Genome最新文献

Wheat defenses against Pyrenophora tritici-repentis (Ptr), the cause of tan spot disease, are complex and require further characterization. We previously identified two wheat genotypes, Robigus (resistant) and Hereward (susceptible), and characterized their differentially expressed genes (DEGs) and accumulated metabolites (DAMs) following challenge with Ptr. In this study we uncover coordinated shifts in gene expression and metabolism triggered by Ptr. The DEGs and DAMs from each genotype were integrated using Regularized Canonical Correlation Analysis (RCCA), yielding scale-free networks with 69,745 edges in Robigus and 760,433 in Hereward. In Robigus, hub genes were upregulated at 48 and 96 h post-inoculation and included hst2 (encoding hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2), located within a QTL for Ptr resistance (QTs.fcu-5D locus), a receptor-like kinase, and a late embryogenesis abundant protein (which play roles in cell wall organization). Pathway enrichment showed significant involvement of catalytic activity, chitinase activity, and cell wall metabolic processes. In contrast, Hereward hub genes were mostly downregulated, except for a hexosyltransferase, with enriched pathways related to energy metabolism, such as ATP binding and phosphorylation. These results suggest that cell wall modifications and chitinase activity are part of an effective defense response against Ptr, whereas costly energetic processes may contribute to tan spot susceptibility.

Plant biotechnology has revolutionized modern agriculture by enabling precise and efficient crop improvement strategies. This review explores the evolution of selective breeding, mutation breeding, and precision breeding, highlighting their applications in Canada's agricultural sector. Conventional selective breeding has been instrumental in developing high-yielding and disease-resistant cultivars, while mutation breeding, through physical and chemical mutagenesis, has introduced valuable genetic diversity. The advent of transgenic breeding allowed for the direct insertion of foreign genes, leading to the development of crops with herbicide tolerance, pest resistance, and improved nutritional content. However, concerns over regulatory restrictions and public acceptance have driven the rapid adoption of genome editing tools, which enable precise modifications without introducing foreign DNA. Canada has played a key role in applying these biotechnological innovations, successfully developing genetically modified canola, CRISPR-edited wheat, stress-resistant soybean, and barley and oat cultivars improved for stress resistance and yield. While each breeding approach presents distinct advantages and limitations, integrating conventional and molecular techniques is essential for maximizing genetic potential, ensuring agriculture, and effectively food security challenges.

This study investigates the selection signatures of 11 Indigenous goat breeds from diverse eco-topographies of India, using whole-genome re-sequencing (WGRS) data from 103 individuals. We identified population-wide copy number variable regions (CNVRs) as well as selection signatures through a variance-stabilizing transformation (VST) approach for utility traits. A total of 32,711 polymorphic sites were analyzed, revealing 327 potentially significant and 32 highly significant signatures under selection. Key genes identified in selection signatures include GHR, PLAG1, and MTOR, which play crucial roles in growth, development, and reproductive traits across different utility groups. Notable reproduction-related genes such as ITPR3, ESRRG, and SOX6 were found to be associated with fertility, hormone regulation, and reproductive system. Network analysis revealed ESR1 as a central hub gene forming significant interactions with RUNX2, HDAC2, and BCL2, indicating its vital role in muscle development and metabolism. The MTOR signaling pathway emerged as another crucial hub, connecting with DEPDC5 and SESN1, suggesting its importance in nutrient sensing and metabolic regulation for production traits. Gene ontology analysis of the selection signatures revealed pathways for functional categories between meat, milk, and fiber-producing breeds, reflecting the genetic architecture underlying their specialized phenotypes. Identified selection signatures and hub genes can be used in marker-assisted and genomic selection to improve growth, reproduction, and adaptability in indigenous goats, aiding precision breeding and conservation programs.

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 Yr^IARI276 is a novel stripe rust resistance gene with putative chromosomal locations on 1BL, 1DL, 5AL, or 7BL. Furthermore, genetic analysis revealed that Yr^IARI276 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.

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.

The actin cytoskeleton is a dynamic mesh of filaments that provide structural support for cells and respond to external deformation forces. Active sensing of these forces is crucial for the function of the actin cytoskeleton, and some actin crosslinkers accomplish it. One such crosslinker is filamin, a highly conserved actin crosslinker dimeric protein with an elastic region capable of responding to mechanical changes in the actin cytoskeleton. Filamins are required across various cells and tissues. In Drosophila early and recent studies have provided many details about filamin functions. This review centers on the two Drosophila filamins encoded by the cheerio and jitterbu g genes. We examine the structural and evolutionary aspects of filamin genes in flies, contrasting them with those of other model organisms. Then, we synthesize phenotypic data across diverse cell types. Additionally, we outline the genetic tools available for both genes. We also propose to divide filamins into typical and atypical based on the number of actin-binding domains and their relationship with other filamins.

Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.

Brassica napus, commonly known as rapeseed or canola, is an economically valuable oilseed crop grown throughout Canada that currently faces several challenges due to industrial farming practices as well as a changing climate. Calcium-dependent protein kinases (CDPKs) are key regulators of stress signaling in multiple plant species. CDPKs sense changes in cellular calcium levels via a calmodulin-like domain and are able to respond to these changes via their protein kinase domain. In this mini-review, we provide a quick guide to BnaCDPKs. We present an updated phylogeny of the BnaCDPK family in relation to CDPKs from Arabidopsis thaliana and Oryza sativa and we provide a standardized nomenclature for the large BnaCDPK family that contains many co-orthologs. We analyze expression patterns of BnaCDPKs across tissue types and in response to abiotic and biotic stresses, and we summarize known functions of BnaCDPKs. We hope this guide is useful to anyone interested in exploring the prospect of harnessing the potential of BnaCDPKs in the generation of elite cultivars of B. napus.

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.

Chromosomes, as carriers of genes, are the fundamental units of heredity, with the eukaryotic genome divided into multiple chromosomes. Each species typically has a consistent number of chromosomes within its lineage. Ants, however, display remarkable diversity in chromosome numbers, and previous studies have shown that this variation may correlate with ant diversity. As ants evolved, various karyotypes emerged, primarily through chromosomal fissions, leading to an increase in chromosome number and a decrease in chromosome size. In this study, we investigate chromosome evolution in ants from a phylogenetic perspective using ancestral reconstruction. Our analysis indicates that the most recent common ancestor of ants had an ancestral haploid chromosome number of 11, likely composed of biarmed chromosomes. The bimodal distribution of karyotypes and the trend toward increased chromosome numbers align with previous assumptions. However, both dysploidy and ploidy changes have been indicated as likely mechanisms of chromosome number evolution. Descending dysploidy occurs consistently throughout the phylogeny, while changes in ploidy are believed to occur occasionally within the subfamilies during genus diversification. We propose, based on our results and previous evidence (e.g., genome size in ants), that both fusions and fissions contribute equally to karyotype changes in Formicidae. Additionally, changes in ploidy should not be fully ignored, as they can occur across specific lineages.