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.

Recombination landscape divergence between populations is marked by larger low-recombining regions in domesticated rye.

The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, individuals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) individuals. By analysing population structure among individuals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analysed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye individuals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harbouring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected for during domestication to achieve more homogeneous populations for agricultural use.

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.

Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley.

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

Bacillus pasinlerensis sp. nov., a thermophilic bacterium isolated from a hot spring in Turkey.

A Gram-reaction-positive, endospore-forming bacterium, designated strain P1T, was isolated from water samples collected from Pasinler Hot Spring and characterized using a polyphasic approach to clarify its taxonomic position. Strain P1T was found to have chemotaxonomic and morphological characteristics consistent with its classification in the genus Bacillus. The strain shared the highest 16S rRNA gene sequence identity values with Bacillus thermolactis R-6488T (97.6 %) and Bacillus kokeshiiformis MO-04T (97.2 %) and formed a distinct clade with both type strains in the phylogenetic trees based on 16S rRNA gene sequences. Strain P1T could grow optimally at 55 °C and in the presence of 2 % NaCl. The organism was found to contain meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The predominant menaquinone was determined to be MK-7. The major cellular fatty acids were identified as iso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. Based upon the consensus of phenotypic and phylogenetic analyses, strain P1T represents a novel species of the genus Bacillus, for which the name Bacillus pasinlerensis sp. nov. is proposed. The type strain is P1T (=DSM 107529T=CECT 9885T=NCCB 100674T).

The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny.

Wheat belongs to the most important crops domesticated in the Fertile Crescent. In this region, fortunately, locally adapted wheat landraces are still present in farmers' fields. This material might be of immense value for future breeding programs. However, especially wheat germplasm adapted to the central part of the Fertile Crescent has been poorly characterized for allelic variation at key loci of agricultural importance. Grain hardness is an important trait influencing milling and baking quality of wheat. This trait is mainly determined by three tightly linked genes, namely, Puroindoline a (Pina), Puroindoline b (Pinb), and Grain softness protein-1 (Gsp-1), at the Hardness (Ha-D) locus on chromosome 5DS. To investigate genetic diversity and haplotype structure, we resequenced 96 diverse wheat lines at Pina-D1, Pinb-D1, Gsp-A1, Gsp-B1, and Gsp-D1. Three types of null alleles were identified using diagnostic primers: the first type was a multiple deletion of Pina-D1, Pinb-D1, and Gsp-D1 (Pina-D1k), the second was a Pina-D1 deletion (Pina-D1b); and the third type was a deletion of Gsp-D1, representing a novel null allele designated here as Gsp-D1k. Sequence analysis resulted in four allelic variants at Pinb-D1 and five at Gsp-A1, among them Gsp-A1-V was novel. Pina-D1, Gsp-B1 and Gsp-D1 sequences were monomorphic. Haplotype and phylogenetic analysis suggested that (1) bread wheat inherited its 5DS telomeric region probably from wild diploid Ae. tauschii subsp. tauschii found within an area from Transcaucasia to Caspian Iran; and that (2) the Ha-A and Ha-B homoeoloci were most closely related to sequences of wild tetraploid T. dicocco ides. This study provides a good overview of available genetic diversity at Pina-D1, Pinb-D1, and Gsp-1, which can be exploited to extend the range of grain texture traits in wheat.

Low radiation dose computed tomography coronary angiography: evaluation of the variations in coronary arteries.

OBJECTIVE: Despite attempts to decrease the radiation dose, coronary computed tomography angiography (CCTA) generally uses higher doses than computed tomography scans of other organs. The purpose of this study was to evaluate the incidence of the variations of the coronary arteries using the adaptive statistical iterative reconstruction technique to perform low-dose coronary computed tomography (CTA). METHODS: Diagnostic CCTA scans were performed in 3433 patients (from November 2010 to January 2015) using an Optima CT660 (GE Healthcare, USA) 64-slice and analyzed retrospectively. RESULTS: The mean effective dose was 2.1 mSv (1.2-4.9 mSv) for prospective and 4.5 mSv (3.6-9.1 mSv) for retrospective ECG-gated scans. The variations of the coronary arteries (CA) excluding myocardial bridge (MB) were detected in 76 (2.2 %) of the 3433 patients. A myocardial bridge was the most common variation (n = 288, 8.3 %). The second most common variation (n = 13, 17.1 %) was an absence of the left main coronary artery (LMCA) with separate starting points for the left anterior descending (LAD) and left circumflex (LCX) arteries. In addition, there was a rare variation (n = 1, 1.3 %) consisting of the LAD artery originating from the right coronary artery (RCA). CONCLUSIONS: The present retrospective study was conducted using CCTA on patients with a coronary artery variations in Turkey (n = 3433). Our data show that low-dose CCTA can be used to detect common coronary variations.

Mutagenic assessment of three synthetic pyridine-diaryl ketone derivatives.

Nowadays, there are increasing numbers of studies about synthetic chemicals according to the supply demands of bioactive chemicals. The current study aims to investigate genotoxic potential of bioactive synthetic pyridine compounds, phenyl-3-pyridinylmethanone (1), p-tolyl-3-pyridinylmethanone (2), and 4-methoxyphenyl-3-pyridinylmethanone (3), using Ames/Salmonella and Escherichia coli WP2 bacterial reversion mutagenicity test systems. The mutant bacterial tester strains sodium azide-sensitive Salmonella typhimurium TA1535, 9-aminoacridine-sensitive S. typhimurium TA1537, and N-methyl-N'-nitro-N-nitrosoguanidine-sensitive E. coli WP2uvrA were used to detect the mutagenic potential of the test compounds. The results indicated that none of the test substances showed significant mutagenic activity on S. typhimurium TA1535, TA1537, and E. coli WP2uvrA bacterial strains up to 1 µg/plate concentrations.

Effects of caffeic acid phenethyl ester on wound healing of nasal mucosa in the rat: an experimental study.

PURPOSE: Wound healing of the nasal mucosa is a highly complex process that restores the anatomical and functional integrity of tissue that has been exposed to trauma. In this experimental study, our aim was to use histopathological examination to investigate the effects of caffeic acid phenethyl ester on the wound healing of rat nasal mucosa after mechanical trauma. MATERIALS AND METHODS: The rats were randomly divided into 3 experimental groups: a non-treated group (n=7), a control saline group (n=7) and a caffeic acid phenethyl ester group (n=7). The non-treated group received no treatment for 15 days. The second group was administered saline (2.5 mL/kg, intraperitoneal) once a day for 15 days. The third group received caffeic acid phenethyl ester intraperitoneally at a dose of 10 µmol/kg once a day for 15 days. At the beginning of the study, unilateral mechanical nasal trauma was induced on the right nasal mucosa of all rats in the three groups using a brushing technique. Samples were stained using hematoxylin and eosin solution and were examined by a pathologist using a light microscope. RESULTS: The severity of inflammation was milder in the caffeic acid phenethyl ester group compared with that in the non-treated and saline groups (P<0.05). The subepithelial thickness index was lower in the experimental group (P<0.05). Goblet cell and ciliated cell loss was substantially reduced in the experimental group compared with the non-treated and saline groups (P<0.05). CONCLUSIONS: Caffeic acid phenethyl ester decreases inflammation and the loss of goblet cells and ciliated cells. Therefore, caffeic acid phenethyl ester has potential beneficial effects on the wound healing of nasal mucosa in the rat.

Determination of genotoxic and antigenotoxic properties of essential oil from Ferula orientalis L. using Ames/Salmonella and E. coli WP2 bacterial test systems.

The essential oils having many application fields such as medicine, flavoring, cosmetics are natural products obtained from aromatic plants. As the natural products of Ferula species have a wide range of use in folk medicine, this study was planned to evaluate the mutagenic and antimutagenic activities of essential oils of leaves and flowers of Ferula orientalis grown in Erzurum, through the bacterial reverse mutation assay. Furthermore, the chemical compositions of essential oils isolated by the hyrodistillation method were analysed by gas chromatography (GC) and gas chromatography-mass spectroscopy (GC-MS), as their biological activities were connected to their contents. According to our results, any tested essential oil at any used concentration on Salmonella typhimurium TA1535 and TA1537 strains and in Escherichia coli WP2 uvrA strain showed no mutagenic activity. However, the tested materials at different concentrations showed antimutagenic activities against the used mutagens. The inhibition rates ranged against sodium azide (NaN3) on S. typhimurium TA1535 from 29% to 36%, against 9-aminoacridine (9-AA) on S. typhimurium TA1537 from 40% to 68% and against N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) on E. coli WP2 uvrA from 23% to 52%, respectively. Also, it is revealed by GC and GC/MS analysis of the essential oils isolated from the leaves and flowers, respectively. The major compounds in these oils were determined as α-cadinol, δ-cadinene and germacrene D-4-ol. The results of this study indicate that as the essential oils of F. orientalis have many constituents, they show no mutagenic activity but significant antimutagenic activity, and these materials can be safely used in medicinal applications after further investigations.

Utilizing the Potential of Waste Hemp Reinforcement: Investigating Mechanical and Thermal Properties of Polypropylene and Polylactic Acid Biocomposites.

Hemp has gained significant popularity for its diverse applications; however, this study explores the untapped potential of waste hemp (wH) as a cost-effective and sustainable bioadditive for the development of high-performance biocomposites. wH offers advantages such as low cost, easy availability, and suitability for extrusion. Polypropylene (PP) and poly(lactic acid) (PLA) served as polymer matrices for this investigation. In order to enhance the interaction between the wH and polymer matrices, alkaline and silane pretreatments were applied to the wHs of both matrices. At the same time, the MA-g-PP additive was used exclusively for the PP matrix. The resulting PP biocomposite demonstrated Young's modulus (2986 MPa) and flexural modulus (2490 MPa), surpassing those of neat PP by 109 and 77%, respectively. Similarly, wH40-PLA-A showed enhancements in the PLA biocomposite, with Young's modulus (6214 MPa) and flexural modulus (5970 MPa) representing an increase of 81 and 56% over that of neat PLA, respectively. The thermal properties and behaviors of the resulting biocomposites were minimally affected by the inclusion of wH as a bioadditive. This study contributes to the advancement of sustainable materials and provides valuable insights into the utilization of wH as a valuable resource for the development of high-performance biocomposites.

Should an Inoue balloon larger than suggested by guidelines be used for percutaneous balloon mitral valvuloplasty?

BACKGROUND AND AIM OF THE STUDY: The study aim was to evaluate the immediate and long-term results of single inflation using a larger balloon size in patients with symptomatic rheumatic mitral stenosis (MS) METHODS: Among a study population of 231 patients with MS, percutaneous balloon mitral valvuloplasty (PBMV) was performed using the Inoue balloon technique. The ideal balloon size was measured according to the patients' height. Patients were allocated at random to two groups: a stepwise method was used in 115 patients (group 1), and a single-inflation method (with +2 mm larger balloon size) in 116 patients (group 2). Follow up was scheduled at six-month intervals for the first year, and annually thereafter. Patients were followed up until 2009. RESULTS: The mitral valve area (MVA) was increased from pre-PBMV values of 1.2 +/- 0.3 cm2 and 1.1 +/- 0.21 cm2 in groups 1 and 2, respectively, to post-PBMV values of 1.9 +/- 0.34 cm2 and 2.0 +/- 0.28 cm2 in groups 1 and 2, respectively; the increase in MVA for each group was statistically significant (p < 0.01) The mean transmitral pressure gradient (MMG) was decreased from pre-PBMV values of 14.1 +/- 5.5 mmHg and 13.2 +/- 5.9 mmHg in groups 1 and 2, respectively, to post-PBMV values of 5.9 +/- 2.3 mmHg and 5 +/- 2.5 mmHg in groups 1 and 2, respectively. One patient in group 2 underwent surgery due to severe mitral regurgitation. The procedure time was significantly shorter in group 2 (32 +/- 11.5 min versus 25 +/- 11 min; p < 0.001). The mean follow up duration was 49.5 +/- 19.2 months (range: 24-84 months). At the last follow up examination, the MVA was shown to be significantly larger in group 2 than in group 1 (1.65 +/- 0.3 versus 1.42 +/- 0.34 cm2; p = 0.02), while the MMG was lower (9 +/- 3.6 versus 6.7 +/- 3 mmHg; p = 0.017). CONCLUSION: The study results suggested that using a +2 mm larger balloon size with single overinflation may represent an alternative and effective therapy, with a shorter procedure time.

Experimental and Statistical Study on the Properties of Basic Oxygen Furnace Slag and Ground Granulated Blast Furnace Slag Based Alkali-Activated Mortar.

Basic oxygen furnace slag (BOFS) is a waste material generated during the steelmaking process and has the potential to harm both the environment and living organisms when disposed of in a landfill. However, the cementitious properties of BOFS might help in utilizing this waste as an alternative material in alkali-activated systems. Therefore, in this study, BOFS and blast furnace slag were activated with varying dosages of NaOH, and the fresh, physical, mechanical, and microstructural properties were determined along with statistical analysis to reach the optimal mix design. The test results showed that an increase in BOFS content decreased compressive and flexural strengths, whereas it slightly increased the water absorption and permeable pores of the tested mortar samples. On the contrary, the increase in NaOH molarity resulted in a denser microstructure, reduced water absorption and permeable pores, and improved mechanical properties. Statistically significant relationships were obtained through response surface methodology with optimal mix proportions, namely, (i) 24.61% BOFS and 7.74 M and (ii) 20.00% BOFS and 8.90 M, which maximize the BOFS content with lower molarity and improve the mechanical properties with lower water absorption and porosity, respectively. The proposed methodology maximizes the utilization of waste BOFS in alkali-activated systems and may promote environmental and economic benefits.

Next-Generation-Sequencing-Based Simple Sequence Repeat (SSR) Marker Development and Linkage Mapping in Lentil (Lens culinaris L.).

Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil (Lens culinaris) breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and diversity of SSR markers in lentil is limited. We used next-generation sequencing (NGS) technology to develop SSR markers in lentil. NGS allowed us to identify regions of the lentil genome that contained SSRs. Illumina Hiseq-2000 sequencing of the lentil genotype "Karacadag" resulted in 1,727,734 sequence reads comprising more than 48,390 Mb, and contigs were mined for SSRs, resulting in the identification of a total of 8697 SSR motifs. Among these, dinucleotide repeats were the most abundant (53.38%), followed by trinucleotides (30.38%), hexanucleotides (6.96%), tetranucleotides (6.59%), and pentanucleotides (3.19%). The most frequent repeat in dinucleotides was the TC (21.80%), followed by the GA (17.60%). A total of 2000 primer pairs were designed from these motifs, and 458 SSR markers were validated following their amplified PCR products. A linkage map was constructed using these new SSRs with high linkage disequilibrium (209) and previously known SSRs (11). The highest number of SSR markers (43) was obtained in LG2, while the lowest number of SSR markers (19) was obtained in LG7. The longest linkage group (LG) was LG2 (86.84 cM), whereas the shortest linkage group was LG7 (53.46 cM). The average length between markers ranged from 1.86 cM in LG1 to 2.81 cM in LG7, and the map density was 2.16 cM. The developed SSRs and created linkage map may provide useful information and offer a new library for genetic diversity analyses, linkage mapping studies, and lentil breeding programs.

Evaluation of wool protein hydrolysate as peptone for production of microbial enzymes.

Peptones are one of the most expensive components of microbial culture media. The present study was conducted to test the usability of low-cost sheep wool peptone (SWP) as an organic nitrogen source in the production of six industrially important enzymes (lipase, amylase, tannase, pectinase, cellulase and invertase). SWP was prepared by alkaline hydrolysis and acid neutralization. Bacillus licheniformis and Aspergillus niger were selected as test microorganisms for enzyme production. To evaluate the efficacy of SWP in enzyme production, it was compared with commercial tryptone peptone (TP) in the shaking flask cultures of the test microorganisms. The optimum concentration of both SWP and TP was determined to be 8 g/L for the production of B. licheniformis-derived enzymes, but 6 g/L for the production of A. niger-derived enzymes. It was determined that SWP was superior to TP in the production of four enzymes (lipase, amylase, tannase and pectinase) of both B. licheniformis and A. niger. This is the first study about the usage of sheep wool protein hydrolysate (SWP) as an organic nitrogen source or a peptone in fermentative production of microbial enzymes.

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.

Prognostic value of CHA2DS2-VASc score for the long-term cardiovascular events after coronary artery bypass grafting.

Background: This study aims to investigate the value of the CHA2DS2-VASc score in predicting long-term major cardiovascular events following coronary artery bypass grafting. Methods: Between January 2008 and January 2010, a total of 559 patients (445 males, 114 females; mean age: 62.7±9.1 years; range, 35 to 84 years) who underwent elective coronary artery bypass grafting were retrospectively analyzed. At a mean of 10.7±3.1-year follow-up, major cardiovascular events were considered as the primary endpoint. Results: The multivariate Cox hazard analysis identified the CHA2DS2-VASc score as an independent predictor of major cardiovascular events (hazard ratio: 1.615; 95% confidence interval: 1.038-2.511; p=0.034). The receiver operating characteristic curve analyses revealed that 3.5 was the most optimal cut-off value of the score predicting major cardiovascular events and the patients were divided into two groups accordingly. The Kaplan-Meier analysis demonstrated a significantly higher incidence of major cardiovascular events in proportion to a higher CHA2DS2-VASc score (p<0.001). Conclusion: CHA2DS2-VASc score ≥4, which includes many risk factors for cardiovascular events, can be used as an independent predictor of long-term major cardiovascular events after coronary artery bypass grafting.

A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [Triticum turgidum L. subsp. dicoccoides (Körn. ex Asch. & Graebn.) Thell] accessions, representative of the entire Fertile Crescent region where wild emmer naturally occurs, was assembled, genotyped, and characterized for population structure, genetic diversity, and rate of linkage disequilibrium (LD) decay. Then, the collection was employed for mapping Pgt resistance genes, as a proof of concept of the effectiveness of genome-wide association studies in wild emmer. The collection was evaluated in controlled conditions for reaction to six common Pgt pathotypes (TPMKC, TTTTF, JRCQC, TRTTF, TTKSK/Ug99, and TKTTF). Most resistant accessions originated from the Southern Levant wild emmer lineage, with some showing a resistance reaction toward three to six tested races. Association analysis was conducted considering a 12K polymorphic single-nucleotide polymorphisms dataset, kinship relatedness between accessions, and population structure. Eleven significant marker-trait associations (MTA) were identified across the genome, which explained from 17% to up to 49% of phenotypic variance with an average 1.5 additive effect (based on the 1-9 scoring scale). The identified loci were either effective against single or multiple races. Some MTAs colocalized with known Pgt resistance genes, while others represent novel resistance loci useful for durum and bread wheat prebreeding. Candidate genes with an annotated function related to plant response to pathogens were identified at the regions linked to the resistance and defined according to the estimated small LD (about 126 kb), as typical of wild species.

Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.

Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.