Search Results (52)

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a highly destructive disease prevalent across most wheat-growing regions globally. The most effective strategy for combating this disease is through the exploitation of durable and robust resistance genes from the relatives of wheat. Thinopyrum intermedium (Host) Barkworth and D.R. Dewey has been widely hybridized with common wheat and has been shown to be a valuable source of genes, conferring resistance and tolerance against both the biotic and abiotic stresses affecting wheat. In this study, a novel wheat–Th. intermedium 2StS.2J^SL addition line, named Th93-1-6, which originated from wheat–Th. intermedium partial amphidiploid line, Th24-19-5, was comprehensively characterized using nondenaturing-fluorescence in situ hybridization (ND-FISH) and Oligo-FISH painting techniques. To detect plants with the transfer of resistance genes from Th93-1-6 to wheat chromosomes, 2384 M₁-M₃ plants from the cross between Th93-1-6 and the susceptible wheat cultivar MY11 were studied by ND-FISH using multiple probes. A total of 37 types of 2StS.2J^SL chromosomal aberrations were identified. Subsequently, 12 homozygous lines were developed to construct a cytological bin map. Ten chromosomal bins on the 2StS.2J^SL chromosome were constructed based on 84 specific molecular markers. Among them, eight alien chromosome aberration lines, which all contained the bin 2StS-3, showed enhanced stripe rust resistance. Consequently, the gene(s) for stripe rust resistance was physically mapped to the 92.88-155.32 Mb region of 2StS in Thinopyrum intermedium reference genome sequences v2.1. Moreover, these newly developed wheat–Th. intermedium 2StS.2J^SL translocation lines are expected to serve as valuable genetic resources in the breeding of rust-resistant wheat cultivars. 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

Non-glaucous wheat can reduce solar light reflection in low-light cultivation regions, enhancing photosynthetic efficiency and potentially increasing yield. In previous work, a non-glaucous cuticular line, YL-429, was discovered in derivatives of pentaploid hybrids by crossing the synthetic wheat LM/AT23 (non-glaucous cuticular) with its tetraploid donor parent LM (glaucous) and selfing to F₇ generations. In the present study, multicolor fluorescence in situ hybridization was used to characterize the karyotype of the YL-429 line; genome resequencing was performed to identify the breakpoint of the 2D-2A chromosome translocation of YL-429; and bulk sequencing analysis was conducted to detect the SNP in the translocated fragment and accordingly develop specific kompetitive allele-specific PCR markers for use in breeding. The line YL-429 was preliminarily determined as a 2DS and 2AS translocation (LM T2DS-2AS.2AL) line through karyotyping. Genome alignment identified an approximately 13.8 Mb segment, including the wax inhibitor gene Iw2, in the telomeric region of the 2DS chromosome arm replacing an approximately 16.1 Mb segment in that of the 2AS chromosome arm. According to the bulk DNA sequencing data, 27 specific KASP markers were developed for detecting the translocated fragment from the 2DS of Aegilops tauschii. The LM T2DS-2AS.2AL translocation line YL-429 could be helpful in improving the photosynthesis of durum wheat cultivated in low-light cultivation regions. The developed markers can assist the screening of the T2DS-2AS.2AL translocation in breeding. Full article

Distant hybridization between Brassica napus and related genera serves as an effective approach for rapeseed germplasm innovation. Isatis indigotica, a wild relative of Brassica, has emerged as a valuable genetic resource for rapeseed improvement due to its medicinal properties. This study employed anchor mapping of alien chromosomal fragment localization (AMAC) method to efficiently identify alien chromosomal fragments in the progeny derived from distant hybridization between I. indigotica and Brassica napus, ‘Songyou No. 1’. Based on the AMAC method, we developed 193,101 IP and SSR markers utilizing the I. indigotica reference genome (Woad-v1.0). Through Electronic-PCR analysis against the Brassica and I. indigotica pan-genome, 27,820 specific single-locus (SSL) IP and SSR markers were obtained. Subsequently, 205 pairs of IP primers and 50 pairs of SSR primers were synthesized randomly, among which 148 pairs of IP markers (72.20%) and 45 pairs of SSR markers (90%) were verified as SSL molecular markers for the I. indigotica genome with no amplification product in four Brassica crops. These 193 SSL markers enable precise identification of one complete I6 chromosome and three chromosomal fragments (I1:1.17 Mb, I5:2.61 Mb, I7:1.11 Mb) in ‘Songyou No. 1’. Furthermore, we traced 32 genes involved in bioactive compound biosynthesis within/near these alien segments in ‘Songyou No. 1’ and developed seven functional markers. This study not only validates the efficacy of SSL markers for detecting exogenous chromatin in intergeneric hybrids but also provides valuable insights for the precise identification and mapping of desired chromosomal fragments or genes embedded in the derivatives from distant hybridization and potential applications in marker-assisted breeding for medicinal plant via distant hybridization strategy between I. indigotica and Brassica crops. Full article

Kluyveromyces marxianus is an emerging yeast cell host for diverse products, but multiple-gene expression in K. marxianus faces challenges due to limited current knowledge of cis-regulatory elements and insertion loci. Our previous study transferred an alien Saccharomyces cerevisiae chromosome I (R1) into K. marxianus, resulting in the creation of the monochromosomal hybrid yeast KS-R1. All R1 genes were actively transcribed, providing a series of loci with varying transcriptional activities. Here, we explore the use of R1 as a novel platform for stable, multi-gene integration and expression. By deleting three essential K. marxianus genes while complementing their functions with orthologs on R1, we achieved stable propagation of R1 in the absence of selective pressure. We characterized several loci on R1 that exhibit stable transcriptional activities under various conditions. GFP inserted in place of genes at six such loci demonstrated varying expression levels. Strains with GFP at two loci exhibited significantly higher expression than those with GFP at a single locus. Furthermore, we replaced five R1 genes with disulfide bond formation genes from Pichia pastoris at distinct loci, resulting in the active expression of all five genes and significantly enhanced production of heterologous glucoamylases BadGLA and TeGlaA. Our findings demonstrate that alien chromosomes offer a stable and versatile platform for the coordinated expression of multiple heterologous genes, serving as valuable tools for metabolic engineering and synthetic biology. Full article

When glufosinate-resistant transgenic Brassica napus (transgene PAT located on C chromosome) were backcrossed with wild Brassica juncea, 50% of the progeny expressed PAT under favourable conditions. However, exposure to stress (drought, salt, flooding, and intraspecific competition) increased the proportion of plants expressing the PAT gene (r-e plants) by approximately 20% compared to those under unstressed conditions. In the self-pollinated progeny of the stressed plants, the proportion of r-e plants increased by a nearly 30% compared to that of the unstressed plants. Composite fitness was comparable between plants developed under drought stress at the seedling stage and those grown under favourable conditions. Abscisic acid (ABA) content and expression of the Repressor of Silencing 1 (ROS1) in leaves increased significantly after stress treatment in the progeny, with r-e plants exhibiting higher levels. Exogenous ABA treatment significantly up-regulated ROS1 expression in progeny leaves, and the ABA treatment of seeds increased the survival of progeny exposed to glufosinate by 15%. Results suggest that increasing ABA under stress may enhance the demethylation of PAT’s promoter by promoting ROS1 expression, thereby inhibiting transgene silencing of PAT, indicating that transgene located on the C chromosome of transgenic B. napus may pose a higher risk of gene flow to wild B. juncea under stress, especially drought stress. Full article

Rape (Brassica napus) is an important oilseed crop widely cultivated worldwide. Due to its relatively short evolutionary and domestication history, its intra-species genetic diversity is limited. Radish (Raphanus sativus), belonging to a different genus but the same family as B. nupus, possesses an abundance of excellent gene resources. It is commonly used for B. nupus germplasm improvement and genetic basis expansion, making it one of the most important close relatives for distant hybridization. In the present study, a novel method for detecting alien chromosome fragments, called Anchor Mapping of Alien Chromosome (AMAC) was used to identify radish chromosome segments in the progeny of rape–radish interspecific hybrids. Based on the AMAC method, 126,861 pairs of IP (Intron Polymorphism) and 76,764 pairs of SSR (Simple Sequence Repeat) primers were developed using the radish Rs1.0 reference genome. A total of 44,176 markers (23,816 pairs of IP and 20,360 pairs of SSR markers) were predicted to be radish genome specific-single-locus (SSL) markers through electronic PCR analysis among four R. sativus, one B. napus, one B. rapa, one B. juncea, and one B. juncea reference genome. Among them, 626 randomly synthesized SSL markers (478 SSL IP markers and 148 SSL SSR markers) were used to amplify the genome of 24 radish samples (R. sativus), 18 rape (B. napus), 2 Chinese cabbage (B. rapa), 2 kale (B. oleracea), and 2 mustard (B. juncea) samples, respectively. Then, 333 SSL markers of the radish genome were identified, which only amplified in the radish genome and not in any Brassica species genome, including 192 IP markers and 141 SSR markers. Furthermore, these validated SSL markers were used to identify alien chromosome fragments in Ogura-CMS restorer line 16C, Ogura-CMS sterile line 81A, and their hybrid-Yunyouza15. In 16C, one marker, Rs1.0025823_intron_3, had an amplification product designated as anchor marker for the alien chromosome fragment of 16C. Afterwards, four novel radish genome-specific IP markers were found to be flanking the anchor marker, and it was determined that the alien chromosome segment in 16C originated from the region 8.4807–11.7798 Mb on radish chromosome R9, and it was approximately 3.2991 Mb in size. These results demonstrate that the AMAC method developed in this study is efficient, convenient, and cost-effective for identifying excellent alien chromosome fragments/genes in distant hybrid progeny, and it can be applied to the molecular marker-assisted breeding and hybrid identification of radish and Brassica crop species. Full article

Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and reproduction of D. macrophthalmus have been successful and this species has become an economic species locally. However, there is still little research on D. macrophthalmus. Methods: In this study, a high-quality genome of D. macrophthalmus was assembled and annotated. The genome was sequenced and assembled using the PacBio platform and Hi-C method. Results: The genome size is 1.01 Gb and N50 is 37.99 Mb. The assembled contigs were anchored into 24 chromosomes. BUSCO analysis revealed that the genome assembly has 95.6% gene coverage completeness. A total of 455.62 Mb repeat sequences (48.50% of the assembled genome) and 30,424 protein-coding genes were identified in the genome. Conclusions: This study provides essential genomic data for further research on the evolution and conservation of D. macrophthalmus. Meanwhile, the high-quality genome assembly also provides insights into the genomic evolution of the genus Distoechodon. Full article

Rye (Secale cereale L.) genes, which contribute to the tertiary gene pool of wheat, include multiple disease resistance genes useful for the genetic improvement of wheat. Introgression lines are the most valuable materials for wheat breeding because of their small alien segments and limited or lack of linkage drag. In the present study, wheat–rye derivative lines SN21627-2 and SN21627-6 were produced via distant hybridization. A genomic in situ hybridization analysis revealed that SN21627-2 and SN21627-6 lack alien segments, while a multi-color fluorescence in situ hybridization analysis detected structural changes in both introgression lines. At the seedling and adult plant stages, SN21627-2 and SN21627-6 were highly resistant to stripe rust and powdery mildew. Primers for 86 PCR-based landmark unique gene markers and 345 rye-specific SLAF markers were used to amplify SN21627-2 and SN21627-6 genomic DNA. Eight markers specific to rye chromosome 2R were detected in both introgression lines, implying these lines carry chromosome 2R segments with genes conferring stripe rust and powdery mildew resistance. Therefore, SN21627-2 and SN21627-6 are resistant to more than one major wheat disease, making them promising bridging parents for breeding disease-resistant wheat lines. Full article

Climate change has resulted in an increased demand for Japanese bunching onions (Allium fistulosum L., genomes FF) with drought resistance. A complete set of alien monosomic addition lines of A. fistulosum with extra chromosomes from shallot (A. cepa L. Aggregatum group, AA), represented as FF + 1A–FF + 8A, displays a variety of phenotypes that significantly differ from those of the recipient species. In this study, we investigated the impact of drought stress on abscisic acid (ABA) and its precursor, $\beta$-carotene, utilizing this complete set. In addition, we analyzed the expression levels of genes related to ABA biosynthesis, catabolism, and drought stress signal transduction in FF + 1A and FF + 6A, which show characteristic variations in ABA accumulation. A number of unigenes related to ABA were selected through a database using Allium TDB. Under drought conditions, FF + 1A exhibited significantly higher ABA and $\beta$-carotene content compared with FF. Additionally, the expression levels of all ABA-related genes in FF + 1A were higher than those in FF. These results indicate that the addition of chromosome 1A from shallot caused the high expression of ABA biosynthesis genes, leading to increased levels of ABA accumulation. Therefore, it is expected that the introduction of alien genes from the shallot will upwardly modify ABA content, which is directly related to stomatal closure, leading to drought stress tolerance in FF. 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

The inoculation of Epichloë endophytes into modern cereals, resulting in systemic infection, depends on the genetics of both the host and the endophyte strain deployed. Until very recently, the only modern cereal to have been infected with Epichloë, in which normal phenotype seed-transmitted associations were achieved, is rye (Secale cereale). Whilst minor in-roads have been achieved in infecting hexaploid wheat (Triticum aestivum), the phenotypes of these associations have all been extremely poor, including host death and stunting. To identify host genetic factors that may impact the compatibility of Epichloë infection in wheat, wheat–alien chromosome addition/substitution lines were inoculated with Epichloë, and the phenotypes of infected plants were assessed. Symbioses were identified whereby infected wheat plants were phenotypically like uninfected controls. These plants completed their full lifecycle, including the vertical transmission of Epichloë into the next generation of grain, and represent the first ever compatible wheat–Epichloë associations to be created. Full article

Thinopyrum intermedium (2n = 6x = 42, E^eE^eE^bE^bStSt or JJJ^sJ^sStSt) contains a large number of genes that are highly adaptable to the environment and immune to a variety of wheat diseases, such as powdery mildew, rust, and yellow dwarf, making it an important gene source for the genetic improvement of common wheat. Currently, an important issue plaguing wheat production and breeding is the spread of pests and illnesses. Breeding disease-resistant wheat varieties using disease-resistant genes is currently the most effective measure to solve this problem. Moreover, alien resistance genes often have a stronger disease-resistant effect than the resistance genes found in common wheat. In this study, the wheat-Th. intermedium partial amphiploid line 92048 was developed through hybridization between Th. intermedium and common wheat. The chromosome structure and composition of 92048 were analyzed using ND-FISH and molecular marker analysis. The results showed that the chromosome composition of 92048 (Octoploid Trititrigia) was 56 = 42W + 6J + 4J^s + 4St. In addition, we found that 92048 was highly resistant to a mixture of stripe rust races (CYR32, CYR33, and CYR34) during the seedling stage and fusarium head blight (FHB) in the field during the adult plant stage, suggesting that the alien or wheat chromosomes in 92048 had disease-resistant gene(s) to stripe rust and FHB. There is a high probability that the gene(s) for resistance to stripe rust and FHB are from the alien chromosomes. Therefore, 92048 shows promise as a bridge material for transferring superior genes from Th. intermedium to common wheat and improving disease resistance in common wheat. 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

We applied a genomic in situ hybridization (GISH) to analyze the genomic constitution of and meiotic pairing in interspecific somatic hybrids, and in a wide subset of backcrossing derivatives (BC₁–BC₅), from three interspecific combinations involving the cultivated potato, Solanum tuberosum (AAAA genome), and three diploid (1 EBN) wild Mexican potato species (genome BB)—S. tarnii, S. pinnatisectum, and S. bulbocastanum. The theoretically expected genomic composition was detected in the somatic hybrids (AAAABB) and in the BC₁ progeny (AAAAB), whereas in the subsequent BC₂–BC₄ generations, the partial loss of alien chromosomes was observed and almost all the BC₅ genotypes showed a complete chromosome elimination of wild species. GISH revealed a homoeologous pairing between the chromosomes of the A- and the B-genomes in each of the hybrid progenies. Using GISH, we selected introgression lines with a single chromosome of the wild species in a potato genome background, as well as introgression lines with intergenomic recombinant chromosomes. Moreover, via molecular screening, BC hybrids with diagnostic markers for the R-genes conferring resistance to late blight disease and to the quarantine pest of the potato–Columbia root-knot nematode—were selected. The potential application of the results obtained for the planning of introgressive schemes directed to the breeding of advanced lines with multiple disease and pest resistance is discussed. Full article