Search Results (32)

Boron (B) toxicity is one of the major abiotic stresses limiting wheat productivity in arid and semi-arid regions of the world. Thus, it is important to understand the molecular basis of tolerance in boron-tolerant wheat genetic resources for effective breeding. Wild emmer wheat is a valuable genetic resource for tolerance to multiple abiotic stresses; however, the molecular mechanisms behind boron toxicity tolerance in this species has not been sufficiently characterized. Here, we present the first RNA sequencing-based transcriptomic analysis of B toxicity response in a boron-tolerant Triticum dicoccoides genotype, PI362036. Shoot tissues exposed to high boron (10 mM B) for 7 days showed extensive transcriptional reprogramming with 2783 differentially expressed genes. Functional enrichment analyses showed that B toxicity significantly altered the genes associated with biosynthesis of secondary metabolites, metabolic pathways, ribosomal activity, carbon metabolism, RNA transport, photosynthesis–antenna proteins, and citrate cycle pathway. Several transcription factor families, including TIG, MYB, MYB-related families, NAC, C2H2-GATA, ARF, and AP2-EREBP families, showed significant differential regulation, emphasizing their regulatory roles in B stress adaptation. Collectively, this study provides the first comprehensive transcriptomic framework of boron toxicity tolerance in T. dicoccoides under short-term high boron exposure, identifying candidate genes and pathways that may be exploited for improving boron tolerance in cultivated wheat through targeted breeding strategies. Given that boron toxicity in agricultural systems primarily arises from excessive boron accumulation in soils and irrigation water, the identified pathways offer insight into early adaptive responses of shoot tissues to elevated boron availability. Full article

In response to the growing genetic uniformity within wheat populations, developing efficient wheat–alien translocation strategies has become critically important. We observed that several offspring of the common wheat (Triticum aestivum L.)–wild emmer (Triticum turgidum L. var. dicoccoides) chromosome arm substitution line (CASL4AL) exhibited stunted growth, including significantly reduced plant height, spike length, spikelet number, and stem width compared to normal plants. Integrative transcriptomic analyses (RNA-Seq and BSR-Seq) revealed a statistically significant depletion (p < 0.01) of single nucleotide polymorphisms (SNPs) on chromosome 4B in compromised plants. Chromosome association analysis of differentially expressed genes (DEGs, up- or downregulated) revealed that downregulated genes were predominantly located on chromosome 4B. The 1244 downregulated DEGs on Chr4B were employed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and RNA metabolic processes, DNA repair, and transport systems were significantly enriched by GO analysis; however, only the mRNA surveillance pathway was enriched by KEGG enrichment. Molecular marker profiling showed a complete absence of target amplification in the critical 0–155 Mb region of chromosome 4B in all weak plants. Pearson’s correlation coefficients confirmed significant associations (p < 0.01) between 4B-specific amplification and weak phenotypes. These results demonstrate that 4B segmental deletions drive weak phenotypes in CASL4AL progeny, and provide experimental evidence for chromosome deletions induced in wild emmer chromosome substitution lines. This study highlights the potential of wild emmer as a valuable tool for generating chromosomal variations in wheat breeding programs. Full article

To effectively mine and utilize the valuable genes of wild emmer wheat (Triticum dicoccoides, 2n = 4x = 28, AABB), this study conducted an investigation of agronomic traits using two sets of chromosome arm substitution lines (CASLs) of wild emmer wheat in the backgrounds of the common wheat varieties Bethlehem (BLH) and Chinese Spring (CS). The results indicated significant differences in growth parameters, including seedling agronomic traits, heading date (HD), and yield traits among the various CASLs in both the BLH and CS backgrounds. In both genetic backgrounds, the number of tillers in CASL7BS was significantly fewer than that of the parents. Additionally, the average leaf width of six CASLs (2BS, 1AL, 7AL, 5BS, 4AS, and 2BL) was significantly narrower compared to the parents. Among CASLs in the CS background, CASL2BS exhibited a significantly narrower average leaf width and shorter average plant height compared to both the parents and early-maturing CASLs. Conversely, CASL4AL exhibited significantly more tillers and a shorter average plant height than the other CASLs. In the BLH background, the spike phenotypes of all CASLs showed no significant differences from BLH. However, in the CS background, CASL6AS and CASL5AL demonstrated significantly longer spike lengths than CS. Moreover, CASL6BL had more spikelets per spike than CS. CASLs 4AS, 4AL, 6BS, and 6BL exhibited basal short awns and apical long awns, whereas the remaining CASLs displayed no awns, a pattern consistent with CS. We hypothesize that genes governing physiological traits such as seedling tiller number, leaf width, plant height, and spike traits are likely located on the corresponding chromosome arms. Full article

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the ancestral species of cultivated tetraploid wheat with BBAA genomes. Because of its full interfertility with domesticated emmer wheat, this wild species can serve as one of the most important genetic resources to improve durum and bread wheat. To clarify the magnitude of genetic diversity between and within populations of Turkish wild emmer wheat, 169 genotypes of ssp. dicoccoides selected from the 38 populations collected from the three sub-regions (East-1, West-1, and West-2) of the Southeast Anatolia Region of Turkey were molecularly and morphologically characterized. The populations showed significant variation in plant height, heading date, flag leaf area, spike length and number, spikelet, peduncle, lemma, palea, glume and anther lengths, glume hull thickness, anther width, and days to maturity. According to the results of nuclear-SSR analysis, the populations collected from the sub-regions East-1 and West-2 were the most genetically distant (0.539), while the populations collected from the sub-regions West-1 and West-2 were the most genetically similar (0.788) populations. According to the results of AMOVA, there was 84% similarity within the populations studied, while the variation between the populations of the three sub-regions was 16%. In the dendrogram obtained by using nuclear-SSR data, the populations formed two main groups. The populations from the sub-region East-1 were in the first group, and the populations from the sub-regions West-1 and West-2 were in the second group. From the dendrogram, it appears that the populations from the sub-region East-1 were genetically distant from the populations from the sub-regions West-1 and West-2. The results highlight the potential diversity in Southeast Anatolia for wild emmer discovery and utilization. Full article

Wild emmer is one of the progenitors of wheat, with a high genetic potential for breeding. Continuous evaluations of emmer and other progenitor species are necessary for long-term improvement in yield, agronomic, and stress-related traits. For this purpose, genetic diversity and relationships among 43 wild emmer (Triticum dicoccoides) and 5 durum wheat (Triticum durum) accessions were determined using two DNA marker systems, CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) markers. CAAT and SCoT markers generated 63 and 76 polymorphic bands, averaging 9 and 7.6 bands per primer, respectively. The discriminating power, effective multiplex ratio, expected heterozygosity, mean heterozygosity, marker index, polymorphism information content, and resolving power parameters obtained for both marker systems showed the high efficiency of these markers in detecting genetic variation in wild emmer and durum wheat. The results showed that CAAT and SCoT markers with average polymorphism are suitable marker systems for detecting genetic variation between a pool of accessions or populations. These markers would be employed for gene-targeted breeding, and the results indicate that genetic analysis with these markers would be practicable for agricultural improvement and development initiatives. Full article

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a disease that seriously harms wheat production and occurs in all wheat-producing areas around the world. Exploring Pm gene(s) and developing resistant cultivars are preferred to control the disease. Wild emmer wheat (Triticum dicoccoides, 2n = 4x = 28, AABB) has accumulated abundant gene resources for resistance to powdery mildew during the long process of natural evolution. In the current study, the WEW accession D430 was highly resistant to powdery mildew at the whole-growth stage. Genetic analysis showed that the powdery mildew resistance in D430 was conferred by a single dominant locus or gene by the cross of D430 and susceptible durum wheat 647, tentatively named PmD430. Combining BSR-Seq analysis, molecular mapping, and sequence alignment, PmD430 was finally mapped to Pm4 locus, and the sequence was identical to Pm4b. Subsequently, 1871 DEGs between resistant and susceptible bulks were annotated and analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Eight disease-related genes were evaluated by qRT-PCR and exhibited a unique expression pattern when invaded by Bgt isolate E09 and was, therefore, presented as latent targets for regulating powdery mildew resistance in D430. Full article

Over the years, alien chromosome substitution has attracted the attention of geneticists and breeders as a rich source of remarkable genetic diversity for improvement in narrowly adapted wheat cultivars. One of the problems encountered along this way is the coadaptation and realization of the genome of common wheat against the background of the introduced genes. Here, using RNA-Seq, we assessed a transcriptome response of hexaploid wheat Triticum aestivum L. (cultivar Chinese Spring) to a 5B chromosome substitution with its homolog from wild emmer (tetraploid wheat T. dicoccoides Koern) and discuss how complete the physiological compensation for this alien chromatin introgression is. The main signature of the transcriptome in the substituted line was a sharp significant drop of activity before the beginning of the photoperiod with a gradual increase up to overexpression in the middle of the night. The differential expression altered almost all biological processes and pathways tested. Because in most cases, the differential expression or its fold change were modest, and this was only a small proportion of the expressed transcriptome, the physiological compensation of the 5B chromosome substitution in common wheat seemed overall satisfactory, albeit not completely. No over- or under-representation of differential gene expression was found in specific chromosomes, implying that local structural changes in the genome can trigger a global transcriptome response. Full article

Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent discoveries have revealed that expansin proteins also have significant functions in plant growth, development, and response to resistance. However, the expansin gene family, particularly in emmer wheat, has not been thoroughly studied, particularly in terms of evolution. In this study, we identified 63 TdEXPs and 49 TtEXPs from the latest genome versions of wild emmer wheat (WEW) and durum wheat (DW), respectively. The physicochemical properties of the encoded expansin proteins exhibited minimal differences, and the gene structures remained relatively conserved. Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide “T” in expansin proteins throughout the evolution of WEW and DW. Collinearity analysis demonstrated higher orthology between the expansin proteins of WEW and DW, with a Ka/Ks ratio ranging from 0.4173 to 0.9494, indicating purifying selection during the evolution from WEW to DW. Haplotype analysis of the expansin gene family identified five genes in which certain haplotypes gradually became dominant over the course of evolution, enabling adaptation for survival and improvement. Expression pattern analysis indicated tissue-specific expression of expansin genes in emmer wheat, and some of these genes were quantified through qRT-PCR to assess their response to salt stress. These comprehensive findings present the first systematic analysis of the expansin protein gene family during the evolution from WEW to DW, providing a foundation for further understanding the functions and biological roles of expansin protein genes in emmer wheat. Full article

Wheat was one of the crops domesticated in the Fertile Crescent region approximately 10,000 years ago. Despite undergoing recent polyploidization, hull-to-free-thresh transition events, and domestication bottlenecks, wheat is now grown in over 130 countries and accounts for a quarter of the world’s cereal production. The main reason for its widespread success is its broad genetic diversity that allows it to thrive in different environments. To trace historical selection and hybridization signatures, genome scans were performed on two datasets: approximately 113K SNPs from 921 predominantly bread wheat accessions and approximately 110K SNPs from about 400 wheat accessions representing all ploidy levels. To identify environmental factors associated with the loci, a genome–environment association (GEA) was also performed. The genome scans on both datasets identified a highly differentiated region on chromosome 4A where accessions in the first dataset were dichotomized into a group (n = 691), comprising nearly all cultivars, wild emmer, and most landraces, and a second group (n = 230), dominated by landraces and spelt accessions. The grouping of cultivars is likely linked to their potential ancestor, bread wheat cv. Norin-10. The 4A region harbored important genes involved in adaptations to environmental conditions. The GEA detected loci associated with latitude and temperature. The genetic signatures detected in this study provide insight into the historical selection and hybridization events in the wheat genome that shaped its current genetic structure and facilitated its success in a wide spectrum of environmental conditions. The genome scans and GEA approaches applied in this study can help in screening the germplasm housed in gene banks for breeding, and for conservation purposes. Full article

Wild emmer, the direct progenitor of modern durum and bread wheat, has mostly been studied for grain quality, biotic, and abiotic stress-related traits. Accordingly, it should also have a certain amount of diversity for morphological and agronomic traits. Despite having a high chance of huge diversity, it has not been deeply explored. In the current study, 263 wild emmer accessions collected from different regions of Israel, Turkey, Lebanon, and Syria were characterized for a total of 19 agronomic and shoot morphological traits. Three trials were carried out in Western Australia, which demonstrated a large variation in these traits. The average phenotypic diversity (H’) was 0.91 as quantified by Shannon’s diversity index. A high heritability was recorded for most of the traits, where biomass/plant and yield/plant were identified as the most potential traits. Correlation analysis revealed several significant associations between traits, including significant positive correlation between yield and tiller number, first leaf area, spike length, and biomass/plant. The principal component analysis (PCA) demonstrated that most of the traits contributed to the overall observed variability. The cluster analysis categorized 263 accessions into five clusters on average. On the other hand, accessions were categorized into eight populations based on the collection region and a comparative analysis demonstrated considerable variations between populations for plant height, spike length, and flag leaf area. Despite the low yield, several wild emmer accessions demonstrated superior performance compared to modern bread wheat cultivars, when selection was based on combining yield with multiple traits. These observations indicate that wild emmer contains a broad gene pool for several agronomic and shoot morphological traits, which can be utilized for bread and durum wheat improvement. Full article

Wheat production losses due to boron (B) toxicity can be reduced by breeding and growing modern wheat cultivars with a greater tolerance to high B. However, breeding of tolerant genotypes is possible by identifying B-tolerant wheat genetic resources and understanding their underlying molecular mechanism. Triticum dicoccum, despite being one of the oldest cultivated wheat species, mostly remained neglected and has been less explored for its potential towards abiotic stresses. In this study, for the first time, we report a B-toxicity-tolerant T. dicoccum genotype, PI94655, and its transcriptomic response towards high-B treatment (10 mM B) using RNA sequencing and RT-qPCR. More than 450 genes were significantly differentially expressed in the shoots of PI94655 under high B. A total 3237 novel genes and 12,206 novel transcripts were determined in the study. AP2-EREBP, MYB, and C3H were the families with the highest percentages of differentially expressed transcription factors (TFs) under B toxicity. Interestingly, KEGG pathway photosynthesis–antenna proteins showed the most significant enrichment. The obtained results suggested potential candidate genes that can be focused on to improve wheat tolerance to high B in future breeding programs. These genes can be functionally characterized to elucidate their role in providing tolerance to high B. Full article

Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F_2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning. Full article

The NAC transcription factor (TF) family is one of the largest TF families in plants, which has been widely reported in rice, maize and common wheat. However, the significance of the NAC TF family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of NAC genes was conducted in the wild emmer genome and 249 NAC family members (TdNACs) were identified. The results showed that all of these genes contained NAM/NAC-conserved domains and most of them were predicted to be located on the nucleus. Phylogenetic analysis showed that these 249 TdNACs can be classified into seven clades, which are likely to be involved in the regulation of grain protein content, starch synthesis and response to biotic and abiotic stresses. Expression pattern analysis revealed that TdNACs were highly expressed in different wheat tissues such as grain, root, leaves and shoots. We found that TdNAC8470 was phylogenetically close to NAC genes that regulate either grain protein or starch accumulation. Overexpression of TdNAC8470 in rice showed increased grain starch concentration but decreased grain Fe, Zn and Mn contents compared with wild-type plants. Protein interaction analysis indicated that TdNAC8470 might interact with granule-bound starch synthase 1 (TdGBSS1) to regulate grain starch accumulation. Our work provides a comprehensive understanding of the NAC TFs family in wild emmer wheat and establishes the way for future functional analysis and genetic improvement of increasing grain starch content in wheat. Full article

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from “;”, “;N”, “;N1” to “;NC”. PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust. Full article

To meet the ever-growing global population necessities, integrating climate-change-relevant plant traits into breeding programs is required. Developing new tools for fast and accurate estimation of chlorophyll parameters, chlorophyll a (Chl-a) content, chlorophyll b (Chl-b) content, and their ratio (Chl-a/b), can promote breeding programs of wheat with enhanced climate adaptability. Spectral reflectance of leaves is affected by changes in pigment concentration and can be used to estimate chlorophyll parameters. The current study identified and validated the top known spectral indices and developed new vegetation indices (VIs) for Chl-a and Chl-b content estimation and used them to non-destructively estimate Chl-a/b values and compare them to hyperspectral estimations. Three wild emmer introgression lines, with contrasting drought stress responsiveness dynamics, were selected. Well-watered and water-limited irrigation regimes were applied. The wheat leaves were spectrally measured with a handheld spectrometer to acquire their reflectance in the 330 to 790 nm range. Regression models based on calculated VIs as well as all hyperspectral curves were calibrated and validated against chlorophyll extracted values. The developed normalized difference spectral indices (NDSIs) resulted in high accuracy of Chl-a (NDSI_415,614) and Chl-b (NDSI_406,525) estimation, allowing for indirect non-destructive estimation of Chl-a/b with root mean square error (RMSE) values that could fit 6 to 10 times in the range of the measured values. They also performed similarly to the hyperspectral models. Altogether, we present here a new tool for a non-destructive estimation of Chl-a/b, which can serve as a basis for future breeding efforts of climate-resilient wheat as well as other crops. Full article