Fruit aroma is an important quality with respect to consumer preference, but the most important aroma compounds and their genetic regulatory mechanisms remain elusive.VvCYP (VIT_08s0007g07730), 2 VvCCR , 3 VvADH , and 1 VvSDR (VIT_08s0040g01200) in the phenylpropanoids synthesis pathway, and 1 VvDXS (VIT_05s0020g02130) and 6 VvTPS  in the methylerythritol phosphate pathway (involved in the production and accumulation of aromatic compounds). Additionally, 2 VvMYB  and 1 VvGATA (VIT_15s0024g00980) transcription factor played important regulatory roles in the accumulation of key biosynthetic precursors of these compounds in grapes. Our results indicated that downstream genes, specifically 1 VvBGLU (VIT_03s0063g02490) and 2 VvUGT  are involved in regulating the formation and volatilization of bound compounds in grapes.In this study, we qualitatively analysed volatile compounds in the pulp and skin of five table grape cultivars with three aroma types  using solid-phase microextraction gas chromatography/mass spectrometry. We identified 215 aroma compounds, including 88 esters, 64 terpenes, and 29 alcohols, and found significant differences in the number of compounds between the pulp and skin, especially for terpenes. Skin transcriptome data for the five grape cultivars were generated and subjected to aroma compound-gene correlation analysis. The combined transcriptomic analysis and terpene profiling data revealed 20 candidate genes, which were assessed in terms of their involvement in aroma biosynthetic regulation, including 1 The results of this study shed light on the volatile compounds and “anchor points” of synthetic pathways in the pulp and skin of muscat and strawberry grapes, and provide new insight into the regulation of different aromas in grapes.The online version contains supplementary material available at 10.1186/s12870-023-04191-1. Aroma is one of the most important indicators of fruit quality. Aroma involves both taste and smell. Aroma is influenced by a variety of factors that are important for breeding . VolatilPathways for the synthesis of aromatic substances in plant fruits include fatty acid metabolism, amino acid metabolism, terpene metabolism, and monosaccharide and glycoside metabolism. The aromatic substances in fruit are mainly derived from saturated and unsaturated fatty acids, which are metabolized by the aerobic pathway of fatty acid metabolism (including lipoxygenase and β-oxidation pathways) to form straight-chain fatty alcohols, aldehydes, ketones, acids, and esters . Amino aHorticultural research has shown that fruit flavour varies greatly depending on the species of fruit tree. Generally, the aromatic composition of fruit is “purer” than that of other foodstuffs, and most have a natural (light or strong) aromatic smell , 9. MoreVitis vinifera L.) is one of the most widely cultivated and economically important fruit crops. Because a rich aroma is essential for table and wine grape quality, numerous studies have focused on aroma characteristics. At present, more than 2,000 volatile components have been identified in grapes [6 compounds and alcohols. Rocha [Grape , our understanding of volatile compounds has increased dramatically. These volatiles, acting as free or bound chemicals, contribute to fruit aroma. However, only volatiles with odour activity values  > 1 are considered to contribute to the characteristic aroma. The aroma of grapes is complex, of which it is mainly known for its muscat and strawberry. The aroma of muscat grapes has been extensively studied; however, little attention has been paid to strawberry aroma or differences in aroma substances between strawberry- and muscat-scented grapes. Compared with other fruits, the genetic mechanisms underlying the biosynthesis and metabolism of grape berries have only just begun to be elucidated. The compounds underlying the different aromas of grape cultivars have yet to be fully resolved, and the regulatory genes also remain to be elucidated. To fully evaluate the aroma characteristics of strawberry and muscat aromas, the volatile compounds and regulatory genes must be analysed in more detail.In this study, we evaluated volatile compounds in the pulp and skin of five table grapes with two aroma types, muscat aroma  and strawberry aroma (‘Summer Black’), as well as a neutral grape (‘Victoria’), using SPME-GC-MS. The unscented ‘Victoria’ was used as a control to investigate the specific composition of each aroma type. The skins of the grapes with different aromas were subjected to transcriptome sequencing. Association analysis of volatile compounds with differentially expressed genes (DEGs) revealed by transcriptome sequencing was used to identify candidate genes after controlling for the different aromas of the grapes. The results from this provide insight into the main substances in muscat and strawberry grapes and lay a foundation for further investigations of the genetic mechanisms of grape aroma.Basic parameters of the grapes, including the TSSs (A), TA (B), berry weight (C), and skin CIRG (D) were measured Fig. . The meaThe volatile aroma components in the five cultivars of cultivated grapes with different aromas were analysed by SPME-GC-MS, and ion flow diagrams of the volatile aroma components in the skins and pulps of the grapes were obtained Figure  and S2. The total volatile compound contents exhibited significant differences between the skin and pulp in the five grape cultivars . Among these compounds, terpenes and aldehydes were dominant in the skin of strawberry and muscat cultivars, whereas ester and aldehydes were the main volatiles in the skin of the neutral cultivar. Notably, terpenes and esters were the dominant compounds in the pulp of strawberry and muscat cultivars. The differences in composition and content of volatile compounds between the skin and pulp suggest that the aroma may be synthesized and metabolized in different ways in these compartments.The volatile compound contents in the skin were significantly higher than those in pulp  than in Victoria . In the pulp, however, there was no significant difference in the extracted compounds with and without aromas.In the skins, terpenes (with the exception of 1-nonene) were detected only in aromatic grapes, in widely varying amounts; specifically, citronellol, 4-terpineol, and terpinen-4-ol were detected only in Summer Black, which has a strawberry aroma. 3-carene, cis-geraniol, and citral were only detected in the muscat-fragranced species. Hexanal and octanal in the aldehyde species, benzyl alcohol and 1-undecanol in the alcohols, and 2-hydroxy-benzoicacimethylester in the esters were detected in the neutral grapes. In addition, 1-octanol, geranyl butyrate, (E)-3,7-dimethyl-2,6-octadienal, and damascene were detected only in the muscat-scented cultivars.In the pulp, very few threshold aroma components were detected. Terpenes and ketones were found only in the aromatic grapes. Dipentene, 1-nonene, linalool, geranic acid (among the terpenes), and geranyl acetone (among the ketones) were detected only in the muscat cultivars. Among the esters, with the exception of octyl formate, which was detected only in the aromatic grapes, the amount of octyl formate did not vary significantly between the different aromas; methyl dodecanoate and diisobutyl phthalate were detected only in the aromatic cultivars, and their OVA values were small. Beta-damascenone belonged to ‘C13-norisoprenoids’ and 1-Octanol belonged to the ‘alcohols’, but was detected in all five grape cultivars. Moreover, the differences were not significant, so it was not a major contributor to the differences in pulp aroma. Among these substances, some had an OVA value < 3 still contributed significantly to the aroma of the grape berries, due to their low threshold values. The alcohols and aldehydes presented with little odour due to their high thresholds; for example, trans-2-hexenal was the active aldehyde in Victoria, but had neutral. The differences in these components contributed to the fruity aroma of the cultivars.There was no clear pattern in the volatile content of the various aroma types, and few volatiles contributed to the aroma of the fruit. PCA is a multivariate analysis technique used to downscale datasets to resolve the correlations between variables and samples , 23. As The results of the multivariate analysis of the five grape cultivars with different aromas are shown in Fig. To identify the key compounds responsible for differences in aroma, OPLS-DA was conducted between pairs of the three cultivar aroma types, and showed that the samples could be classified effectively by the models Fig. . SignifiAfter analysis of the physiological parameters and terpene profiles of the skins and pulps of five cultivars of grapes in the three growth periods, samples in the ripening stage were subjected to RNA-seq gene expression analysis. The HiSeq™ 2500 system  was used to sequence CK1-3, XP1-3, MP1-3, WP1-3, and YP1-3 cDNA libraries. After rigorous quality checks and data cleaning, a total of 97.67 Gb of clean data was obtained, with each sample having 5.78 Gb of clean data. The percentage of Q30 bases was > 92.69%  ≥ 2 and FDR ≤ 0.01 were considered significantly different. There were 1,814 DEGs between neutral and strawberry grapes in the ripening stage, of which 656 DEGs were up-regulated and 1,158 were down-regulated. Of the 537 DEGs between neutral and muscat aroma grapes, 358 were up-regulated and 179 were down-regulated , one VvSDR (VIT_08s0040g01200), two VvCCR , and three VvADH  genes. Of these genes, only VIT_08s0007g07730 and VIT_13s0047g00940 were highly expressed in neutral grapes; the rest were highly expressed in aromatic grapes.Combining the GO and KEGG enrichment results revealed128 genes that may be directly involved in the biosynthesis of grape aroma compounds. The biosynthesis of benzene-containing aroma compounds in plants involves the conversion of shikimic acid to phenylalanine, which enables primary and secondary metabolism. Analysis of aroma synthesis and metabolic processes revealed that 4-coumarate: coenzyme A ligase (4CL) and cinnamoyl-CoA reductase (CCR) were mainly enriched in upstream floral aroma synthesis processes. The DEGs included one Furthermore, combining our previous aroma studies with the transcriptome sequencing results of this experiment indicated that one 1-deoxy-d-xylulose-5-phosphate synthase  gene was differentially expressed among cultivars with different aromas, and high expression was seen in grapes with muscat aroma. Among the other five MEP pathway genes, DXR , MCT , CMK , CMS , HDR (4-hydroxy-3-methylbut-2-enyl diphosphate), UDP-glycosyltransferase , and β-glucosidase  were mainly enriched in the downstream stages of floral aroma compound synthesis. However, the gene VIT_17s0000g07060 was highly expressed in neutral grapes.VvTPS genes were found , the first five of which were highly expressed in grapes with strawberry aroma. VIT_00s0271g00010 was present in grapes with muscat aroma and VIT_13s0067g00050 was expressed in unscented grapes. These results suggest that different genes in the same family have different functions.The final step of terpenoid biosynthesis is catalysis by terpene synthase (TPS) enzymes. TPS expression is usually associated with terpene-rich grapes. However, in this experiment, six Transcription factors (TFs) can control and regulate the expression levels of target genes by binding to promoter regulatory elements. The differential TFs in this experiment and previous studies on grape aroma identified one GATA (VIT_15s0024g00980) and two MYB  TFs, suggesting that these TFs may be important for regulating the biosynthesis of volatile compounds. Furthermore, of the three TFs, only VIT_03s0063g02620 was highly expressed in aromatics, suggesting a negative regulatory role.−ΔΔct from qRT-PCR, correlation coefficients near 0.8 were obtained for these gene, respectively, indicating that the RNA-Seq data were reliable.To validate the reliability of the RNA-seq data, gene expression analyses of 20 putative terpene biosynthesis genes were performed by qRT-PCR across different cultivars Fig.  and S6. Grapes, as the second most produced fruit in the world, are widely grown and have an important role in winemaking, due to the differences in flavour among the many cultivars. The distinctive flavour of fresh grapes arises from the balance between sweet and sour tastes in the fruit, and the content of volatile substances. In recent years, identifying the aromatic compounds in grapes has been a key target for studies of aroma . Grape bMuscat aroma is closely related to the content of terpenes, the most abundant of which are monoterpenes including linalool, geraniol, nerolidol, citronellol, geranic acid, and α-terpinol . Fenoll Strawberry aromas are mainly found in American grape cultivars and hybrids with other species, and the characteristic aroma substances are mainly esters , 28. Lin6 compounds account for the majority of aromatic substances [6 compounds to be important flavour compounds in grapes. Moreover, they are of great value for evaluating the quality of grapes and determining their origin. In the current study, two alcohols and three aldehydes, along with one ketone and one ester, were the main aroma components of the neutral cultivar, with trans-2-hexenal being the most abundant compound, followed by octanal and hexanal. These substances contributed less to the aroma due to their high threshold values, in agreement with previous studies [Terpenoids and esters are rare in neutral cultivars of grapes; their concentrations tend to be low or almost non-existent, mainly because Cbstances . Oliveir studies . DihydroVvCYP DEG, two VvCCR DEGs, three VvADH DEGs, and one VvSDR DEG were detected in the transcriptome of grapes. VvCCR (VIT_13s0047g00940) and VvCYP were highly expressed in grapes without an aroma; VvCCR (VIT_13s0067g00620), VvADH, and VvSDR genes were highly expressed in grapes with an aroma, but their specific regulatory roles are still unknown.Phenylpropanoids volatiles were mainly synthesized from phenylalanine and produced via the shikimate, prephenate, and arogenate synthesis pathways. A number of enzymes were involved in the synthesis of phenylalanine, including CCR, ADH, SDR, and CYP. Notably, SDR genes are involved in many aspects of primary and secondary metabolism, especially in carbonyl-alcohol redox . The SDRVvDXS DEG and six VvTPS DEGs were identified. When volatile components were analysed in different aromatic grapes, differences in terpenoid composition and content were found between strawberry and muscat aromatic grapes, just as the expression of relevant genes differed among aromatic grapes. VvDXS (VIT_05s0020g02130) and VvTPS (VIT_00s0271g00010) were highly expressed in muscat grapes. VvTPS  were highly expressed in the strawberry grape. In contrast, TPS (VIT_13s0067g00050) was highly expressed in the neutral grape. These results suggest that different VvTPS genes have different functions, and that these genes  play an important role in terpene synthesis in muscat and strawberry grapes.The metabolic pathways of terpenoids are well understood and conserved across species. DXS is the rate-limiting enzyme in the MEP pathway, and phylogenetic analysis of DXSs from other species revealed that this protein is primarily involved in terpenoid synthesis . TPS catVvUGT genes (VIT_17s0000g07070 and VIT_17s0000g07060) potentially involved in the synthesis and volatilization of grape terpenoids by comparative transcriptome analysis.GTs are a multi-member gene family, and glycosylation refers to the process of covalent binding of some sugars or non-sugar biomolecules to additional glycosyl groups catalysed by GTs . GTs regPmBGLU produces more fragrance, which allows the flowers to release more aromatics [One DEG (VIT_03s0063g02490) was annotated as BGLU in this study. BGLU is widely expressed in plant tissues and acts mainly in the pre-hydrolysis of aroma compounds, converting aromatic substances in plants from the bound to the free state and releasing aroma volatiles , 43. BGLromatics . In thisPhMYB indirectly inhibits the synthesis of coumaric acid derivatives in Petunia [PmMYB4 gene was significantly more abundant in ‘Xiangxuegongfen’ than in ‘Xiao lve’, and was enriched in of phenolic-containing compounds and phenylpropanoid biosynthesis, which can affect the aroma of plum blossom [Previous studies have shown that TFs known as trans-acting molecules can regulate proteins in gene transcription during plant growth and associated with fragrance synthesis. A variety of TFs were found that could play various roles in the regulation of aroma biosynthesis. The expression profiles of some TFs, including MYB, GATA were also found to be positively related to the monoterpenoid content in this study. MYB TF are commonly in plants. The plant MYB TF family consists of four subclasses: 1R-MYB, R2R3-MYB, R1-MYB, and 4R-MYB. of which R2R3-MYB is the largest class, not only involved in the physiological processes of plant stress resistance, but also responds to JA signals and is an important transcription factor regulating the synthesis of flavonoids and terpenoids , 46. In  Petunia . In plum blossom . GATA TF blossom . GNC, a  blossom , which hIn the current study, analysis of transcriptome data showed that two MYB TFs  and one GATA TF (VIT_15s0024g00980) were differentially expressed in grapes with versus without aroma. However, the expression of the three TFs showed opposite trends: VIT_17s0000g07950 and VIT_15s0024g00980 were highly expressed in grapes with an aroma, whereas gene VIT_03s0063g02620 was highly expressed in neutral grapes; this indicates that these TFs are not involved in aroma metabolism. These results also indicate that VIT_17s0000g07950 and VIT_15s0024g00980 are more important in the aroma synthesis pathway in grape. The synthesis of plant terpenoids is a complex process in which a series of enzymes encoded by structural genes are involved in the synthesis of various compounds related to the terpene pathway. Transcription factors specifically bind to recognizable cis-elements in the promoters of structural genes, and ultimately regulate the synthesis of terpenoids by up- or down-regulating the expression of structural genes. However, the regulatory role of TFs in grape volatile compound synthesis needs to be further explored if the molecular mechanisms involved in the biosynthesis of these aromatic compounds are to be fully elucidated.VvMYB and VvGATA TFs may play important regulatory roles in the accumulation of aromatic compound biosynthetic precursors in grapes. In addition, the VvCYP, VvCCR, VvADH, VvSDR, VvDXS and VvTPS genesplay important roles in the production and accumulation of aromatic compounds. VvBGLU and VvUGT genes may be key for controlling the morphology of bound compounds. These results show that volatiles play a key role in the formation of aroma in grape and transcriptome provides a basis for further exploration of the regulatory mechanisms of grape aroma compounds.This study revealed some differences in the aroma composition and active aromatic substances among neutral, muscat, and strawberry grapes. The neutral grape had the lowest number of aromatic components. The concentration of terpenes was significantly higher in the muscat grapes than in the other aroma cultivars. Diisobutyl phthalate, citronellol, and phenethyl alcohol were unique to strawberry grapes and contributed strongly to its aroma. Based on the aroma characteristics and taste experience as well as the holding of experimental materials, four table grape cultivars, including ‘Summer Black’ (XP), ‘Shine Muscat’ (YP), ‘Midnight Beauty’ (MP), ‘Centennial Seedless’ (WP), which had one of typical aroma types , and neutral grape ‘Victoria’ (VP), were collected from a single vineyard . The 5-year-old plants were planted with a spacing of 3 m × 2 m. In the 2019 growing season, samples were collected between 2 weeks before the ripening stage (− 2 wrs) and 2 weeks thereafter (2 wrs). The pulp and skin samples at the three maturity stages  were used to determine aroma composition and content, and skin samples corresponding to the three maturity stages were used for RNA-sequencing (RNA-seq). For each sample, three bunches of grapes were randomly picked from three vines as one replicate and then transported to the laboratory at 4℃. After standard physicochemical analyses, including of total soluble solids (TSSs), titratable acidity (TA), berry weight, and fruit skin colour, the remaining samples were frozen at − 80°C until the aroma analysis was performed. TSSs were determined using an Abbé refractometer . TA is expressed as grams of tartaric acid per 10 g of fresh weight, as determined by titration with NaOH to a final pH of 8.1 using an automatic titration system .L, a, and b values of skin colour differences were determined using a CR-400 portable colorimeter , and the colour saturation chroma (C), hue (h), and colour index of red grape (CIRG) values were calculated from these values, as follows:The where L is the colour brightness, which ranges from 0 to 100, and a* and b* are chromaticity components with values between − 60 and 60. Positive a* represents red, and negative values of a* indicate green; the higher the absolute value, the greater the degree of red or green. A positive value of b* indicates a yellow sample and a negative value of b* indicates a blue sample; a higher absolute value indicates a deeper yellow or blue colour. Specifically, CIRG < 2 for yellow-green, 2 < CIRG < 4 for pink, 4 < CIRG < 5 for red, 5 < CIRG < 6 for dark red, and CIRG > 6 for blue-black.The samples were prepared according to the method of . About 5The free state-treated sample, 5 mL of ultrapure water, 1 g of NaCl, and 50 µL of 1-octanol were transferred together into a 22mL glass vial. After the vials were capped, the volatiles were equilibrated for 30 min at 60 °C. An extraction head aged at 300℃ for 1 h was then inserted into the vials, 0.8 cm above the liquid level. After the 60-min extraction, the extraction head was removed and inserted immediately into the GC injection port to undergo desorption after 5 min at 280℃.The desorbed volatiles were separated in an Agilent 7890 gas chromatograph  equipped with a DB-5 mass spectrometer (30 m × 0.25 mm × 0.25 μm) , and coupled with a 5975MS system. The carrier gas was high-purity helium with a flow rate of 1 mL/min. The injector temperature was set at 250℃ in non-divergent mode. The temperature was set to 60℃ for 2 min and then increased to 180℃ at a rate of 5℃/min. Subsequently, the temperature was ramped up to 240℃ at 5℃/min and held at this temperature for 2 min. The ionization voltage was 70 eV, with the source at 230 °C. The quadrupole was set at 150 °C. The acquisitions were performed in full-scan mode over the scanning range of 35–500 m/z. The detected volatiles were identified by comparing spectra and retention times with commercially available NIST 14 libraries. The peak area of each metabolite was normalized using the percentage of the identified component peak area in the area of the internal standard component multiplied by the inner standard mass.The skins of five cultivars ‘XP’, ‘YP’, ‘MP’, ‘WP’, and ‘VP’ were collected at − 2, 0, and 2 wrs for RNA sequencing. These 15 tissue types were denoted as XP-1, XP-2, XP-3, YP-1, YP-2, YP-3, MP-1, MP-2, MP-3, WP-1, WP-2, WP-3, VP-1, VP-2 and VP-3. Total RNA was extracted using a previously described method . Quantithttp://plants.ensembl.org/Vitis_vinifera/Info/Index. The clean reads were mapped to the grape reference genome (PN40024 assembly 12X) sequence using Bowtie2 (v2.2.5), and the gene expression level was calculated using RSEM (V1.2.12). The expression quality of unigenes is expressed in terms of fragments per kilobase of exon per million mapped fragments (FPKM). The DESeq R package  was used to identify DEGs between groups. The p-value was adjusted based on the q-value [2 (fold change) | ≥ 1 were set as the thresholds for significantly differential expression. Gene Ontology (GO) enrichment analysis of the DEGs was performed using the GOseq R packages based on the Wallenius non-central hyper-geometric distribution, which can adjust for gene length bias in DEGs [www.kegg.jp/kegg/kegg1.html) [The grape genome and annotations were downloaded from  q-value . A q-val in DEGs . The Kyog1.html) . We usedg1.html) .−ΔΔCt method was applied to calculate the relative transcript levels of each gene [Twenty genes related to the aroma metabolism in grape skin were analysed using qRT-PCR to verify the accuracy of transcriptome sequencing. The primers for qRT-PCR were synthesized by Sangon Biotech ; the details are shown in Supplementary Table ach gene . Three rAll data were subjected to one-way analysis of variance after testing their normality. Orthogonal partial least squares-discriminant analysis (OPLS-DA) and principal components analysis (PCA) were performed using SIMCA14.1; both analyses were weighted using unit variance scaling. Significant differences between cultivars were assessed by Tukey’s post-hoc test (p < 0.05) using SPSS software .Below is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2


Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass  accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei’s genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs.Bermudagrass ( Cynodon L. C. Rich. is a genus consisting of nine warm-season grass species in the Cynodonteae tribe, Chloridoideae subfamily, and grass family (Poaceae)  is the most important species economically and ecologically. Cynodon dactylon var. dactylon is a C4 perennial grass used as a turfgrass, forage, and soil stabilizer  . Cynodonabilizer . It has abilizer . Cynodoniculture , as welliculture . Anothernditions . AfricanCynodon vary widely. Flow cytometry studies revealed diploidy to hexaploidy levels in Cynodon . Species including C. arcuatus, C. dactylon var. dactylon, C. dactylon var. coursii, C. dactylon var. elegans, and C. dactylon var. polevansii are largely tetraploid (2n = 4x = 36). Other species with both diploid and tetraploid cytotypes are C. aethiopicus, C. dactylon var. afghanicus, C. incompletus var. hirsutus, C. nlemfuensis var. nlemfuensis, and C. nlemfuensis var. robustus   , simple m (AFLP) , random m (AFLP) , inter-sm (AFLP) , and seqm (AFLP) . Moleculirmation . The useirmation .1 progeny population derived from C. dactylon ‘T89’ (4x = 36) × C. transvaalensis ‘T574’ (2x = 18) was analyzed to construct genetic maps for each parent  and 13 African bermudagrass  genotypes) were studied  were ligated to fragmented DNA sequences. DNA libraries were sequenced with 101 bp single end reads on an Illumina Novaseq SP platform at UMGC.The germplasm was cultured in separate containers under greenhouse conditions at Mississippi State University. Plant leaf material was harvested and freeze-dried. Leaf samples were then shipped to the University of Minnesota Genomic Center (UMGC), where DNA extraction, library preparation, and sequencing were performed. Genomic sequencing libraries were prepared following the GBS protocol with I enzyme . A totalhttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/). All GBS libraries were sequenced with high-quality reads. The raw GBS data generated by the UMGC did not have inline barcodes, but instead contain variable length padding sequences (0–10 bp) added in front of the enzyme cut site. Therefore, a Perl script  was used to trim padding sequences. The SNPs were then called de novo using the UNEAK pipeline  based on its inferred ancestry from ADMIXTURE. In brief, a Cynodon accession was assigned to a given population if its ancestry fraction from this subpopulation was highest among four subpopulations. Pedigree relationship and ancestry coefficients (Q) from the optimum K were used for visualization of population structure. Principal component analysis (PCA) was also conducted in TASSEL 5.2.77 (Fst) between subpopulations were calculated using the adegenet package  have transition substitutions, whereas 14,172 (37.79%) have transversions—a transition to transversions ratio (Ts/Tv) of 1.64:1. The frequency of transitions and transversions observed is given in A total of 600,380,494 reads were generated, with a mean of 2.9 million reads per sample. After trimming padding sequences, a total of 537,127,057 reads were retained. The UNEAK pipeline identified a total of 536,993,374 reads that contained an Cynodon accessions, missing data rate ranged from 14% to 40%. Although missing data pose a problem, high number of SNPs is desirable in genetic diversity analyses and could partially offset the negative effect of missing data.Across 37,496 SNPs, missing data rate ranged from 0 to 50%, with an average missing data rate of 32.68%. The average minor allele frequency across all SNPs was 0.13. Among 206 dactylon accessions collected from seventeen different countries ranging across Africa, Asia, North America, Australia, and Europe  were also assigned to subpopulation 1, suggesting admixture or possibly misidentification of these two accessions. Subpopulation 2 consisted of 36 (17.4%) accessions—22 of African origin, 12 from the United States, and two from Europe. In this cluster, 9 out of 13 C. transvaalensis accessions clustered with 27 C. dactylon accessions. The third cluster (subpopulation 3) contained 54 (26.2%) accessions—52 of which were C. dactylon and two were C. transvaalensis (PI 289922 and PI 647878). Again, hybridization or misidentification should be considered for these two C. transvaalensis. A majority of the accessions in subpopulation 3 were from five African countries, with two from the U.S., one from India, and one from Australia. The fourth cluster (subpopulation 4) contained the remaining 32 (15.5%) accessions of solely C. dactylon. In subpopulation 4, 17 accessions collected in the United States by the Oklahoma State University turfgrass breeding program grouped with 14 accessions collected in neighboring European and Asian countries maintained at the USDA NPGS .One of the major objectives of this study was to assess the relationship among 206 accessions and determine the overall population structure. A total of 37,496 SNPs were analyzed in ADMIXTURE and PCA. ADMIXTURE revealed four bermudagrass subpopulations (K=4) based on maximum likelihood clustering model and five-fold cross-validations, which were designated as subpopulations 1–4  analysis indicated that PC1, PC2, and PC3 explained 15.6%, 10.1%, and 3.8% of the genetic variation in the panel, respectively  evaluates genetic differences between subgroups within a population. In plants, Fst values greater than 0.15 are considered to significantly differ while values below 0.05 are considered insignificant  accessions, many of which clustered in subpopulation 2 with C. dactylon of African origin  of modern diploid African bermudagrass may have substantially contributed to the formation of tetraploid common bermudagrass. When whole genome sequences of the two species are available, comparative analysis may validate this hypothesis. In Miscanthus (Panicoideae subfamily), two major species, M. sinensis (largely diploid) and M. sacchariflorus (largely tetraploid) are used for biomass breeding. Genetic analyses in these two Miscanthus species revealed unidirectional gradient introgression from diploid M. sinensis to tetraploid M. sacchariflorus  grouped with 46 C. dactylon , ADMIXTURE and phylogenetic analysis all support that most of African accessions formed a unique cluster with the remaining accessions exhibiting admixture 4. The d factors . These aCynodon species are predominantly outcrossing, breeding programs have mainly relied on small subset. Observed heterozygosity ranged from 0.07 to 0.12, which were considerably smaller than expected heterozygosity which ranged from 0.17 to 0.22 , which will improve bermudagrass breeding and serve as foundation for genetic mapping of important traits.This study revealed extensive genetic diversity in the two https://figshare.com/articles/dataset/Genomic_Diversity_Bermudagrass/21941333. R scripts used in data analysis and visualization are available on Github: https://github.com/SinghLovepreet2363/Bermudagrass_GenomicDiversity.The SNP datasets generated and analyzed in this study are available in the Figshare repository: LS and HD conceptualized the study, analyzed the data, drafted the manuscript. YW contributed to the germplasm collection, assisted in interpreting the results and edited the manuscript. MW, JM, BS, BB edited and reviewed the manuscript. HD obtained the funding for the project. All authors contributed to the article and approved the submitted version.


Cluster analysis grouped all genotypes into two main clusters with eight subgroups that corresponded to the country of origin of cultivars and their maturity group. Pairwise Fst values between countries of origin showed the highest differentiation of Swiss cultivars from the rest of the European gene pool, while the lowest mean differentiation was found between American introductions and all other European countries. On the other hand, Fst values between maturity groups were much lower compared to those observed between countries. In analysis of molecular variance, the total genetic variation was partitioned either by country of origin or by maturity group, explaining 9.1% and 3.5% of the total genetic variance, respectively. On the whole, our results suggest that the European soybean gene pool still has sufficient diversity due to the different historical breeding practices in western and eastern countries and the relatively short period of breeding in Europe.Soybean is the most grown high-protein crop in the world. Despite the rapid increase of acreage and production volume, European soybean production accounts for only 34% of its consumption in Europe. This study aims to support the optimal exploitation of genetic resources by European breeding programs by investigating the genetic diversity and the genetic structure of 207 European cultivars or American introductions registered in Europe, which were genotyped by the SoySNP50K array. The expected heterozygosity (H Soybean is the most grown high-protein crop in the world, with beans containing high levels of protein 39–42%) and oil 19–22%) [9–22% [1,% and oilSoybean acreage in Europe has nearly doubled over the past decade, and soybeans are now grown on 5.3 million hectares, representing 4.4% of the total global soybean acreage , as wellA basic requirement for successful crop breeding is the continuous provision and exploitation of genetic diversity, which serves as a reservoir of tolerance/resistance traits for crop adaptation to new environmental conditions and the changing climate. The common use of just few elite cultivars by farmers reduces the ability to maintain sufficient crop production under increasingly frequent extreme climatic events and associated environmental stresses. The genetic diversity of many crops declines over time as commercial plant breeding focuses on improving one or a few traits and/or uses only a small number of elite genotypes to develop breeding populations . The stuThe development of DNA marker technology, such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), has created the technical tools required to evaluate the genetic relationships within soybean germplasm. Due to the minor role of soybean in European agriculture, few studies investigated the genetic diversity of European germplasm ,15,16,17Although some insights into the genetic background of European soybean germplasm have been gained recently, there are still many uncertainties about its origin, diversity, and genetic structure. This work focuses on the molecular diversity of a geographically broad germplasm collection of 207 historical and modern soybean cultivars (MG000 to MGII) relevant to commercial production and breeding under Southeast European conditions. It aims to support the optimal exploitation of genetic resources by European breeding programs by (a) assessing the genetic diversity and the genetic structure of the collection based on a large number of SNP markers, and (b) comparing genetic diversity parameters among country breeding programs and maturity groups.The germplasm collection, consisting of 207 soybean cultivars, was genotyped by the Soy50k Illumina Bead Chip , resultie), polymorphic information content (PIC), and minor allele frequency (MAF) for the entire collection were 0.34, 0.27, and 0.25, respectively  based on the SNP marker data was used to assess the population structure of the collection. The proportion of total genetic variability explained by the first two principal components was 13% . The anaModel-based structure analysis revealed two groups (Q1 and Q2), corresponding to the best-fit K-value of 2 . There wn = 90) in the dendrogram consisted mainly of Italian cultivars (35/39), French cultivars (15/22), and introductions from America, divided into three subgroups as follows: A1 consisted only of Italian cultivars; A2 mainly of French cultivars and introductions from America; while A3 was dominated by cultivars from Italy, America, and Serbia. The larger cluster B (n = 117) consisted mainly of Croatian, Serbian and Romanian cultivars, followed by Austria, America and Switzerland. Subcluster B1, included mainly Croatian and some Serbian cultivars; B2 was dominated by Central European cultivars from Switzerland and Austria, along with some American cultivars; B3 consisted mainly of Southeastern European cultivars from Romania, Croatia and Serbia; B4 contained mainly Serbian cultivars; B5 contained the majority of Noah’s Ark with some Southeastern European cultivars and two introductions from America. With respect to maturity groups  showed that the variation among countries of origin and that among maturity groups explained 9.8% and 4.5% of the total variation, respectively, confirming the fairly modest variation accounted for by these cultivar classification criteria .st, as a measure of population differentiation due to genetic structure, revealed low average differentiation among countries of origin (average Fst = 0.128), while differentiation between maturity groups was much lower (average Fst = 0.053) (st = 0.22) and the lowest for American cultivars (Fst = 0.08), whereas the average Fst for other countries ranged from 0.10 to 0.15. In addition to the American cultivars, relatively low average differentiation was also found for Austrian and Serbian cultivars (Fst = 0.10). These three groups showed the highest similarity among themselves with the respective Fst values ranging from 0.05 to 0.08.F= 0.053) . The higAlthough soybean has become one of the most important sources of high-protein feed and plant-based food, little is known about the diversity and interrelationships in the European commercial germplasm gene pool. The observed value of 0.34 for gene diversity (expected heterozygosity) of the entire collection is similar to results in Hahn and Würschum , who repWe investigated the population structure with different approaches, which provided fairly similar indications. Structure analysis indicated the presence of two subpopulations in the European gene pool, in agreement with previous results for European commercial germplasm based on SSR and SNP markers ,17. The Agenzia regionale per lo Sviluppo Rurale del Friuli Venezia Giulia), whose breeding activities started only recently (in 1987) with the main objective to create new cultivars with high grain yield and low level of antinutritional factors, such as the Kunitz trypsin inhibitor [Cluster analysis revealed two main clusters, which corresponded to the two subgroups obtained by structure analysis. These subgroups may be related to the history of soybean introductions to Europe, which took different paths in the historical eastern and western blocks . The smanhibitor . Therefonhibitor .In the present study, extremely low genetic distance values (high genetic similarity) based on high number of SNP loci were observed in nine pairs of cultivars and within one cluster consisting of four Croatian cultivars. However, the four Croatian cultivars have been released 3–5 years one after another and had similar but not identical pedigree. All these four cultivars passed the DUS and VCU test and had significant market success in Croatia.Extremely low genetic distance within soybean germplasm has been observed in a similar study by Fu et al.  It is knGenerally, there is very modest information and a lack of tools for public but reliable genotype verification at the international level. The CPVO Variety Finder is a simple, helpful tool (database) to discover some basic information on breeding companies, seed maintainers and providers, as well as synonyms  at European markets, but it is not consistently compiled and maintained. In conclusion, so far there is no reliable referent database of soybean cultivars in Europe that would provide basic morphological, biological, and genetic identification data. Our results might contribute to soybean germplasm management and utilization.st estimates showed the high differentiation of Swiss cultivars from the rest of the European gene pool. In addition, Swiss cultivars showed higher differentiation from American germplasm than cultivars from other European countries. The differentiation between Swiss cultivars and Central European germplasm and their weaker relationship with American lines was reported earlier [st as a function of the difference in maturity class. A similar genetic separation of very early material was observed earlier [F earlier  and may  earlier , as well earlier , concurr earlier ,20. Low  earlier . The exp earlier  may part earlier ,30. OtheOur results can inform the introduction of genetic resources by regional European breeding programs that aim to widen the available genetic diversity for soybean selection. For example, the Swiss germplasm was most divergent within the European gene pool and has particular interest for breeding programs aimed to select very early cultivars. This phenological type is important to expand soybean production to Northern European regions, or for breeding varieties suitable as a second crop in Southern Europe. Our results suggest that genetic diversity of soybean germplasm in Europe is not a limiting factor for further progress in soybean breeding. The introduction of extra-European genetic resources has high interest as well for European breeding programs, especially in the context of climate change, as devised by Haupt and Schmid  by meanswww.arche-noah.at), and the North and South American continents  were also included in this investigation because these were introduced in the European soybean breeding program during the past decades. Specific information for plant material is listed in The plant material used in this study consisted of 207 soybean cultivars representing the European gene pool with suitable maturity groups ranging from MG000 to MGII . TraditiSnpReady R package. All heterozygous markers were removed, and imputation was performed according to Wright’s method [Seeds from each accession were sent to TraitGenetics Ltd. in Gaterslaben for genotyping. Single nucleotide polymorphism genotyping was conducted on SoySNP50K Illumina Infinium BeadChips  followed by the InfiniumH HD Assay Ultra protocol  as described by Song et al. . Genotyps method .popgen R package [e, PIC, MAF). Genetic diversity measures by country of origin were calculated only for countries represented by 10 or more cultivars. The clustering of cultivars was performed using the R package “stats” and Ward’s minimum variance method based on Nei’s genetic distances. The Bayesian model-based method STRUCTURE, version 2.3.4 [Cultivars, prior to the analysis itself, were classified into the countries of their origin and maturity groups. Principal component analysis was performed to summarize the genetic structure and variation present in the collection using  package . The samon 2.3.4 , was useon 2.3.4 . Softwaron 2.3.4  was usedhierfstat R package [The hierarchical F statistic was used to estimate the proportion of genetic variance accounted for by origin and maturity group using ancestry estimates for K = 2 and calculated using the  package .poppr R package [Analysis of molecular variance (AMOVA) was performed to determine within and between-group variation using poppr.amova function in the  package . GeneticThe hierarchical F statistic and AMOVA only groups, which contains 10 or more cultivars, were included in the analysis.


Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat–matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic ( The island of Madagascar is a globally important biodiversity hotspot with high rates of endemism ,2,3. YetMicrocebus ravelobensis, between edge and interior habitats within the same forest. However, the negative effects of smaller and more isolated populations may be mitigated if connectivity is high within landscapes and organisms are able to disperse across matrix and edge zones between habitat patches [When organisms are subjected to habitat loss and fragmentation, genetic and genomic methods are useful to explore and quantify negative outcomes on population genetic compositions ,23. Popu patches ,29. Afte patches .Eliurus myoxinus) and the invasive black rat (Rattus rattus). As a geographically widespread species across Madagascar, E. myoxinus are found throughout the western and northern dry deciduous forests [E. myoxinus. As with other Malagasy fauna, studies on forest loss and fragmentation have found mixed or unclear effects. Species-specific and regional differences appear to play a large role in determining the direction and scale of effect, rather than a single unifying ecological pattern. For example, capture rates of Eliurus spp. increased with increasing forest area in some dry forest sites [Eliurus spp. in the North and West of Madagascar display relatively consistent biogeographic patterns, with weak signals of genetic differentiation from large-scale geographic barriers such as rivers, and a lack of strong isolation by distance pattern suggesting that ecological factors such as habitat preference and elevational gradients play a more important role in the biogeography of these rodents [To evaluate the effects of habitat fragmentation, our study focused on two species of rodents in northwestern Madagascar: the endemic western tuft-tailed rat , more gregarious species with a generalized diet that is found in a variety of habitats from urban and rural human settlements to primary and secondary forests [R. rattus do not disperse over long distances, preferring to stay in close proximity to kin [R. rattus in Madagascar very likely occurred recently, within the last 1000 years, in port cities like Tôlanaro in the east or Antsiranana in the North via trading routes from Africa and Asia [R. rattus, perhaps due to the complicated nature of defining habitat preference for an invasive generalist species. Capture rates of R. rattus declined with increasing forest area in western dry forest sites [R. rattus were only weakly affected by habitat heterogeneity, and significant patterns of isolation by distance were detected as is expected in an invasive generalist [R. rattus genetic differentiation, and suggested dispersal alongside humans in a non-Euclidean pattern, such as via boats along coastlines, was responsible for the spatial genetic patterns observed. Several studies have investigated the potential for competition between introduced and endemic rodent species, but found no effect or inconclusive results [In comparison,  forests . When eny to kin . The intand Asia ,42. A cost sites , while fst sites ,33. In Cneralist . However results ,33. EvenE. myoxinus and R. rattus, in two fragmented forest landscapes in northwestern Madagascar. Given one arboreal, relatively specialized, and forest-dependent endemic species and one ecologically flexible, invasive species with a generalized diet that has colonized a variety of habitat types, different outcomes can be expected for these two species. We aimed to answer three main research questions for each of these two species in order to compare and contrast their movement patterns and the resulting population connectivity when living in fragmented landscapes: (1) Do endemic and invasive rodents use non-forest matrices for local movement or dispersal? (2) Are connectivity and genetic structure within these landscapes affected primarily by isolation, by distance, or by habitat-related factors? (3) Which ecological factors affect the genetic diversity of subpopulations living in fragmented landscapes?The goal of our study was to investigate the influence of habitat loss and fragmentation on the genetic variation of these two contrasting species of rodents, Bismarckia nobilis) and a generally anthropogenic landscape featuring villages, rice fields, and roads [We systematically captured animals across two landscapes in northwestern Madagascar  that contain a network of forest patches ranging in area from 0.8 to 114.6 ha, with adjacent continuous forest sites ranging from 3,683 to 130,390 ha . Both land roads . ANP is E. myoxinus collected from two other sites  in ANP in 2004 for comparative spatial analyses; see Rakotondravony and Radespiel [http://qgis.osgeo.org (accessed on 15 April 2022)) to determine the distance to the next edge, distance to the next continuous forest, and forest area for each individual animal captured.In ANP, we established 31 transects in 27 forest fragments and 4 transects in continuous forest sites. In MCF, we established 18 transects in 13 forest fragments and 8 transects across 3 patches of continuous forest . All traadespiel  for furtAll field protocols were reviewed and approved by the appropriate ethics committees at the University of Toronto, Canada (Protocol # 20011950) and the Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Germany. All fieldwork adhered to the legal requirements of Madagascar and were approved by the Ministère de l’Environnement, de l’Ecologie et des Forêts and Madagascar National Parks .E. myoxinus  and 106 samples of R. rattus  for RADseq.We used restriction site-associated DNA sequencing (RADseq) to generate genetic data for the population genetics analyses . RADseq RADseq libraries were prepared using 100–200 ng of genomic DNA and the TruSeqNano DNA HT kit (Illumina). The restriction enzyme SbfI was used to generate DNA fragments. Libraries were prepared in sets of 24 samples sorted based on their measured DNA concentration. Each sample was ligated to one of 48 available P1 adapters with a unique five base pair molecular identifier allowing individual identification of the samples after sequencing. All fragments were randomly sheared, resulting in fragments with an average size of 550 bp. We ligated sheared DNA fragments to the P2 adapter, and all fragments with both P1 and P2 adapters were amplified in 10 polymerase chain reaction cycles. We verified DNA concentration and fragment sizes of the amplified libraries using a Qubit Fluorometer and a Bioanalyzer 2100. Finally, we sequenced the libraries using 150 bp paired-end reads on an Illumina HiSeq3000 at the GeT-PlaGe platform .E. myoxinus, we used a de novo alignment method in Stacks vs. 2.5 [https://catchenlab.life.illinois.edu/stacks/) to call SNPs. We first filtered out low quality reads using process_radtags, clone_filter, and kmer_filter. We created a catalog and aligned our samples using the de novo_map pipeline in Stacks 2.5 utilizing ustacks, sstacks, and tsv2bam. We set m, M, and n parameters to two, seven, and eight after optimization using protocols from Rochette and Catchen [gstacks and populations retaining only loci found in at least 80% of samples (r = 0.80), with a minor allele frequency of at least 5% (min_maf = 0.05), and a maximum heterozygosity of 0.7 (max_het = 0.7), and we retained only one random single nucleotide polymorphism (SNP) per RAD locus (--write_random_snp) in order to avoid linkage disequilibrium in downstream analyses. After filtering, we retained 66 samples of E. myoxinus, 52 from ANP and 14 from MCF  using the Burrows–Wheeler alignment (BWA) with BWA-MEM vs. 0.7.17 [https://github.com/lh3/bwa). We then ran gstacks and removed read pairs of the same length (--rm-PCR-duplicates). We ran populations, retaining only loci found in at least 80% of samples (r = 0.80), with a minor allele frequency of at least 5% (min_maf = 0.05) and a maximum heterozygosity of 0.7 (max_het = 0.7), and we retained one random single nucleotide polymorphism (SNP) per RADtag (--write_random_snp). After filtering, we retained 81 samples of R. rattus, 43 from ANP and 38 from MCF . We tested a varying number of ancestral populations (K = 2–10) and calculated cross-validation errors (CV) for each K-value to determine the most likely K. We then used the CLUMPAK program 1.1 [http://clumpak.tau.ac.il/) to infer cluster assignments across 20 independent runs of ADMIXTURE 1.3.0, which revealed that each landscape contained a distinct population with comparably low levels of admixture between them   . Thereforelatedness2 function in VCFtools 0.1.16 [https://vcftools.github.io/) by two, and assigned dyads into discrete kinship classes based on these r values. Classes were defined as first-order relatives (r ≥ 0.375), second-order relatives (0.375 > r ≥ 0.1875), or distantly related individuals (0.1875 > r > 0) in congruence with Combs et al. [http://www.rstudio.com/ (accessed on 10 January 2021)) to test for significant differences in geographic distances between second-order relatives and distantly related dyads within and between each species. First-order dyads were not statistically analyzed in both species due to low sample sizes.We calculated a coefficient of genetic relatedness for each dyad for each landscape separately to investigate the distribution of related individuals in space. Distribution of related individuals accurately reflects the dispersal patterns within a species and can be used to detect potential dispersal events . We genes 0.1.16  ). We used these two matrices to create Mantel correlograms using the mantel.correlog function in the Vegan R package 2.6-4 with 999 permutations [R. rattus [E. myoxinus for comparability. Only dyads from individuals of less than half the maximum Euclidean geographic distance were included in this analysis to reduce a potential bias due to individuals from the edges of the sampling space [We additionally created a genetic dissimilarity matrix using the BED2DIFFS_V1 function, which calculates average genetic dissimilarity based on allelic differences observed between samples  and geneutations . Mantel . rattus , and useng space .In order to assess the effect of isolation by distance (IBD) across the entire population in each landscape, we first conducted Mantel tests using the genetic dissimilarity matrix and the geographic distance matrix described above. We ran Mantel tests with 999 permutations on each species and landscape separately using the Vegan R package 2.6-4 .n = 4 individuals removed). First, we ran ADMIXTURE 1.3.0 [We used three complementary methods to determine sub-population connectivity and genetic structure within the two landscapes. For all three analyses, we used a slightly reduced dataset with one individual of each closely related dyad being removed (RE 1.3.0  to asseshttps://github.com/dipetkov/eems) to investigate migration rates and potential barriers to gene flow across each landscape. EEMS uses a stepping-stone model to estimate effective migration rates between adjacent subpopulations (demes) and produces a visual migration surface of estimated genetic barriers and connectivity [R. rattus for the Northern and Southern patches of forest in MCF due to the large spatial scale of the site and sufficient sample size. Our analyses used two MCMC chains, each with a length of 25,000,000 iterations, with a burn-in of 1,000,000 iterations. We examined the log posterior between the chains and combined results from both using the rEEMSplot package 0.1.0. We then plotted surfaces of effective migration rates across each landscape to identify geographic barriers and areas of connectivity.Secondly, we used the Estimating Effective Migration Surfaces (EEMS) software package 0.0.0.9000 , which estimates resistance to dispersal across landscapes. ResDisMapper 1.1 calculates IBD residuals for each dyad of individuals and maps resistance values based on their deviations from the general IBD trend. Genetic data were input into ResDisMapper 1.1 using the GENEPOP format, and a Euclidean distance matrix was used to produce IBD residuals using the “relative similarity method” (Method 1). We ran ResDisMapper 1.1 with default values of a final resolution of 50, confidence intervals set to 0.95, for 1,000 repetitions. The significance threshold for resistance contours was set to 0.05. For MCF, we set the maximum distance for dyads at 10,000 m to ensure a continuous distribution of IBD values [rdm_mapper function to produce a resistance map which was then overlaid on a map of each landscape produced in QGIS 2.18.9.Thirdly, we ran the ResDisMapper program 1.1  , observed heterozygosity (HO), and expected heterozygosity (HE). These three parameters were calculated using the VCFtools --het command [E. myoxinus and R. rattus. Generalized additive models (GAMs) were built for each of these dependent variables  using maximum likelihood estimation in the R package mgcv 1.8.42 [E. myoxinus, R. rattus), region , sex , forest type , body mass (a proxy for body condition), forest area , distance to edge , distance to continuous forest , and the percentage of edge habitat (area of the fragment within 50 m of the forest edge). Normality of all continuous variables was assessed using Shapiro–Wilk’s tests [n = 123 individuals) and (b) just with the individuals caught in forest fragments  to also test for variables that are not relevant for continuous forest sites . The separation of correlated variables into different models resulted in two GAMs built for the overall data set (Models A-B) and three GAMs built for the fragment-only data set  from ANP, and 53,070–69,657 RAD loci per individual with a mean depth of 10.09x coverage  for E. myoxinus individuals (n = 14) from MCF  from ANP, and 34,451–48,855 RAD loci per individual with a mean depth of 10.42x coverage  for R. rattus individuals (n = 38) from MCF. SNP sets were generated for each species separately and individuals were grouped for different downstream analyses based on need  for from MCF . We reco on need .E. myoxinus dyads at ANP .We identified 26 related R. rattus at ANP  and 6 at MCF  were trapped within 110 m of each other, while distantly related R. rattus (r < 0.1875) were trapped within 760 m of each other. Related R. rattus dyads were trapped in different forest patches in only one case . For both second-order and distant relatives, R. rattus dyads were in closer proximity to each other than the respective E. myoxinus dyads .In both E. myoxinus at ANP and for R. rattus at both ANP and MCF, but spatial autocorrelation could not be tested for E. myoxinus at MCF due to small sample size   .E. myoxinus at ANP , and in R. rattus at both ANP  and MCF . No such effect was detected for E. myoxinus at MCF , possibly due to small sample size.Significant IBD effects were identified in both species . GeneticE. myoxinus in ANP, although one cluster (= blue) was dominant in the southwestern part of the landscape and rarer in the other parts  with mixed results; between two fragments, there was a low effective migration rate, while between another set of fragments and the continuous forest, there were high effective migration rates. In the southern forest sites  and significantly lower observed and expected heterozygosity than R. rattus , we did not observe any long-distance dispersal events, and all closely related dyads (r ≥ 0.1875) were captured within ~100 m of each other. These results suggest philopatric tendencies and kin-biased spatial clustering in R. rattus which has already been described from other study sites in Madagascar [R. norvegicus in an urban landscape, a decline in correlations was also observed beyond 200 m but in a much more gradual pattern [E. myoxinus [R. rattus in our study seemed to be reduced due to fragmentation as well, although dispersal across the matrix was possible but probably relatively rarer due to a preference for staying close to their natal site and not necessarily a lesser ability to cross matrix than in E. myoxinus. While R. rattus are generally able to exploit a breadth of habitat types, our results indicate that they do not use savanna as habitat, although it is clearly permeable to dispersal.The invasive dagascar . This fi pattern . Correlomyoxinus ,71. ThusR. rattus dyads in closer proximity than related E. myoxinus dyads, which was unexpected, as invasive species tend to have greater dispersal abilities than native species [E. myoxinus is a solitary, frugivorous, arboreal rodent [R. rattus [R. rattus forms gregarious groups of related members and has an opportunistic, omnivorous diet [E. myoxinus are in concordance with the solitary lifestyle of a dietary specialist [R. rattus seems to be largely philopatric, with less dispersal across the matrix as a by-product of individuals preferring to stay near kin rather than an inability to disperse across open spaces. Thus, it is possible that the forest fragments we studied contain enough resources for R. rattus, while E. myoxinus are dispersing greater distances due to a lack of suitable habitat in fragmented landscapes. While our study did not directly test for this, it is also possible that human-mediated dispersal is occurring in these landscapes. While R. rattus and E. myoxinus both have different life history strategies, both species are able to maintain dispersal across non-habitat matrices and inhabit isolated forest fragments.We found related  species . These dl rodent ,34 and w. rattus . In contous diet . While tecialist , their lE. myoxinus at ANP showed a pattern of isolation by distance. Previous research on Eliurus spp. did not find significant effects of IBD using mitochondrial DNA [E. myoxinus sub-populations at MCF showed strong signals of genetic differentiation between the two large forest patches separated by savanna, while a more complex patchwork of connectivity was observed at ANP, not directly connected to a matrix–forest dichotomy. This effect is in line with range-wide patterns of E. myoxinus, which has a wide distribution and is mainly structured by altitudinal gradients [E. myoxinus, which may also explain the lack of unifying ecological patterns seen in other studies [rial DNA ,37, but radients  with higradients . Howeverradients  or micro studies ,21,73.R. rattus sub-populations at both ANP and MCF showed significant effects of IBD. However, we also observed different patterns of connectivity across the landscape, suggesting that other habitat factors such as matrix composition and quality may also structure these sub-populations. We observed two distinctive areas of high connectivity in larger forest patches at ANP and a more complicated pattern at MCF, but similar areas of high connectivity in larger forest patches. These movement patterns suggest a general preference for larger patches of forest but also may be explained by the population dynamics of R. rattus in the landscapes. More specifically, the high degree of genetic connectivity among the larger fragments in ANP points towards a larger and well-established population nucleus consisting of multiple, largely philopatric matrilines that are rather isolated from neighboring lineages inhabiting the smaller, isolated fragments due to a scarcity of long-distance dispersal. Anthropogenic influences may also be structuring R. rattus populations in the region. R. rattus have been observed to follow human paths and settlements rather than dispersing in a Euclidean manner [n manner . There an manner , while tn manner .R. rattus populations in Madagascar. Eradication is unfeasible, especially in a country with limited conservation resources. R. rattus are able to exploit and colonize continuous forest and forest fragments likewise, and the only habitat type they seem not to use, savanna matrix, cannot be expanded as it would also negatively affect endemic species such as E. myoxinus. It is likely that some of habitat-related factors structuring these two species are similar, such as vulnerability to predation [From a conservation management standpoint, our study showcases the difficulty in managing invasive redation , while mE. myoxinus, distance to edge. The regional differences in the case of E. myoxinus were rather unexpected, since both the inbreeding coefficient and the observed and expected heterozygosity were higher in MCF compared to ANP. These rather inconsistent findings may have been driven by the small sample size from MCF, which precludes further interpretation.Only three ecological factors influenced the genetic diversity of the studied rodents, and these were region, species and, in the case of IS and distance to edge, HO decreased significantly with increasing distance to edge, but only in E. myoxinus. Taken together, these findings suggest that genetic diversity, at least in E. myoxinus, was higher closer to edges than towards the center of forests. Previous research from the same two landscapes found a decreased abundance of E. myoxinus in fragments with a higher percentage of edge zone, and it was concluded that E. myoxinus shows negative effects of habitat edges and of extensive habitat fragmentation [E. myoxinus near edges. Alternatively, the higher levels of genetic diversity near edges may have resulted from an increased diversity of mating opportunities with unrelated conspecifics near edges, since immigrants from other fragments arrive first in the edge zone of any given site, and long-distance dispersal was confirmed for E. myoxinus in the present study. Radespiel et al. [E. myoxinus if individuals born in edge zones of fragments would rather disperse across the matrix to other edge zones than towards interior sub-populations. Such a behavior would lead to an increasing genetic diversity in edge zones, despite a lack of high-quality habitat creating an ecological trap. Molecular edge effects are understudied and represent an important upcoming topic in fragmentation research, especially given the adoption of next-generation sequencing which may be able to parse out smaller-scale patterns in genetic differentiation [E. myoxinus or other endemic rodents.In congruence with the overall significant and positive relationship between Fentation . If thatl et al.  found dentiation . Given tntiation , major cR. rattus when analyzed individually was region; we observed higher levels of genetic diversity at ANP. This may reflect the invasion dynamics of R. rattus in northwestern Madagascar. At least two founder events occurred in Madagascar, one in the North and one in the South, followed by a relatively slow range expansion across the island. The populations in northwestern Madagascar were suggested to have resulted from the southern invasion [R. rattus would lie at the edge of the range of the southern expansion and thus may have been more recently colonized than ANP and undergone a founder effect, which is known to coincide with a population bottleneck and lower genetic diversity. The lack of other significant ecological impacts on genetic diversity may also suggest ecological flexibility, lack of habitat preference, and their principal ability to cross the matrix and mitigate its isolation effects. Future research, using methods such as approximate Bayesian computation (ABC) to infer demographic history of R. rattus could help tracing and reconstructing the original invasion(s) into Madagascar and its spread throughout the North into our study landscapes.The only significant factor affecting the genetic diversity of invasion ,75. ConsR. rattus was higher compared to E. myoxinus at both sites. Invasive species with a limited number of invasion points in recent history should have lower levels of genetic diversity compared with established populations of native species in a given landscape due to founder effects [R. rattus and E. myoxinus population abundances are not correlated in this site, suggesting a lack of competition [R. rattus are better equipped to expand into and establish viable populations within fragmented landscapes compared with E. myoxinus. Compared with R. rattus, E. myoxinus has more specialized habitat requirements, such as tree holes for sleeping sites and a frugivorous diet [E. myoxinus may still be at greater risk of extirpation in these fragmented landscapes over time, especially as deforestation continues and the amount of remaining habitat subject to edge effects increases. Given that distance to edges was the only significant ecological variable we found affecting E. myoxinus, we encourage further research in the microhabitat preference and natural history of this species in order to more effectively inform conservation.Genetic diversity of  effects . While ppetition ,21, our ous diet . Thus, wE. myoxinus, a solitary species with more specialized habitat requirements dispersed large distances between habitat patches across an open savanna matrix. However, decreased abundance, lower levels of genetic diversity overall, and lower genetic diversity with increasing distances from habitat edges suggest that the long-term persistence of this endemic species in fragmented landscapes is not secured. These overall threats are increased by the rapid rates of deforestation in Madagascar [R. rattus, a gregarious and ecologically flexible, invasive species, is well adapted to living in fragmented landscapes of northwestern Madagascar, although it maintains connectivity with short-distance rather than long-distance dispersal. Our results add further complexity to the literature on mammal populations in fragmented forests of Madagascar and suggest further research is needed. In particular, basic natural history information  is missing for many species, which would ultimately help to improve conservation initiatives.We found variation in local movement, connectivity, and genetic diversity for rodents in Malagasy fragmented dry forests. Certain aspects of these species’ life histories seem to allow them to colonize and/or persist in fragmented landscapes. dagascar  and prob


Enterobius vermicularis occurs worldwide. The most common clinical manifestation of a pinworm infection is an itchy anal region. This parasite is incidentally found in appendicitis. This study aims to characterize and genotype this parasite from different samples inferred by mt-DNA.Human infection with cox1) gene.Forty appendectomies for acute clinical appendicitis, 40 positive scotch-tape samples, and 10 adult females worm isolated from patients. Genetic differentiation, haplotype differences, and isolates population structure were analyzed based on the cytochrome c oxidase subunit I (It has been demonstrated that all isolations in the appendectomies specimens are similar, and the genetic difference divergence is seen in adult worm specimens. The neutral indices of the samples did not show a significant difference and show that there is no intra-specific and population distribution diversity.Our results show different haplotypes in the B type of E. vermicularis population and add new information about genotyping of these parasites in Iran. In comparison with other studies, intra-specific variation of this parasite from Iran was observed. Enterobius vermicularis is a cosmopolitan distributed intestinal nematode in children that cause pinworm disease Oxyuriase. The transmission of this parasite is directly in the human population. The infection of this parasite is often asymptomatic. Other symptoms attributed to this parasite include itchy nose, appendicitis, vulvovaginitis, runny mouth, and gnashing of teeth at night with ectopic migration  is the center of West Azerbaijan province in Iran, and it is situated at an altitude of 4,360 ft above sea level. Also, Maragheh city (37°23′21″N 46°14′15″E) is located in the southwest of East Azarbaijan province on the south hillside of Sahand Mountain and situated at an altitude of 4,845 ft above sea level. The climate of the two cities is temperate, disposed to cold and humid , according to the instructions, and all of which were stored at - 20 °C until use. The cox1 gene was amplified using primers based on Piperaki et al. study  and reverse primers (EVM2: 5-CACATTATCCAAAATAGGATTAGCC-3).The total volume of the reaction was 30 µl containing 3 µl DNA template, 10 µl distilled water, 10 pmol of each primer, and 15 µl master mix (amplicon).Reaction cycles consisted of an initial denaturing step at 94°C for 5 min, followed by 35 cycles at 94°C for 90 s, 57°C for 60 s, and 72°C for 45 s, with a final extension at 72°C for 10 min using a gradient thermocycler. DNA fragments were analyzed by 1.5% agarose gel electrophoresis and sequenced by Bioneer Company using the same primers.Phylogenetic analysis: Sequences have been aligned and unlike the sequences from the region. In contrast to existing sequences from the area associated with E. vermicularis available in the GenBank, using Chromas 2.2 and multiple, some alignment was done with the data linked to E. vermicularis from Iran deposited in GenBank. Phylogenic analyses based on cox1 sequence data were conducted to the fullest possible using MEGAX , and neutrality values (Tajima's D and Fu's Fs tests) were calculated by DnaSP software version 5.10 (sion 5.10. The degtistics) , 15.E. vermicularis as positive control samples. Sequence analysis was performed for 24 PCR products consisting of appendectomy, egg isolates from tapes, and adult worms (8 from each group) to characterize the genotype of E. vermicularis. Phylogenic analyses of E. vermicularis haplotypes based on the cox1 gene and type of nucleotides in Iran were conducted by Maximum likelihood (ML) using MEGAX with Syphacia obvelata designated as an out-group shown in An approximately 390 bp band was amplified from 22 appendectomy samples and 35 egg isolates from tapes and ten adult worms of Using DnaSP 5.10 software, haplotype differences (Hd), nucleotide differences (π = Nd), and neutrality indices of the samples studied in this study and recorded from different parts of Iran in GeneBank were calculated .The results show that the haplotype diversity in the samples of Azerbaijan is 0.712, and the number of haplotypes in this region is 3. On the other hand, the neutral indices of the samples of Azerbaijan did not show a significant difference and show that there is no intra-specific and population distribution diversity in the samples of Azerbaijan (this study).E. vermicularis were calculated by the Dnasp5 software package with the nucleotide data set of cox1 gene. The results showed that there was the slightest difference in the genetic structure of the population in our studied samples, such as Azerbaijan, Khorramabad, and Gilan north of Iran (Fst = 0), and the highest genetic population distance of Azerbaijan with the samples of Shiraz in the southwest of Iran (Fst = 0.34524). This index  shows the genetic variability in the studied E. vermicularis population (The  in 2020 . It seembranches , but ourpulation . A studypulation . Like ouNeutrality indices of the isolates from appendectomies did not show significantly different intra-specific diversities. In other words, despite the haplotype diversity in Iranian samples, these changes did not lead to intra-specific diversity.FST will seriously underestimate differentiation in highly structured populations. Fst values between the E. vermicularis population of this study and Gilan and Khorramabad are 0, indicating low genetic differentiation in or same population. This finding could be attributed to little direct movement or interaction of infected human populations. The limitation of this study was that the number of sequences was related to isolates for more comprehensive details to compare the sequences with each other.Balloux describes genetic discrimination grade from infra-population in 2002 , 26. FSTE. vermicularis population and add new information about genotyping of these parasites in Iran. In comparison with other studies, intra-specific variation of this parasite from Iran was observed.In conclusion, our samples show different haplotypes in the B type of


Fhb1 and resistance genes from emmer wheat and by selection against adverse alleles of elite durum wheat.FHB resistance of durum wheat was improved by introgression of Triticum aestivum, T. dicoccum and T. dicoccoides. The lines were phenotyped for FHB resistance, anthesis date, and plant height in artificially inoculated disease nurseries over 5 years. A broad variation was found for all traits, while anthesis date and plant height strongly influenced FHB severities. To correct for spurious associations, we adjusted FHB scorings for temperature fluctuations during the anthesis period and included plant height as a covariate in the analysis. This resulted in the detection of seven quantitative trait loci (QTL) affecting FHB severities. The hexaploid wheat-derived Fhb1 QTL was most significant on reducing FHB severities, highlighting its successful introgression into several durum wheat backgrounds. For two QTL on chromosomes 1B and 2B, the resistance alleles originated from the T. dicoccum line Td161 and T. dicoccoides accessions Mt. Hermon#22 and Mt. Gerizim#36, respectively. The other four QTL featured unfavorable alleles derived from elite durum wheat that increased FHB severities, with a particularly negative effect on chromosome 6A that simultaneously affected plant height and anthesis date. Therefore, in addition to pyramiding resistance genes, selecting against adverse alleles present in elite durum wheat could be a promising avenue in breeding FHB-resistant durum wheat.Durum wheat is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is impeded by the low genetic variation within the elite gene pool. To extend the genetic basis for FHB resistance in durum wheat, we analyzed 603 durum wheat lines from crosses of elite durum wheat with resistance donors carrying resistance alleles derived from The online version contains supplementary material available at 10.1007/s00122-023-04426-7. Triticum aestivum L.) and durum wheat (Triticum durum Desf.) and is caused by fungi of the genus Fusarium  is one of the most destructive diseases of bread wheat  include two elite durum lines and two resistant donor lines, 361 lines (subpopulations 5–10) originate from crosses of one elite durum wheat cultivar and three resistance donors and subpopulation 4, comprising 89 lines, descents from crosses of four resistance donors.A total of 603 durum wheat recombinant inbred lines Table S1a) developed at the University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln) was used in this study. According to the parents the lines were grouped into ten subpopulations (Table a developT. aestivum (DBC480), T. dicoccum , and T. dicoccoides  and were developed at the University of Natural Resources and Life Sciences, Vienna  and I19 has Mt. Gerizim#36 (aka T. dicoccoides 52A) as FHB resistance source , the Austrian durum wheat cultivars Durobonus (registered 2004 by Saatzucht Donau GesmbH & Co KG) and Floradur (registered 2003 by Saatzucht Donau GesmbH & Co KG) as well as the Austrian breeding line SZD1029K (Saatzucht Donau GesmbH & Co KG). All elite durum wheat parents possess the semi-dwarfing allele The lines were tested in nine artificially inoculated field trials at the University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Austria , following crop management standards described by Buerstmayr et al. . Each liF. culmorum 'Fc91015' was prepared and stored at − 80 °C  based on the formula delineated by Buerstmayr et al. .Correction of each FHB scoring by anthesis date and accumulated thermal time was done as described in Moreno-Amores et al.  to avoiduncorrected, AUDPCcorrected), date of anthesis (defined in days after May 1st) and plant height (cm) were used for the analysis. Single trials were analyzed for each trait with the linear mixed model:kth replication (block), and FHB severities , anthesis date, and plant height were estimated for all pairwise trial combinations, and correlations among the traits were calculated for BLUEs across all trials and for each trial individually. All statistical analyses of the phenotypic data were performed with R 3.5.1 , 0 = heterozygous (AB), − 1  = homozygous (BB). The DArTseq PAV and UMN10 were coded as 1 (presence) and − 1 (absence). The physical positions of the markers were determined by aligning the marker sequences to the T. turgidum durum wheat Svevo (RefSeq Rel. 1.0) reference genome  as described in Weir  of the filtered and imputed genotypic data with the R function  Wickham . The pai in Weir  using thsommer (Covarrubias-Pazaran α = 0.05. Quantile–quantile (Q–Q) plots based on observed and expected − log10p values were drawn using the R package qqman (Turner corrected) data. Additive effects were estimated as half the difference between the averages of the BLUEs value of the homozygote for each marker.Genome-wide association mapping was performed with the R package n Turner  to checkn Turner . Furtheruncorrected), date of anthesis and plant height but with high correlations between FHB severity and anthesis date (r = 0.47**) and plant height (r =  − 0.64**), such that later flowering and shorter lines tended to have higher disease severities (Table corrected) considering anthesis date and thermal accumulation during the evaluation period nearly eliminated the association of FHB severity with anthesis date (r =  − 0.06**) and also reduced the significant negative correlation between FHB severity and plant height (r =  − 0.45**)  Tables , S2.Tablcorrected was used as the measure for FHB severity for all further analysis. The 603 durum wheat lines displayed large and continuous variation for FHB severity, which was slightly skewed toward resistance with an AUDPC mean of about 270 .The genotypic variance was much larger than the genotype-by-year interaction, yielding a high across-year broad-sense heritability for FHB severity . The PCA analysis divided the 603 durum wheat lines into two main distinct clusters based on the number of elite durum wheat cultivars used for crossing Fig. . The twor2) over physical distance in Mbp . The intrachromosomal LD decay, below a r2 critical threshold lower than 0.2, showed a mean value of 39 Mbp for the whole genome  and varied between chromosomes from 16.02 Mbp (chromosome 6A) to 103.5 Mbp (chromosome 2A) .The LD patterns of the 603 durum wheat lines are graphically displayed by scatter plots of pairwise LD  for which the favorable allele originated from parental lines with a T. dicoccum genetic background and on chromosome 2BS  with T. dicoccoides parental lines as the donors. Haplotype comparisons for markers in the QTL intervals revealed for the ‘1B QTL’ T. dicoccum line Td161 and for the ‘2B QTL’ the T. dicoccoides lines Mt. Hermon#22 (aka T. dicoccoides 1A) and Mt. Gerizim#36 (aka T. dicoccoides 52A) as the sources of resistance.Seven QTL had a significant association with FHB severity when correcting for anthesis date by thermal accumulation and including plant height as a covariate in the GWAS model Table , Fig. 3aThe four QTL on chromosomes 3A, 3B, 5A, and 6A detected susceptibility alleles in elite durum wheat that increased FHB severities. Several elite durum wheat parents inherited the unfavorable alleles for the significant marker associations on chromosomes 3A, 3B, and 5A Table a. The 6ARht-B1, which was the predominant regulator of FHB severities but completely disappeared when using plant height as a covariable . Nevertheless, the resistance QTL derived from hexaploid wheat, Fhb1, was significantly associated with FHB severity regardless of statistical adjustment for plant height or temperature correction on AUDPC values, confirming its robustness and importance.Adjusting FHB severities for anthesis date and accumulated temperature and using plant height as a covariable diminished colocalization of markers associated with FHB severity and simultaneously with anthesis date or plant height. Particularly evident is the corrective effect on the semi-dwarfing locus Ppd-B1  was the most significant, revealed the highest explained genetic variance (17.88%) and colocalized with the major determinant of anthesis date Rht-B1 detected the most prominent association  and a large additive effect, the 'short' Rht-B1b allele reduced plant height substantially by − 10.38 cm  given that they did not possess the unfavorable allele at the ‘6A QTL’ from durum wheat SZD1029K  compared to lines with no resistance QTL (µ = 509.03)  has been repeatedly reported to strongly increase FHB susceptibility in durum wheat  suggesting that Fhb1 significantly and consistently reduces FHB severity in durum wheat even under field conditions. These results underlined thus the usefulness of Fhb1 in practical FHB resistance breeding programs for durum wheat.The most significant association was detected for the n et al.  confirmeFhb1 can improve FHB resistance significantly, pyramiding resistance genes is important to increase the level and the durability of resistance  and the identification of the same QTL associated with FHB resistance and DON accumulation. Additionally, Scarpino and Blandino . Yet, quantifying DON content is more expensive and technically more challenging compared to assessing FHB disease symptoms on the plants. For bread wheat, a comprehensive meta-analysis conducted by Paul et al.  examinedo et al.  assessedBlandino  reportedT. aestivum, T. dicoccum and T. dicoccoides in durum wheat background. Pyramiding the favorable alleles from these resistance donors at the detected marker-trait associations revealed that such a strategy can achieve an increase in FHB resistance. Moreover, identification of susceptibility alleles in the elite durum wheat germplasm and the selection against these alleles can further boost resistance levels. Hence, combining multiple resistance QTL from wild and cultivated relatives of durum wheat can be considered a promising strategy in breeding, which will lead to the development of new cultivars with increased FHB resistance in the long term.Harnessing the potential of genetic resources can enlarge the durum wheat gene pool and accelerate the genetic improvement of FHB resistance. We, therefore, conducted genome-wide association mapping to decipher the genetic architecture of FHB resistance in a large durum wheat panel with multiple parents. It was thereby pivotal to adjust the FHB severity scorings for temperature fluctuations during the anthesis period to prevent spurious associations. The plant material itself was derived from crosses between durum wheat elite germplasm and resistance donors carrying introgressions of resistance alleles from Supplementary file1 (XLSX 26560 KB)Supplementary file2 (DOCX 2726 KB)Below is the link to the electronic supplementary material.