly the declining distribution of Triticum boeoticum and Triticum urartu over the last 30 years, as well the absence of Cicer taxa in the two years of surveys. The collection of 500 CWR occurrence data points for the target taxa provides a solid ground for future analyses, including ecogeographic and predictive characterization approaches, to identify the best areas for establishing genetic reserves for active in situ protection of these crucial taxa in Lebanon, which is urgently needed.

Genetic diversity of 139 accessions of diploid Triticum species including Triticum urartu , Triticum boeoticum and Triticum monococcum was studied using 11 SSR (simple sequence repeats) markers. A total of 111 alleles with an average of 10 alleles per locus were detected. The polymorphism information content (PIC) of each SSR marker ranged from 0.30 to 0.90 with an average value of 0.62. Among the three Triticum species T. urartu had the highest number of total alleles (Na = 81), private alleles (Npa = 15) and showed higher genetic diversity (Hex = 0.58; PIC = 0.54). The genotypes from Turkey exhibited the highest genetic diversity (PIC = 0.6), while the least diversity was observed among 4 Georgian accessions (PIC = 0.11). Cluster analysis was able to distinguish 139 wheat accessions at the species level. The highest genetic similarity (GS) was noted between T. boeticum and T. monococcum (GS = 0.84), and the lowest between T. urartu and T. monococcum (GS = 0.46). The grouping pattern of the PCoA analysis corresponded with cluster analysis. No significant differences were found in clustering of T. urartu and T. monococcum accessions with respect to their geographic regions, while within T. boeoticum species, accessions from Iran were somewhat associated with their geographical origin and clustered as a close and separate group. The results from our study demonstrated that SSR markers were good enough for further genetic diversity analysis in einkorn wheat species.

Key messageAllotetraploidization drives Glu-1Ay silencing in polyploid wheat.The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41.21% accessions), 13 alleles with PTCs and 1 allele with a WIS 2-1A retrotransposon were present in wild tetraploid wheat; and only silenced alleles with PTC or WIS 2-1A were in cultivated tetra- and hexaploid wheat. Both the PTC number and position in T. urartu Glu-1Ay alleles (one in the N-terminal region) differed from its progeny wild tetraploid wheat (1–5 PTCs mainly in the repetitive domain). The WIS 2-1A insertion occurred ~ 0.13 million years ago in wild tetraploid wheat, much later than the allotetraploidization event. The Glu-1Ay alleles with PTCs or WIS 2-1A that arose in wild tetraploid wheat were fully succeeded to cultivated tetraploid and hexaploid wheat. In addition, the Glu-1Ay gene in wild einkorn inherited to cultivated einkorn. Our data demonstrated that the silencing of Glu-1Ay in tetraploid and hexaploid wheat was attributed to the new PTCs and WIS 2-1A insertion in wild tetraploid wheat, and most silenced alleles were delivered to the cultivated tetraploid and hexaploid wheat, providing a clear evolutionary history of the Glu-1Ay gene in the wheat polyploidization and domestication processes.

The majority of cultivated wheat varieties have glaucous spikes, leaves and leaf sheaths, and the non-glaucous phenotype is rare in modern varieties. The glaucousness/non-glaucousness phenotype is not selectively neutral. It was expected that wild wheat may be the source of the allele to control non-glaucousness. We developed near-isogenic lines of durum wheat ‘LD222’ for glaucousness inhibitor loci Iw1, Iw3 and Iw4 derived from wild relatives. The Iw1 locus was derived from ‘MG4343’, an accession of Triticum dicoccoides (Körn. ex Asch. et Graebn.) Schweinf. (2n = 4x = 28, BBA u A u genome), and Triticum aestivum L. s. str. (2n = 6x = 42, BBA u A u DD genome) ‘Shamrock’. The Iw3 locus in chromosome arm 1BS is unique in tissue specificity of wax regulation in the spikes. The Iw3 locus was introduced from the lines that originated from crosses with T. dicoccoides and Aegilops speltoides Tausch (2n = 2x = 14, SS genome) for two near-isogenic lines. The allelic variation for A-genome non-glaucous gene has not been recorded in polyploid wheat. The Iw4 m allele for non-glaucousness was introduced from the wild einkorn, Triticum boeoticum Boiss. (2n = 2x = 14, A m A m genome).

Einkorn wheat is known as the donor of ‘A’ genome to cultivated wheat and source of many important genes. Therefore, genetic erosion in cultivated wheat provides a good reason to investigate genetic diversity in these species. In the present study, genetic diversity of 14 populations of Triticum urartu and Triticum boeoticum collected from west and north-west of Iran was examined by IRAP and REMAP markers. In total, 26 out of 36 IRAP and 41 out of 88 REMAP combinations amplified polymorphic and scorable banding patterns. IRAP and REMAP combinations produced 6.53 and 5.21 polymorphic bands per assay, respectively. Mean of polymorphism information content for IRAPs and REMAPs were 0.38 and 0.40 and marker index values for them were 2.60 and 2.09, respectively. Analysis of molecular variance based on IRAP and REMAP data revealed significant within and among population variances, although within population variance was higher than that of among population. Primer combinations based on Sukkula and Nikita retrotransposons produced the highest number of markers in the whole population. Cluster and principal coordinate analyses using REMAP data grouped the populations based on the species and geographical origin, but grouping based on IRAP could not separate the two species. However, based on both marker systems considerable diversity was observed among and within the studied populations.

The status of Triticum boeoticum subsp. aegilopoides (Link) Schiem. is somehow confusing, suggesting a need to verify whether this subspecies is a truly wild or a feral form. After reviewing some rather inaccessible older literature, a half-diallel of three pure einkorn lines (truly wild, domesticated and aegilopoides ) was performed. The F 2 and F 3 analyses of brittleness and microscope-based studies of the abscission scars on rachis fragments were combined with extant genome maps. Two QTL segregated in the cross domesticated × wild (one on chromosome 4 and one on chromosome 7), but only one segregated in the cross feral × wild (same as before on chromosome 7), indicating that the feral form carried a wild (or equivalent) allele. Within the cross domesticated × feral, quantitative segregation occurred and could be caused by some neat abscission scars, but without the typical ‘fish-mouth-like’ appearance of the truly wild form. We suggest that aegilopoides and domesticated einkorn emerged in patches of semi-brittle mutants in the Karacadağ Mountains and were collected and maintained by humans. When agriculture moved from South-East Turkey into Western Turkey and later into the Balkans, aegilopoides became the feral form we know today, characterized by a semi-brittle rachis that makes it less wild compared to the truly wild Triticum boeoticum subsp. thaoudar (Reut. ex Hausskn.) Grossh.