Genome

Soybean seeds are rich in oil and protein; however, the seed composition is influenced by genotype and environment. For years, it has been observed that soybeans grown in western Canada have lower seed protein concentration (by ∼1%–5% total seed weight) than those grown in eastern Canada. In this study, soybean seeds harvested from five varieties were grown in four different locations in Canada (east and west growing regions) and analyzed using RNA-sequencing. Using gene ontology and biological pathway mapping, we identified a difference in cysteine and methionine metabolism between soybeans grown in eastern and western Canada that may attribute to the difference in seed protein concentration. Further, we identified differential gene expression within the oil biosynthesis pathway, specifically upregulation of lipoxygenases in western-grown soybeans, which may also influence seed composition and/or membrane fluidity. The information gained in this study is useful for marker assisted selection in soybean breeding programs across Canada and globally.

Chromosomal rearrangements (CRs) can play an important role in evolutionary diversification by preserving linkage among favourable alleles through reduced recombination and/or by reducing hybrid fitness due to genomic incompatibilities. Our goal was to determine to what extent CRs contribute to known patterns of genetic variation in Arctic charr (Salvelinus alpinus). To address this goal, we compared genetic linkage maps to identify whole arm CRs and smaller scale structural variants (SVs) such as translocations/transpositions and inversions found in groups of populations that reflect the temporal sequence of geographic isolation events. If CRs contribute to genetic differentiation, we expected that CRs would be specific to glacial lineages, geographic clusters of populations within lineages, and sympatric morphs. We detected fusions and fissions of whole chromosome arms and SV involving translocations/transpositions of the sex-determining gene (sdY) and inversions. Several CRs were shared across populations from the Arctic and Atlantic glacial lineages, Canadian and Icelandic populations within the Atlantic lineage, between two Icelandic populations and sympatric morphs within Icelandic populations, suggesting that their origin predates geographic isolation in glacial refugia. Other CRs were specific to single populations, which suggests a more recent origin of these variants in refugia, during post-glacial recolonization and/or in contemporary populations. Thus, CRs contribute relatively little to known patterns of genetic differentiation at different geographic scales but represent a pool of standing genetic variation for evolution.

Advancements in sequencing technologies enabled the assembly and characterization of plant genomes with high resolution. In breeding programs, this data is combined with phenotypic information in genomic prediction to select genotypes based on their genetic profiles. Although SNP arrays are commonly used for genotyping, they capture only a fraction of the genomewide diversity. To address this, one approach involves genotyping the entire population with arrays, sequence a subset using whole-genome sequencing (WGS) or assessing gene expression profiles, followed by imputing the data across the entire population. This study evaluates the effect of imputed WGS markers (SNPs and structural variants) and expression data on genomic prediction in a rapeseed hybrid breeding population. A combination of SNP arrays, WGS, and RNA sequencing was employed, followed by imputation of marker and expression data. Genomic prediction was utilized to estimate general and specific combining ability effects in untested hybrids. However, while adding imputed whole-genome and expression data increased marker density and linkage disequilibrium, it didn´t enhance prediction accuracy compared to SNP array data. This is attributed to redundancy in relationship, imputation errors, or environmental influences on gene expressions. This suggests that SNP arrays continue to be reliable for genomic prediction in rapeseed hybrid breeding.

Prion protein (PrP) plays a central role in bovine spongiform encephalopathy (BSE). Given the structural and biological similarity to PrP, recent research has focused on Doppel (Dpl) protein, which is encoded by the prion-like protein Doppel (PRND) gene. In this study, we characterized the PRND genetic polymorphism in 100 Jeju black cattle, a native Korean breed. We predicted the potential effect of non-synonymous single nucleotide polymorphisms (SNPs) on the Dpl protein function using three in silico tools: SIFT, PANTHER and PolyPhen-2. Finally, we performed a comparative analysis of the genotype distribution of c.395A>G (Q132R) between German BSE-infected cattle and Korean healthy cattle to assess the BSE susceptibility of Korean cattle. We found eight SNPs, including three novel SNPs c.-7C>T, c.172G>A (A58T), and c.537+83C>T. Only c.172G>A was predicted by SIFT to exert a deleterious effect. According to the comparative analysis, Holstein and Jeju black cattle exhibited a higher potential risk for BSE. To the best of our knowledge, this is the first report on the genetic characteristics of the PRND gene in Jeju black cattle.

A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of 3 environmentally relevant genera, Limnohabitans , Aquabacterium , and Novosphingobium . These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans , 10 Aquabacterium , and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.

Environmental DNA (eDNA) has shown promise for the detection of threatened and endangered species and has been implemented for monitoring aquatic spawning events. Freshwater unionid mussels exhibit a rare form of mitochondrial inheritance, in which males possess a unique mitochondrial mitotype that is divergent from the female mitotype. As freshwater mussels are spermcasters, the detection of male mitotype eDNA may provide critical conservation information related to timing of sperm release. This study re-purposed an existing eDNA metabarcoding dataset to detail the unique detection of eDNA pertaining to the male mitotype. Water samples collected alongside an extensive mussel salvage within the Walhonding River, Ohio, detected 16 distinct male mitotypes. However, several constraints limit the proper interpretation of these detections. There is currently a lack of reporting on assay compatibility with the male mitotype within freshwater mussel eDNA literature. Reference genetic databases are critically lacking, with only four of the 16 male eDNA sequences in this study able to be discerned to a species. This study highlights the importance of detailing these detections as the unique inheritance system provides opportunities to document difficult to record spawning behaviors, and eDNA may be employed as a survey tool to evaluate patterns of metapopulation geneflow.

Canada has made significant contributions to the field of plant biochemistry, with numerous researchers actively focusing on elucidating the biosynthetic pathways of plant specialized metabolites and producing these compounds in heterologous systems, such as bacteria, yeast, or other plant species. The review aims to highlight the strengths of Canadian research in this domain over the last three decades. It will describe advances in pathway elucidation, enzyme characterization, and production of enzymes and metabolites in heterologous systems, particularly in the areas of alkaloids, terpenoids, and phenolic compounds. Canadian researchers have not only made pivotal scientific discoveries but have also ensured the continuity of scientific excellence by mentoring new generations of principal investigators in plant specialized metabolites. These advances warrant recognition and financial support to retain future talent and to maintain Canada's leadership in scientific progress on the global stage.

Platycarya longipes is a dominant tree species in karst forests. Due to limited genomic information, its exact phylogenetic position within the family Juglandaceae remains unclear. In this study, the complete chloroplast genome (cp genome) of Platycarya longipes was de novo assembled using Illumina reads. This circular cp genome was 158 592 bp in length, consisting of an 88 066 bp large single-copy region, an 18 524 bp small single-copy region, and a total of 26 001 bp derived from a pair of inverted repeats (IRa and IRb), with an average GC content of 36.15%. It accommodated a total of 113 genes, including 80 protein-coding genes, 29 tRNAs, and 4 rRNAs. Additionally, within the genome, 49 long repeats and 66 simple sequence repeats, which could be utilized as molecular markers, were identified. In comparison to the related Platycarya strobilacea, the Ka/Ks substitution rate values of Platycarya longipes exhibited significant divergence, supporting the differentiation between the species. The conserved gene order and structure of the Platycarya longipes cp genome compared to other Juglandaceae members. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with Fagales genomes showed a close relationship between Platycarya longipes and Platycarya strobilacea.

Luteinizing hormone-releasing hormone A3 (LHRH-A3), a reproductive hormone analog, is widely used to stimulate ovulation in female rabbits. However, the long-term impact of sustained LHRH-A3 administration on the reproductive system, particularly ovarian health, remains unclear. In this study, we compared apoptosis levels in ovaries and molecular regulation between LHRH-A3-treated (A3 group) and untreated female rabbits (N group) after their 5th litter. Western blotting showed a significantly lower Bcl-2/Bax ratio in the A3 group compared with the N group (P < 0.01), indicating higher ovarian apoptosis. Ovarian tissues from four rabbits per group were divided into the A3 group and the N group, and RNA-seq technology was then utilized to conduct transcriptome analysis on these two groups. This analysis revealed 220 differentially expressed genes (DEGs), including BMP6, BMP15, CYP1A1, and other reproductive-related genes. KEGG analysis of these DEGs showed their involvement in processes such as the cell cycle, PI3K-Akt signaling pathway, and ovarian steroidogenesis. Subsequently, we selected the key gene Matrix metallopeptidase 7 (MMP7) for functional analysis using CCK8 and Annexin V-FITC/PI techniques. MMP7 was found to promote the proliferation of granulosa cells (GCs) and inhibit apoptosis (P < 0.01). In conclusion, LHRH-A3 treatment can modulate ovarian molecular regulation, with the key gene MMP7 involved in the proliferation and apoptosis of GCs.

Traditional taxonomic revisions based on macromorphological and leaf anatomical traits may have limitations in accurately distinguishing certain species within the genus. To improve taxonomic clarity, this study applied DNA barcoding to enhance the understanding of the taxonomy and phylogeny of Baccaurea Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including rbcL, ITS2, and trnH-psbA, were used to analyze 64 samples representing 19 Baccaurea species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of rbcL, ITS2, trnH-psbA, and their combinations rbcL + ITS2 and rbcL + ITS2 + trnH-psbA as 21.1%, 89.5%, 87.5%, 89.5%, and 89.5%, respectively. The Neighbor-Joining tree revealed well-defined, monophyletic species clusters that largely align with phylogenetic positions based on macromorphological features. Notably, our results indicate that Baccaurea parviflora and the synonymized Baccaurea scortechinii are distinct species, recommending the re-establishment of B. scortechinii as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.

Regulations within the crop agriculture industry exist to ensure that products undergoing risk assessment prior to commercialization are safe for the environment and human consumption. Since 1995, these regulations have provided safe crops and foods for Canadians to consume, as no commercialized innovative product has caused any post-commercialization health or environmental problems. However, Canada suffers from a gap in its innovation pipeline in that far more investments go into the innovation pipeline than products come out. Canada is a global top ten nation in terms of innovation investments yet drops over ten positions when it comes to outputs. Additionally, Canada is one of the lowest ranked on the G30 list of countries in terms of regulatory burden on the economy. This article describes updates to the regulatory framework for plant biotechnology, highlighting recent changes regarding regulation of gene editing technologies and how these changes respond to previously identified innovation barriers.

Circadian rhythms are important cellular pathways first described for their essential role in helping organisms adjust to the 24 h day–night cycle and synchronize physiological and behavioral functions. Most organisms have evolved a circadian central clock to anticipate daily environmental changes in light, temperature, and mate availability. It is now understood that multiple clocks exist in organisms to regulate the functions of specific organs. Epidemiological studies in humans reported that disruption of the circadian rhythms caused by sleep deprivation is linked to the onset of immune-related conditions, suggesting the importance of circadian regulation of immunity. Mechanistic studies to define how circadian clocks and immune responses interact have profound implications for human health. However, elucidating the clocks and their tissue-specific functions has been challenging in mammals. Many studies using simple model organisms such as Drosophila melanogaster have been pioneering in discovering that the clock controls innate immune responses and immune challenges can impact circadian rhythms and/or their outcomes. In this review, we will report genetic studies using the humble fruit fly that identified the existence of reciprocal interactions between the circadian pathway and innate immune signaling, contributing to elucidate mechanisms in the growing field of chrono-immunology.

Recently developed hybrid assemblies can achieve telomere-to-telomere (T2T) completeness of some chromosomes. However, such approaches involve sequencing a large volume of both Pacific Biosciences high-fidelity (HiFi) and Oxford Nanopore Technologies (ONT) sequencing reads. Along with this, third-generation sequencing techniques are rapidly advancing, increasing the available length and accuracy. To reduce the final cost of genome assembly, here we investigated the possibility of assembly from low-coverage samples and with only ONT corrected by next-generation sequencing (NGS) sequencing reads. We demonstrated that haploid ONT-based assembly approaches corrected by NGS can achieve performance metrics comparable to more expensive hybrid approaches based on HiFi sequencing. We investigated the assembly of different chromosomes and the low-coverage performance of state-of-the-art hybrid assembly tools, including Verkko and Hifiasm, as well as ONT-based assemblers such as Shasta and Flye. We found that even with one-contig T2T assembly Verkko and Hifiasm still have numerous misassemblies within centromere. Therefore, we recommend using a combination of regular R9 or simplex R10 ONT reads and accurate NGS reads for assembly without aiming for T2T completeness. Additionally, we rigorously evaluated the performance of MGI, Illumina, and stLFR NGS technologies across various aspects of hybrid genome assembly, including pre-assembly correction, haplotype phasing, and polishing.

Genome mining has been a key strategy for finding biosynthetic gene clusters (BGCs) coding for secondary metabolites in the recent past. Actinomycetia is among the important bacterial classes found in marine habitats, renowned for producing high-value secondary metabolites. Kocuria is one such gram-positive bacteria that has been reported to produce the potent antibacterial molecule kocurin/PM181104. The objective of this study was to confirm the production of kocurin/PM181104 followed by sequencing, assembly, and mining of the genome of Kocuria flava NIO_001. AntiSMASH analysis predicted the BGCs involved in the production of kocurin along with eight promising secondary metabolite-producing BGCs including non-alpha poly-amino acids like e-polylysin (NAPAA), ribosomally synthesized and post-translationally modified peptide like (RiPP-like), non-ribosomal peptide synthetase like (NRPS-like), NRPS-independent IucA/IucC-like siderophores (NI-siderophore), type III polyketide synthase (T3PKS), ε-Poly-l-lysine (NAPAA), terpene, and betalactone. Kyoto Encyclopedia for Genes and Genomes pathway analysis showed the presence of biosynthetic pathways involved in terpenoid backbone synthesis and the presence of certain hemolysin-like proteins. The present investigation is highly valuable for designing experiments to overproduce this potent antibiotic molecule by using a reverse engineering approach.

Bacteria in the genus Staphylococcus include human and animal pathogens. Although the genomic diversity of these bacteria is increasingly well characterized, the rate of protein evolution in staphylococci remains poorly understood. In this study, the genomic sequences of one representative from each of the 63 Staphylococcus species were downloaded from the RefSeq database. Homologous protein sequences were identified, and their evolutionary rates were inferred using a phylogenetic approach. The results demonstrated that some proteins evolve significantly faster than others, with several being involved in DNA-mediated transformation. Further analyses of the genomic sequences revealed that the evolutionary rate of proteins is correlated with codon adaptation of their genes, and that certain protein regions are more prone to accumulating mutations. This study highlights the more rapid evolution of specific proteins in staphylococci, likely reflecting the host diversity of these bacteria and their high adaptive capacity.

The second iteration of the international conference “Pathway to Increase Standards and Competency of eDNA Surveys” was held at the University of Guelph, Guelph, Ontario, Canada from 18 June to 20 June 2023. During this environmental DNA (eDNA) conference, 60 oral and 25 poster presentations from academia, government, industry, NGOs, and Indigenous partners discussed the latest developments in eDNA research, explored strategies to inform public policy, and presented future directions in the field. The conference also included three panel discussions focused on prominent themes in the eDNA space, and five workshops dedicated to practical eDNA tools and methods. Recordings of presentations at the conference have been made available on YouTube. Here we summarize the major themes covered during the conference, provide our concluding remarks, and share the conference abstracts.

Natural history museums harbor invaluable resources for conserving endangered species by providing insights into the mechanism of historical population declines. We conducted data synthesis to better understand the extinction factors of the iconic Jambato Harlequin frog, Atelopus ignescens, which was widespread in the Ecuadorian Andes before 1985 but vanished in 1988. We synthesized historical data from natural history museums, the global biodiversity information facility, and mtDNA sequences to examine whether Batrachochytrium dendrobatidis (Bd) fungus infection, climate change, and/or their interaction contributed to the rapid population decline. We found excessive rare alleles reflected in the negative Tajima's D estimated from the mtDNA samples from 1984, indicating a selective sweep or population bottleneck. Sex and geography showed stronger effects on adult body sizes than Bd epizootic timing. The body sizes of adult males formed a geographic cline. Species distribution modeling based on temperature and precipitation accurately predicted the occupancy of A. ignescens in 1960–69, which further projected a rapid decline in species distribution between 1970 and 2020. This investigation revealed strong climate effect and weak epizootics effect on A. ignescens extinction, and inspires future museum genomic studies to dissect the potential climatic maladaptation behind dramatic historical extinctions.

Medicago polymorpha (2n = 2x = 14) is a valuable forage legume, but the identification of its somatic chromosomes has been challenging due to a lack of distinctive chromosome morphological features. With appropriate probes, oligonucleotide-based FISH is a highly effective method for chromosome identification. However, there are no available probes for M. polymorpha. In this study, we isolated five tandem repeats from the M. polymorpha genome, named Mp51, Mp139, Mp167, Mp179, and Mp497. Mp51 showed two pairs of signals located at the pericentromere. Mp139 exhibited four pairs of signals, located at the pericentromere and short arm of chromosomes. Mp167 and Mp179 showed seven pairs of signals, respectively, concentrated in the pericentromere. Mp497 exhibited three pairs of signals, distributed across the pericentromere and proximal position of the chromosomes. The combined FISH results of Mp51 and Mp139 oligo probes with 5S rDNA and 18S-26S rDNA probes demonstrated distinct signal patterns for each chromosome, enabling the precise identification of all chromosome pairs. Finally, the visual identification of M. polymorpha chromosomes was resolved. This will provide useful cytological information for studying the chromosomal structure and behavior of M. polymorpha.

Cytogenetic studies on Potamotrygon motoro (Müller & Henle, 1841) are limited to classical cytogenetic techniques, but they do reveal great karyotypic variation. The main differences are related to the karyotypic formula and the absence/presence of sex chromosome systems. Thus, this study aimed to expand knowledge of the karyotypic composition of Potamotrygon motoro from different locations of the Central Amazon using Fluorescence in situ Hybridization to investigate the distribution of ribosomal DNAs (rDNA) and microsatellites sequences (SSRs). In addition, we used the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) to perform neighbor-joining analysis to investigate the relationships among the individuals sampled. In our study, Potamotrygon motoro presented 2n = 66 chromosomes, with 18m + 12sm + 10st + 26a and heterochromatic blocks on centromeric region of all chromosomes. The 18S rDNA is present in three chromosomal pairs and 5S rDNA is located in the pair 16, which is a feature shared among freshwater stingray species. Regarding the mapping of SSRs, dinucleotide sequences showed a greater number of sites, usually on terminal regions of chromosomal pairs, with an accumulation throughout the long arms of the pair 17. Our molecular analyses did not reveal differences between the sequences used. In general, the karyotypic differences previously reported for Potamotrygon motoro indicate the presence of different cytotypes within the species.

The Physalaemus cuvieri–Physalaemus ephippifer species complex is a Neotropical frog group that encompasses seven well-supported major clades. Although very similar morphologically, the five lineages previously karyotyped show notorious cytogenetic signatures. There is also evidence of ancient secondary contact between P. ephippifer, which has heteromorphic sex chromosomes, and the lineage known as L1B, which lacks sex chromosome heteromorphism. Here, to aid comparative analysis within this complex, we mapped the U2 small nuclear RNA (snRNA) gene using fluorescent in situ hybridization (FISH). All samples presented a U2 snRNA gene cluster terminally in the short arm of chromosome 6. Additional small FISH signals were also revealed, particularly in one lineage with previously noted polymorphism of nucleolar organizer regions. Moreover, one additional site contributed for the analysis of sex chromosomes, since the Z chromosome of P. ephippifer harbors a small FISH signal, which is absent in the W chromosome. In lineage L1B, chromosome 9—which is homologous to the sex chromosomes of P. ephippifer—is polymorphic for a small FISH signal, as did the Z chromosome in the group derived from the contact between these lineages. Finally, nucleotide sequence analysis revealed some truncated gene sequences, suggesting the presence of pseudogenes of the U2 snRNA gene in these frogs.

Advancements in sequencing technologies have dramatically transformed genomics research by enabling the analysis of genetic information with unprecedented scale and efficiency. Next-generation sequencing, renowned for its high-throughput capabilities, has significantly reduced costs and expanded the scope of sequencing applications. Among these, sequencing by synthesis on Illumina systems is predominant, favored for its accuracy and cost-effectiveness. However, emerging technologies like Element Biosciences’ sequencing by Avidity (AVITI) are beginning to challenge this dominance. In this study, we sequenced and genotyped a library of 40 Cannabis samples using both the AVITI and Illumina NovaSeq systems. After filtering out low-quality variants, both technologies showed an 81.2% overlap with 98.9% concordance in genotype calls. AVITI stands out for its flexibility and reduced per-base costs, presenting a viable option particularly for mid-sized laboratories. As the scientific community continues to seek ways to lower genotyping expenses, the combination of the AVITI system with NanoGBS library preparation offers a cost-effective solution adaptable to a wide range of project sizes.

We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (Bombus pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees that suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.

The voles of the Microtus thomasi/Microtus atticus species complex (Arvicolinae) display extensive karyotypic variation, in the number of autosomes and the morphology of sex chromosomes. We analyzed the satellitome of Microtus thomasi and identified 17 satellite DNA (satDNA) families, corresponding to 6.704% of the genome. Homogenization and divergence analyses showed that some satDNA families are more homogeneous, indicative of recent amplification, while others displayed higher variation, suggesting ancient amplification. Twelve of the satDNA families are conserved across Arvicolinae with a substantial variation in the abundance and the composition. These results support the “library” hypothesis, where a shared collection of satDNAs exists across related species, with differential amplification driving species-specific genomic profiles. Localization analysis demonstrated that an increased number of satDNA families are localized in the pericentromeric and the heterochromatic regions of autosomes and sex chromosomes. Our results suggest that the heterochromatin of the X and Y chromosomes co-evolved and that satDNA families might have contributed to the chromosomal rearrangements involved in the karyotypic variation and sex chromosome polymorphism of the chromosomal races. Our study contributes to a deeper understanding of the evolutionary mechanisms underlying karyotype diversification in Microtus species, which exhibit some of the highest rates of karyotypic variation among mammals.

Yellow/stripe rust caused by Puccinia striiformis f. sp. tritici is a major biotic stress in global wheat production. Introgression lines derived from the Triticum spelta accessions PI348764 and IARI276 showed high levels of yellow rust resistance at seedling and adult plant stage. The Yr5 gene located on 2B chromosome was previously the only stripe rust resistance gene described in T. spelta gene pool. By genotyping parental and introgressed material with markers linked with the Yr5 gene, we demonstrate that PI348764 likely carries Yr5, and that it appears to be absent from IARI276. By employing a combination of methods, including screening for adult plant resistance and seedling resistance at multiple field trials, bulked segregant analysis (BSA) on F5 families, and genotyping using wheat Breeders’ 35K array, we show that YrIARI276 is a novel stripe rust resistance gene with putative chromosomal locations on 1BL, 1DL, 5AL, or 7BL. Furthermore, genetic analysis revealed that YrIARI276 showed a goodness of fit to Mendelian ratios for a single dominant gene. As the gene is distinct from Yr5 and the chromosomal location is unique from earlier reported Yr genes, it will be useful in improving diversity of Yr gene repertoire in disease resistance breeding programmes.

Urochloa P. Beauv. (formerly classified as Brachiaria (Trin.) Griseb.) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, Urochloa brizantha, Urochloa decumbens, and Urochloa ruziziensis, form the brizantha agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected Urochloa species belonging to the b rizantha agamic complex; identify and compare major repeat classes across species; and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent in situ hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56%–65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the Athila and Retand lineages, representing the most abundant repeat class. Urochloa decumbens exhibited the highest proportion of Ty3/Gypsy retrotransposons, while U. ruziziensis had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the brizantha agamic complex of Urochloa and revealed genomic relationships among different species and ploidy levels.