Search Results (56)

Fusarium head blight (FHB) is a devastating disease of wheat (Triticum aestivum) globally. Utilizing resistance genes from wild relatives like Thinopyrum elongatum offers a promising approach for genetic improvement. We introgressed FHB resistance from Th. elongatum chromosome 1E into common wheat by inducing homoeologous recombination with wheat chromosome 1B using the ph1b mutant. From a population of 376 BC₁F₂ individuals, we identified 19 independent 1E-1B recombinant lines using KASP markers and fluorescence genomic in situ hybridization (FGISH). High-resolution genotyping with a 130K SNP array precisely mapped recombination breakpoints, revealing a hotspot in the distal long arm. Further phenotypic evaluation revealed that 11 recombinants exhibited significantly enhanced FHB resistance compared to the susceptible Chinese Spring (CS) control. Cytogenetic and physical mapping localized the resistance to a ~48 Mb subtelomeric interval on the long arm of chromosome 1E. This study provides novel wheat germplasm with improved FHB resistance, delineates the physical location of the resistance gene(s) on chromosome 1E, and demonstrates an efficient strategy for precise introgression of valuable genes from wild relatives into cultivated wheat. Full article

Naturally colored cotton offers ecological advantages by eliminating the need for chemical dyeing; however, its limited fiber quality restricts its commercial utilization. The main goal of this study was to evaluate the potential of the SSR marker BNL1604 for marker-assisted selection in naturally colored cotton (G. hirsutum L.) and to assess fiber quality variation among hybrid progenies derived from crosses between colored and elite white-fiber cultivars. As an expected outcome of this approach, we also assessed whether hybridization of naturally colored lines with elite white-fiber cultivars could contribute to the improvement of fiber quality traits in segregating progenies. Five colored lines (brown and green), three elite cultivars, and fifteen derived F₃ progenies were analyzed. Fiber traits, including upper half mean length (UHML), strength, elongation, and micronaire, were measured using HVI. Genotyping was conducted with BNL1604, and in silico mapping localized this marker to chromosome A07, with a homoeologous region on D07. White-fiber cultivars exhibited superior fiber length (33.4–35.4 mm) and strength (>31 g·tex⁻¹) compared with colored lines. Several F₃ hybrids exhibited transgressive segregation (progeny with trait values significantly exceeding those of both parents, as confirmed by frequency distribution and ANOVA analyses). For instance, the F₃ (C-6577 × L-4099) hybrid achieved UHML values of 30.51 mm and strength > 31.93 g·tex⁻¹. Most progenies maintained optimal micronaire (4.0–4.9). It was concluded that the presence of the 107 bp allele of BNL1604 marker was strongly associated with high-quality fiber, specifically improved fiber strength and length. In silico annotation revealed candidate genes near the BNL1604 locus linked to fiber development. These findings highlight the potential of combining hybridization with selection based on the presence of this 107 bp allele to develop high-quality, naturally colored cotton cultivars. Full article

Triticale, a man-made cereal, has been grown worldwide since the 1980s in order to replace established cereals in difficult areas, at least partially. The present cultivars are mostly hexaploid genotypes with 42 chromosomes, of genomic structure AA BB RR. Their agricultural performance does not meet all breeding requirements. In particular, some technological characteristics are inadequate compared to tetraploid (durum) and hexaploid (soft) wheats. Therefore, we aimed to find ways to improve modern triticale varieties by targeted introgression with genes and even chromosomes from wheat, in particular, from the D genome. Through appropriate bridge crossings and embryo culture technique and under cytogenetic control, a series of new stable hexaploid lines with reasonable agronomic stability were finally produced. All of them carried a complete D sub-genome, a complete R sub-genome, plus a mixed genome consisting of various combinations of chromosomes derived from the A and B genomes representing the seven homoeologous groups. It is clear that such mixed genomes can be of genetic and breeding significance. These large introgression lines demonstrate the flexibility of genome organization and offer the opportunity for further regulatory and genetic optimization. Full article

The cultivated peanut (Arachis hypogaea L.) is a globally important oilseed and economic crop, but its narrow genetic base limits breeding progress. Wild Arachis species represent valuable genetic resources for enhancing the resilience of the peanut cultigen. While wild species from section Arachis are widely used in breeding programs, the detection of alien chromosomes in hybrids remains challenging due to limited molecular tools. In this study, a cost-effective and efficient system was established for generating species-specific molecular markers using low-coverage next-generation sequencing data, bypassing the need for whole-genome assembly. Utilizing the Chorus2 software, specific alien-chromosome oligo (SAO) markers were developed for four wild species, A. duranensis (accession A19), A. pusilla (A10), A. appresipilla (A33), and A. glabrata (G2 and G3). A total of 1166 primer pairs were designed, resulting in 220 SAO markers specific to A. duranensis, 77 to A. pusilla, 112 to A. appresipilla, 69 to A. glabrata G2, and 59 to A. glabrata G3, with the highest development efficiency observed in A. duranensis (55.0%). These markers span all chromosomes of the five wild accessions. Genome-wide, chromosome-specific SAO markers enable the efficient detection of introgressed alien chromosomes and provide insight into syntenic relationships among homoeologous chromosomes. These markers offer an effective tool for identifying favorable genes and facilitating targeted introgression for the genetic improvement of the cultivated peanut. Full article

Von Willebrand factor A (vWA) genes play important roles in regulating plant growth and development, as well as biotic stresses. However, limited data are available on the contributions of vWA genes to wheat (Triticum aestivum L.). In this study, 114 TavWA genes were identified in the wheat genome, which were unevenly distributed on 21 chromosomes. According to the phylogenetic analysis, the 114 TavWAs were classified into six groups, two of which (G3 and G6) were unique to wheat. Fifty-five homoeologous gene sets among A, B, and D sub-genomes were detected, which play a crucial role in the expansion of the wheat vWA gene family. Analysis of specific spatiotemporal expression patterns showed that more than 50% of TavWAs (61 out of 114) exhibited tissue-specific expression. These included 71 TavWAs that responded to one or more of the four biotic stress treatments (flg22, chitin, powdery mildew, and stripe rust). Notably, these included TavWA1-7D, a recently reported key growth regulator in wheat, suggesting its additional role in biotic stress responses. RT-qPCR analysis indicated that eight genes (TavWA1-7D, TavWA24-2B, TavWA36-1D, TavWA37-7D, TavWA40, TavWA47, TavWA51, and TavWA53) may play important roles in wheat’s powdery mildew resistance. Collectively, the results of this study provide significant insights for future research on the involvement of vWA genes in the development and stress responses of wheat. Full article

Group 1 LEA proteins are involved in embryo water dynamics during the maturation stage of seed development and contribute to desiccation stress protection in vegetative and embryonic tissues. Nevertheless, their roles in durum wheat remain largely unexplored. This study represents the first comprehensive survey of group 1 LEA proteins and their encoding genes in Triticum turgidum ssp. Durum (durum wheat). Eight group 1 LEA (TtEM1 to TtEM8) genes were identified in the durum wheat genome, which were named according to their chromosomal location. Analyses of the physiochemical characteristics and subcellular location revealed that all TtEM proteins exhibited a highly disordered structure (more than 90% of tendency of disorder) and were located in the nucleus. Evolutionary analysis between the durum wheat family and all other known group 1 LEA proteins from Arabidopsis thaliana, rice (Oryza sativa), barley (Hordeum vulgare), and barrel medic (Medicago truncatula) showed four phylogenetic groups; each group shares the same conserved motifs and gene structure. Interestingly, almost TtEM genes harbor cis-elements related to hormone regulation, stress response, and growth regulation, indicating their function in stress tolerance and developmental control. Subsequently, Expression analysis of two homoeologous genes, TtEM1 and TtEM4, demonstrated that the two genes exhibited distinct expression profiles across different tissues and in response to various stress treatments, suggesting that these genes may be involved in regulating growth, development, and stress adaptation in durum wheat. TtEM1 and TtEM4 purified proteins act as molecular chaperones and protect LDH activity against desiccation, cold, and heat treatments. Moreover, TtEM1 and TtEM4 genes were proved to enhance heat, cold, oxidative, and drought tolerance in yeast. These results clearly described the characteristics and the evolutionary dynamics of the EM gene family in wheat, and unveiled their role in wheat development and response to abiotic stress. Full article

Psathyrostachys huashanica (2n = 2x = 14, NsNs) and Leymus mollis (2n = 4x = 28, NsNsXmXm) are important wild relatives of common wheat. The Ns chromosomes from two species have been successfully introgressed into wheat through distant hybridization. To compare the genetic effects and evolutionary relationship of Ns chromosomes from different genera in a wheat background, wheat-P. huashanica derivative WH15 and wheat-L. mollis derivative WM14-2 were selected. Sequential FISH-GISH showed that both WH15 and WM14-2 contained 40 wheat chromosomes (with 2D deletion) and two Ns chromosomes with different FISH karyotypes. Molecular markers and SNP array analysis revealed that the two lines both introduced 2Ns chromosomes. However, the P. huashanica 2Ns and L. mollis 2Ns had distinct sequence compositions, and the different SNPs between the two species 2Ns chromosomes were primarily clustered on the short arm. WH15 and WM14-2 exhibited significant differences in spike-related morphologies but shared leaf rust resistance and susceptibility to powdery mildew and Fusarium head blight. Cytogenetic analysis confirmed stable meiotic inheritance of the introduced 2Ns chromosomes. We further developed universal diagnostic markers for 2Ns chromosomes based on SLAF-seq. Therefore, substantial divergence likely exists between the Ns genomes of P. huashanica and L. mollis, and P. huashanica is probably not the direct Ns genome donor for Leymus. Our research-developed derivatives provide unique resources for comparative studies of the structural and functional evolution of homoeologous Ns chromosomes across genera, while offering valuable alleles for wheat improvement. Full article

The genus Vigna Savi (Leguminosae Juss.) comprises approximately 150 species, classified into five subgenera, most of which exhibit a diploid chromosome number of 2n = 22. However, the wild species Vigna lasiocarpa (Benth) Verdc. (V. subg. Lasiospron) is notable for its dysploid chromosome number of 2n = 20. This study aimed to elucidate the chromosomal events involved in the karyotype evolution of V. lasiocarpa (Vla). We used oligopainting probes from chromosomes 1, 2, 3, and 5 of Phaseolus vulgaris L. and two barcode probes from the genome of V. unguiculata (L.) Walp. Additionally, bacterial artificial chromosomes (BACs) from V. unguiculata and P. vulgaris, along with a telomeric probe from Arabidopsis thaliana (L.) Heynh., were hybridized to V. lasiocarpa metaphase chromosomes to characterize Vla3, Vla7/5, and Vla9. Our findings revealed conserved oligo-FISH patterns on chromosomes 2, 6, 8, 10, and 11 between V. unguiculata and V. lasiocarpa. Paracentric and pericentric inversions were identified for Vla3 and Vla9, respectively. Our integrative approach revealed that the dysploid chromosome originated from an “end-to-end fusion” of homoeologous chromosomes 5 and 7. This is the first report on the chromosomal mechanisms underlying descending dysploidy in Vigna, providing new insights into the evolutionary dynamics of the genus. Full article

Drought stress is a devastating natural stress that threatens crop productivity and quality. Mitigating the adverse effects of drought stress on wheat is a key object in agriculture. C-repeat binding transcription factor/DROUGHT RESPONSE ELEMENT BINDING FACTOR 1 (CBF/DREB1) transcription factors are well known for their role in cold acclimation. However, the involvement of CBF genes in drought stress and the mechanisms underlying their function remain poorly understood. In this study, 81 CBFs were identified in wheat, which were further clustered into four distinct lineages based on phylogenetic analysis. Chromosomal localization indicated that most CBF genes were dispersed across chromosome 5. We identified three homoeologous genes (TaCBF14A, TaCBF14B, and TaCBF14D) that were simultaneously upregulated under drought stress based on RNA-seq analysis. According to the high expression after drought stress, TaCBF14B was selected for further functional analysis. Subcellular localization and transcriptional activation activity analysis indicated that TaCBF14B likely functions as a transcription factor involved in drought stress tolerance. Overexpression of TaCBF14B in Arabidopsis enhanced the primary root growth by 13.49% (OE1), 12.56% (OE2), and 19.53% (OE3) under 200 mM mannitol treatment, and 21.65% (OE1), 16.63% (OE2), and 28.13% (OE3) under 250 mM mannitol treatment compared to WT. Meanwhile, the water loss rate of transgenic lines was 56% in WT leaves, but only 44%, 50%, and 40% in OE1, OE2, and OE3 lines, respectively. Compared to the wild type, POD activities of OE1, OE2, and OE3 were significantly increased by 42.94%, 29.41%, and 62.52%, respectively. And the Pro activities in OE1, OE2, and OE3 were significantly increased by 16.33%, 5.18%, and 29.09%, respectively, compared to the wild type. Additionally, the MDA content in OE1, OE2, and OE3 was significantly reduced by 40.53%, 15.81%, and 54.36%, respectively. Further analysis showed that the transgenic lines were hypersensitive to abscisic acid (ABA), and exhibited increased expression of AtABI3. We speculate that TaCBF14B plays an important role in enhancing drought tolerance. In summary, our findings provide new insights into the functional roles of CBF genes in drought stress tolerance. Full article

Rice (Oryza sativa) is one of the key staple crops, providing food for nearly half of the world’s population. The past twenty years have seen significant advances in understanding Oryza species through genome sequencing efforts. However, the stability of Oryza genomes during their divergence has not been well characterized. Here, by performing gene collinearity and comparative genomics analysis, we selected ten Oryza species and three other Poaceae species to check their genome stability, with Leersia perrieri as the reference. Intra- and intergenomic analysis showed a ~30% difference in homologous block numbers and a 35.7% difference in collinear gene numbers per block, indicating that Oryza genomes have undergone extensive DNA permutations. Notably, we found that Oryza chromosomes with smaller ordinal numbers have often preserved larger percentages of genes, while those with bigger numbers have undergone more gene losses. This unique observation may be explained by elevated gene losses incurred by illegitimate or homoeologous recombination between homoeologous chromosomes produced by the grass-common tetraploidization (GCT) ~100 million years ago (Mya), e.g., Chro. 11 and 12. However, the lowered gene loss rates in Chro. 1–3 could be explained by earlier restriction of illegitimate recombination after the GCT due to there often being (larger) neo-chromosomes produced by the fusion of ancestral chromosomes. The enriched NBS-LRR (nucleotide-binding site and leucine-rich repeat) genes in chromosomes 11 and 12 are another explanation for the above observation. Further evidence was obtained from other Poaceae plants. Moreover, we revealed around twice as many differences in tandem genes and their densities among Oryza plants, further showing their divergent levels of genome stability. The present efforts may contribute to the understanding of the stability of the Oryza genome and its formation, evolution, and functional innovation. Full article

Plant respiratory burst oxidase homologs (Rbohs) are key enzymes that produce reactive oxygen species (ROS), which serve as signaling molecules regulating plant growth and stress responses. In this study, 39 TaRboh genes (TaRboh01–TaRboh39) were identified. These genes were distributed unevenly among the wheat genome’s fourteen chromosomes, with the exception of homoeologous group 2 and 7 and chromosomes 4A, as well as one unidentified linkage group (Un). TaRbohs were classified into ten distinct clades, each sharing similar motif compositions and gene structures. The promoter regions of TaRbohs contained cis-elements related to hormones, growth and development, and stresses. Furthermore, five TaRboh genes (TaRboh26, TaRboh27, TaRboh31, TaRboh32, and TaRboh34) exhibited strong evolutionary conservation. Additionally, a Ka/Ks analysis confirmed that purifying selection was the predominant force driving the evolution of these genes. Expression profiling and qPCR results further indicated differential expression patterns of TaRboh genes between heat and drought stresses. TaRboh11, TaRboh20, TaRboh22, TaRboh24, TaRboh29, and TaRboh34 were significantly upregulated under multiple stress conditions, whereas TaRboh30 was only elevated in response to drought stress. Collectively, our findings provide a systematic analysis of the wheat Rboh gene family and establish a theoretical framework for our future research on the role of Rboh genes in response to heat and drought stress. Full article

Polyploids are essential in plant evolution and species formation, providing a rich genetic reservoir and increasing species diversity. Complex polyploids with higher ploidy levels often have a dosage effect on the phenotype, which can be highly detrimental to gametes, making them rare. In this study, offspring plants resulting from an autoallotetraploid (RRRC) derived from the interspecific hybridization between allotetraploid Raphanobrassica (RRCC, 2n = 36) and diploid radish (RR, 2n = 18) were obtained. Fluorescence in situ hybridization (FISH) using C-genome-specific repeats as probes revealed two main genome configurations in these offspring plants: RRRCC (2n = 43, 44, 45) and RRRRCC (2n = 54, 55), showing more complex genome configurations and higher ploidy levels compared to the parental plants. These offspring plants exhibited extensive variation in phenotypic characteristics, including leaf type and flower type and color, as well as seed and pollen fertility. Analysis of chromosome behavior showed that homoeologous chromosome pairing events are widely observed at the diakinesis stage in the pollen mother cells (PMCs) of these allopolyploids, with a range of 58.73% to 78.33%. Moreover, the unreduced C subgenome at meiosis anaphase II in PMCs was observed, which provides compelling evidence for the formation of complex allopolyploid offspring. These complex allopolyploids serve as valuable genetic resources for further analysis and contribute to our understanding of the mechanisms underlying the formation of complex allopolyploids. Full article

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids. Full article

The limited culinary utilizations of durum wheat (Triticum turgidum ssp. durum) are partly related to its very hard kernel texture, which is due to the softness genes Puroindoline a (Pina) and Puroindoline b (Pinb) on the Hardness (Ha) locus eliminated during allopolyploid formation. A previous study has reported that the softness genes Dina/Dinb, homologous to Pina/Pinb, were located on the chromosome arm 5VS of wild species Dasypyrum villosum. In the present study, we describe the process of transferring the soft grain texture from D. villosum into durum wheat through homoeologous recombination to develop a Robertsonian translocation. A durum wheat–D. villosum T5AL·5V#5S translocation line, S1286, was developed and characterized by molecular cytogenetic analysis from BC₄F₂ progeny of durum cv. ZY1286/D. villosum 01I140. The translocation line S1286 exhibited a soft grain texture as evidenced by observation through an electron microscope and a Single Kernel Characterization System (SKCS) hardness value of 5.5. Additionally, a newly developed 5VS/5AS co-dominant InDel marker, LW5VS-1, facilitated the transfer of the T5AL·5V#5S translocated chromosome into diverse durum wheat backgrounds. Subsequently, the T5AL·5V#5S translocated chromosome was transferred into five high-yielding durum wheat backgrounds by backcrossing and traced using marker LW5VS-1. Compared with each recurrent parent, T5AL·5V#5S lines showed good viability, similar development, and no yield penalty. Meanwhile, a significant decrease in plant height of about 6.0% was observed when comparing T5AL·5V#5S translocation lines with their recurrent parents. Accordingly, our results provide an efficient strategy for developing soft kernel durum wheat through the combination of T5AL·5V#5S translocation and the co-dominant marker LW5VS-1, which will be crucial for meeting the future challenges of sustainable agriculture and food security. Full article

Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome’s polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era. Full article