Search Results (45)

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

Nile tilapia, as an ideal model for studying sex differentiation, is a popular farmed fish worldwide with a stable XX/XY sex-determination system. In tilapia, ovarian differentiation is triggered by estradiol-17β (E2) production in undifferentiated gonads. In a previous study, we suggested that follicle-stimulating hormone (FSH) signaling might be involved in ovarian differentiation in Nile tilapia. In this study, we further investigated the role of FSH signaling in ovarian differentiation via aromatase expression, which converts testosterone to E2. Masculinization of XX fry by aromatase inhibitor or 17α-methyltestosterone leads to suppression of fshr expression. Feminization of XY fry by E2 treatment increased fshr expression from 15 days after hatching, when E2 treatment was terminated. XX tilapia developed ovaries harboring aromatase expression if fsh and fshr were double knockdowns by morpholino-oligo injections. Finally, the transcriptional activity in the upstream region of the aromatase gene (cyp19a1a) was further increased by FSH stimulation when HEK293T cells were co-transfected with foxl2 and ad4bp/sf1. Collectively, this study suggests that the role of FSH signaling is not critical in tilapia ovarian differentiation; however, FSH signaling may have a compensatory role in ovarian differentiation by increasing cyp19a1a transcription in cooperation with foxl2 and ad4bp/sf1 in Nile tilapia. Full article

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

Interspecific hybridization serves as a crucial strategy for innovating sugarcane germplasms. Currently, nearly all modern sugarcane varieties that incorporate genetic material are derived from Saccharum spontaneum. The number of chromosomes in S. spontaneum ranges from 40 to 128, contributing significantly to the diversity of its genetic resources. However, the genetic mechanisms driving chromosome number variation in S. spontaneum remain to be fully elucidated. Here, oligonucleotide fluorescence in situ hybridization (Oligo-FISH) was conducted to identify individual chromosomes and explore chromosome transmission during the intraspecific hybridization of S. spontaneum. The results indicate that from the progenies generated from S. spontaneum Yunnan2017-22 (2n = 8x = 64) and Yunnan82-1 (2n = 8x = 64) emerged two distinct karyotypes, 2n = 12x = 96 (A1) and 2n = 8x = 64 (A2, A33-1, A18). This implies that the chromosome inheritances were 2n + n and n + n in the progenies. However, self-pollinated samples of A1 (2n = 12x = 96) produced normal offspring C1 (2n = 94) and C2 (2n = 96). The 2n + n inheritance pattern did not continue. In another cross, the progenies derived from S. spontaneum Yunnan2017-41 (2n = 8x = 64) and Yunnan8 (2n = 10x = 80) carried a karyotype of 2n = 9x = 72, with n + n inheritance mode. These findings highlight the existence of two chromosome inheritance modes, 2n + n and n + n, in the context of the intraspecific hybridization of S. spontaneum. Additionally, hybridization between different ploidy S. spontaneum was also accompanied by chromosomal translocations (A1, A2, A18, A18) and loss (A2, A33-1, AA-4, and C2) that further resulted in the complexity of the S. spontaneum genome. Together, these findings highlight diverse chromosome inheritance in S. spontaneum hybridization, and provide a theoretical foundation for the further utilization of S. spontaneum germplasm in sugarcane breeding. Full article

Turbot and brill are two congeneric commercial flatfish species with striking differences in skin organization. The calcified appendages in turbot skin are conical tubercles, while in brill, they are elasmoid scales. A skin injury involving epidermal and dermal levels was evaluated 72 h post-injury to compare the skin regeneration processes between both species. An immune-enriched 4x44k turbot oligo-microarray was used to characterize the skin transcriptome and gene expression profiles in both species. RNA-seq was also performed on the brill samples to improve transcriptome characterization and validate the microarray results. A total of 15,854 and 12,447 expressed genes were identified, respectively, in the turbot and brill skin (10,101 shared) using the oligo-microarray (11,953 and 9629 annotated). RNA-seq enabled the identification of 11,838 genes in brill skin (11,339 annotated). Functional annotation of skin transcriptomes was similar in both species, but in turbot, it was enriched on mechanisms related to maintenance of epithelial structure, mannosidase activity, phospholipid binding, and cell membranes, while in brill, it was enriched on biological and gene regulation mechanisms, tissue development, and transferase and catalytic activities. The number of DEGs identified after skin damage in brill and turbot was 439 and 143, respectively (only 14 shared). Functions related to catabolic and metabolic processes, visual and sensorial perception, response to wounding, and wound healing were enriched in turbot DEGs, while metabolism, immune response, oxidative stress, phospholipid binding, and response to stimulus were enriched in brill. The results indicate that differences may be related to the stage of wound repair due to their different skin architecture. This work provides a foundation for future studies directed at skin defense mechanisms, with practical implications in flatfish aquaculture. Full article

Chicory (Cichorium intybus L., 2n = 18), belonging to the Asteraceae family, exhibits significant edible, medicinal, and pasture values. Moderate research has been performed on identifying Chicory species’ chromosomes using fluorescence in situ hybridization (FISH) and C-banding. Detailed karyotype comparisons with chromosome nomenclature have not yet been performed for Chicory and similar species. In this study, the tandem repeats (TRs) were predicted and mapped to chromosomal regions based on released C. intybus L. ASM2352571 genome assembly v1, and then compared to the genome of Lettuce (Lactuca sativa L.). Nine new oligo probes were then developed and employed for karyotypic investigation of endive, Lettuce, and Chicory mitotic metaphase using non-denaturing FISH (ND-FISH). By combining the conserved oligo probes for 5S rDNA and 18S rDNA with the unique ND-FISH signals of new TR-oligo probes, we can develop a high-resolution standard karyotype for the cultivars of Lettuce and Chicory. The occurrence of chromosome structure variations from the natural population of Chicory and Lettuce was also revealed by ND-FISH with multiple oligo probes. The current observation of the karyotype differences and divergences of Lactuca and Cichorium and the genomic research offers crucial information about the Asteraceae family’s genetic diversity, chromosomal dynamics, and evolutionary routes. Full article

The dietary presence of feed additives is crucial for boosting fish growth and immunity. Accordingly, this feeding trial aimed to investigate the effects of the separate and concurrent dietary supplementation of Spirulina platensis (SP) and bitter lemon (Citrus limon) peel essential oil (LEO) on the growth, immunity, antioxidant capacity, and intestinal health of Nile tilapia (Oreochromis niloticus). Four groups of male Nile tilapia were employed. The first group (control) was given the basal diet, while the second and third groups received the basal diet supplemented with LEO extract (1%) and SP (1 g/kg diet), respectively. The fourth group received the basal diet supplemented with a mix of LEO (1%) and SP at 1 g/kg. After two months of feeding, using LEO or/and SP improved the overall growth and immunological parameters, with their combination yielding the best outcomes. The supplementation of LEO or/and SP improved the Nile tilapia’s growth metrics and transcriptomic levels of growth-regulating genes such as (oligo-peptide transporter 1 (Pep1), growth hormone receptors 1 (GHR1), and insulin-like growth factor (IGF1). The improved growth performance was linked to significant increases in the expression levels of mucin and fat metabolism-related genes. Moreover, fish supplemented with LEO, SP, or their combination showed enhanced non-specific immunological measures, including phagocytic and lysozyme activities and the mRNA copies of its regulating genes. Additionally, remarkable increases in the antioxidant enzyme activities and the mRNA levels of their related genes were detected. The complement (C3) gene’s transcriptomic level was also significantly increased. Furthermore, the dietary supplementation of LEO, SP, or their combination improved the histological structures of the spleen, hepatopancreas, and intestine. The enhanced effects of LEO, SP, or their combination on fish immunity and growth are suggested to be due to their contents of bioactive compounds with anti-inflammatory, antioxidant, and antimicrobial properties. Thus, using the LOE and SP blends as feed additives is recommended for better growth and immunity of Nile tilapia. Full article

In order to understand the community structure of plankton and environmental factors in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes (referred to as the “Reserve”) along the upper Yangtze River, this study investigated phytoplankton and zooplankton in the water body from 2021 to 2022. The results revealed a diverse phytoplankton community with 243 species from 105 genera and 8 phyla, dominated by Bacillariophyta and Chlorophyta. Phytoplankton showed average densities of 1.7 × 10⁶ cells/L and biomass of 2.6221 mg/L, following a seasonal pattern of summer > spring > winter. Zooplankton analysis identified 141 species from 77 genera and 4 phyla, with rotifers most abundant, followed by protozoa. Zooplankton displayed average densities of 0.17 × 10⁴ ind./L and biomass of 0.3226 mg/L, also following a seasonal pattern of summer > spring > winter. Total phosphorus (TP) emerged as the primary environmental factor influencing plankton community structure, positively correlating with phytoplankton density and zooplankton biomass. Plankton biodiversity indices classified water quality in the Chongqing section of the “Reserve” as oligo-/mesotrophic. Overall, plankton diversity in this section is notably rich, with similar species composition between mainstems and tributaries but seasonal variations in community structure. While mainstem water quality generally meets standards, some tributaries exhibit varying degrees of pollution, underscoring the need for improved ecological management and protection measures. This is crucial for maintaining the sustainability of the ecosystem. Full article

An elite hexaploid triticale Yukuri from Australia was used as a bridge for transferring valuable genes from Secale cereale L. into common wheat for enriching the genetic variability of cultivated wheat. Non-denaturing-fluorescence in situ hybridization (ND-FISH) identified that Yukuri was a secondary triticale with a complete set of rye chromosomes and a 6D(6A) substitution. Seed protein electrophoresis showed that Yukuri had a unique composition of glutenin subunits. A set of Yukuri-derived wheat-rye introgression lines were created from a Yukuri x wheat population, and all lines were identified by ND-FISH with multiple probes and validated by diagnostic molecular marker analysis. A total of 59 wheat-rye introgression lines including modified chromosome structural variations of wheat, and new complex recombinant chromosomes of rye were detected through ND-FISH and Oligo-FISH painting based on oligonucleotide pools derived from wheat-barley genome collinear regions. Wheat lines carrying the 1R chromosome from Yukuri displayed resistance to both stripe rust and powdery mildew, while the lines carrying the 3RL and 7RL chromosome arms showed stripe rust resistance. The chromosome 1R-derived lines were found to exhibit a significant effect on most of the dough-related parameters, and chromosome 5R was clearly associated with increased grain weight. The development of the wheat-rye cytogenetic stocks carrying disease resistances and superior agronomic traits, as well as the molecular markers and FISH probes will promote the introgression of abundant variation from rye into wheat improvement programs. Full article

The genome composition of intermediate wheatgrass (IWG) is complex and continues to be a subject of investigation. In this study, molecular cytogenetics were used to investigate the karyotype composition of Th. intermedium and its relative diploid species. St₂-80 developed from Pseudowroegneria strigose and pDb12H developed from Dasypyrum breviaristatum were used as probes in fluorescence in situ hybridization (FISH) to classify the chromosomes of Th. intermedium into three groups, expressed as J^vsJ^vsJ^rJ^rStSt. A combined multiplex oligonucleotide probe, including pSc119.2-1, (GAA)₁₀, AFA-3, AFA-4, pAs1-1, Pas1-3, pAs1-4, and pAs1-6, was used to establish the FISH karyotype of ten accessions of Th. intermedium. Variability among and within the studied accessions of intermediate wheatgrass was observed in their FISH patterns. Results of this study led to the conclusions that J^vs had largely been contributed from Da. breviaristatum, but not the present-day Da. villosum; IWG had only one J genome, J^r, which was related to either Th. elongatum or Th. bessarabicum; and St was contributed from the genus Pseudoroegneria by hybridization with Th. junceiforme or Th. sartorii. Full article

As a perennial herb in Triticeae, Elymus dahuricus is widely distributed in Qinghai–Tibetan Plateau and Central Asia. It has been used as high-quality fodders for improving degraded grassland. The genomic constitution of E. dahuricus (2n = 6x = 42) has been revealed as StStHHYY by cytological approaches. However, the universal karyotyping nomenclature system of E. dahuricus is not fully established by traditional fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). In this study, the non-denaturing fluorescent in situ hybridization (ND-FISH) using 14 tandem-repeat oligos could effectively distinguish the entire E. dahuricus chromosomes pairs, while Oligo-FISH painting by bulked oligo pools based on wheat-barley collinear regions combined with GISH analysis, is able to precisely determine the linkage group and sub-genomes of the individual E. dahuricus chromosomes. We subsequently established the 42-chromosome karyotype of E. dahuricus with distinctive chromosomal FISH signals, and characterized a new type of intergenomic rearrangement between 2H and 5Y. Furthermore, the comparative chromosomal localization of the centromeric tandem repeats and immunostaining by anti-CENH3 between cultivated barley (Hordeum vulgare L.) and E. dahuricus suggests that centromere-associated sequences in H subgenomes were continuously changing during the process of polyploidization. The precise karyotyping system based on ND-FISH and Oligo-FISH painting methods will be efficient for describing chromosomal rearrangements and evolutionary networks for polyploid Elymus and their related species. Full article

Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies. Full article

Green prickly ash (Zanthoxylum armatum) has edible and medicinal value and is an economically significant plant in many countries. Z. armatum has many cultivars and varieties with similar phenotypes that are difficult to distinguish via traditional methods. In this study, we utilized oligo-FISH to distinguish five varieties and cultivars of Z. armatum on the basis of three oligonucleotide probes of 5S rDNA, (AG₃T₃)₃, and (GAA)₆. Karyotype analysis of the five varieties and cultivars of Z. armatum showed that the Z. armatum ‘Tengjiao’ karyotype formula was 2n = 2x = 98m with karyotype type 1C and an arm ratio of 4.3237, including two pairs of 5S rDNA signals and five pairs of (GAA)₆ signals. The karyotype formula of Z. armatum ‘Youkangtengjiao’ was 2n = 2x = 128m + 8sm with karyotype type 2B and an arm ratio of 3.5336, including three pairs of 5S rDNA signals and 17 pairs of (GAA)₆ signals. The karyotype formula of Z. armatum var. novemfolius was 2n = 2x = 134m + 2sm with karyotype type 1C and an arm ratio of 5.5224, including two pairs of 5S rDNA signals and eight pairs of (GAA)₆ signals. The karyotype formula of Z. armatum ‘YT-03’ was 2n = 2x = 2M + 128m + 4sm + 2st with karyotype type 2C and an arm ratio of 4.1829, including three pairs of 5S rDNA signals and nine pairs of (GAA)₆ signals. The karyotype formula of Z. armatum ‘YT-06’ was 2n = 2x = 126m + 10sm with cytotype 2B and an arm ratio of 3.3011, including three pairs of 5S rDNA signals and two pairs of (GAA)₆ signals. The five varieties and cultivars of Z. armatum had (AG₃T₃)₃ signals on all chromosomes. The chromosomal symmetry of Z. armatum ‘Tengjiao’ was high, whereas the chromosomal symmetry of Z. armatum 'YT-03' was low, with the karyotypes of the five materials showing a trend toward polyploid evolution. The phylogenetic relationship between Z. armatum ‘Tengjiao’ and Z. armatum var. novemfolius was the closest, while that between Z. armatum ‘YT-03’ and Z. armatum ‘YT-06’ was closer than with Z. armatum ‘Youkangtengjiao’ according to oligo-FISH. The results provided a karyotype profile and a physical map that contributes to the distinction of varieties and cultivars of Z. armatum and provides strategies for distinguishing other cultivated species. Full article

Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of Populus simonii which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for P. simonii to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current P. simonii genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the P. simonii chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly. Full article

Thinopyrum intermedium (2n = 6x = 42, JJJ^SJ^SStSt) has been hybridized extensively with common wheat and proven to be a valuable germplasm source for improving disease resistance and yield potential of wheat. A novel disease-resistant wheat-Th. intermedium double substitution line X479, carrying 1St(1B) and 4St-4J^S (4B), was identified using multi-color non-denaturing fluorescence in situ hybridization (ND-FISH). With the aim of transferring Thinopyrum-specific chromatin to wheat, a total of 573 plants from F₂ and F₃ progenies of X479 crossed with wheat cultivar MY11 were developed and characterized using sequential ND-FISH with multiple probes. Fifteen types of wheat-Thinopyrum translocation chromosomes were preferentially transmitted in the progenies, and the homozygous wheat-1St, and wheat-4J^SL translocation lines were identified using ND-FISH, Oligo-FISH painting and CENH3 immunostaining. The wheat-4J^SL translocation lines exhibited high levels of resistance to stripe rust prevalent races in field screening. The gene for stripe rust resistance was found to be physically located on FL0–0.60 of the 4J^SL, using deletion lines and specific DNA markers. The new wheat-Th. intermedium translocation lines can be exploited as useful germplasms for wheat improvement. Full article