Malarmathi Muthusamy

Bacteria are continually exposed to stressors, making their ability to sense, acclimate and adapt to changing conditions essential for fitness. Two-component response systems (TCRS) play a primary role in mediating these responses. However, the role of epigenetic modifications in acclimation and adaptation is not well understood. We characterized N6-methyladenine (6mA) and N4-methylcytosine (4mC) DNA methylation patterns in wild-type Escherichia coli K-12 MG1655, four cusS mutants and six silver-adapted mutants with and without exposure to 50 ng/mL AgNO₃ for 1 h using Single-Molecule Real-Time sequencing. The cusS mutants were selected to study the impact of the mutations on DNA methylation. Global mean 6mA fractions were high across all strains with and without silver and were largely driven by the dominant GATC motif in all strains and the AACN₆GTGC/GCACN₆GTT motif in wild-type and silver-adapted mutants, while global mean putative 4mC fractions were lower. Across conditions, variation was observed in extended degenerate motifs with moderate-to-low methylation. Our findings suggest that motif-specific methylation patterns vary across silver exposure and genetic backgrounds, while global methylation levels in E. coli remain remarkably resilient. This study improves understanding of microbial stress adaptation and stress response, raising the possibility that methylation contributes to TCRS-mediated stress tolerance.

Dairy goats offer significant potential to enhance food security, promote climate resilience, and improve rural livelihoods in sub-Saharan Africa (SSA), particularly within women-led smallholder farming systems. This interdisciplinary narrative review integrates findings from nutritional science, climate adaptation studies, recent genomic innovations, and policy analyses (2010–2025) to critically evaluate dairy goats’ roles in addressing persistent malnutrition and vulnerability to climate extremes. Goat milk provides vital macronutrients and micronutrients and can contribute to improved dietary adequacy. Compared with larger ruminants such as cattle, goats—particularly indigenous and locally adapted populations—often exhibit greater tolerance to heat stress, flexible browsing behaviour, and lower water requirements. However, these adaptive advantages vary widely among dairy goat breeds, with high-yielding temperate breeds generally showing lower resilience to climatic extremes than indigenous SSA ecotypes. In addition, the per-kg GHG emissions for goat milk are typically higher than those for bovine milk, although system-level benefits may emerge in drylands where goats fit local heat/feed constraints and where species mix and management differ substantially. Recent genomic advancements, notably genome-wide association studies and selection signature analyses, have identified candidate loci for thermotolerance, disease resistance, and milk yield. Near-term improvement is most plausible where breeding is anchored in community-based programmes supported by minimal identification and phenotyping, with marker use most defensible when validated within target populations. Despite emerging opportunities through microfinance and climate finance, especially for women-centric cooperatives, dairy goats remain underrepresented in national livestock and climate policies, and life cycle assessment data to support formal carbon–credit integration are limited. We therefore recommend dedicated funding to goat-specific extension and animal health, targeted gender-inclusive training, strategic investments in genomic and data infrastructure, and enhanced data collection for carbon accounting. Overall, the evidence synthesised here indicates that scalable dairy goat development in SSA is unlikely without the coordinated implementation of climate-smart management and delivery systems (animal identification and core recording), alongside context-validated genomic approaches (e.g., MAS or genomic prediction integrated within community-based breeding where reference resources and phenotypes exist) and targeted policy and financing.

Indigenous goats in Nigeria and neighbouring countries support livelihoods across forest–savanna–Sahel environments, yet genomic structure, connectivity history, and adaptive signals are rarely investigated in a single corridor-scale transboundary framework. We analysed three Nigerian populations (Sahel, Red Sokoto/Maradi, and West African Dwarf; WAD) and seven neighbouring populations from Burkina Faso, Mali, and Cameroon using 46,431 autosomal markers from 209 unrelated animals (with a South Asian outgroup where needed). We tested whether recurrent vernacular labels map onto shared genomic backgrounds across borders, reconstructed time-layered connectivity, quantified demographic contraction and inbreeding, and prioritised candidate adaptive regions using a structure-aware approach. Model-based ancestry and principal component analysis supported three transboundary genomic backgrounds: (i) a Sahel–Sudan background spanning Nigeria, Burkina Faso, and Mali; (ii) a southern Djallonké/WAD background spanning Nigeria, Burkina Faso, and Mali; and (iii) a distinct Cameroon dwarf lineage, with Guéra representing a drifted subgroup within the Sahel–Sudan background. Admixture-timing analysis, interpreted as approximate dates inferred from linkage-disequilibrium decay, suggested very recent cross-border involving Nigerian Sahel goats (~30–40 years under the assumed generation interval), superimposed on older Sahelian–dwarf exchange (~160–1,000 years). Effective population size declined from ~1,400–2,700 at ~960 generations ago to ~40–111 at 13 generations ago. Runs of homozygosity indicated low-to-moderate genomic inbreeding (0.004–0.040), with long segments (>8 Mb) most pronounced in Guéra and Red Sokoto/Maradi. A multi-statistic composite selection scan identified 53 candidate windows. Enrichment highlighted adhesion and translation quality-control themes in the Djallonké/WAD background background, neuronal/neuroendocrine terms in Guéra, and olfactory transduction in the Sahel–Sudan background. These results define transboundary genomic backgrounds rather than country-bounded “breeds” and provide background-specific hypotheses that can be validated in resilience-oriented breeding under ongoing mobility.

Newcastle Disease (ND) is an important and notable disease among the avian infectious diseases, because of its high contagiousness, and the most virulent strains of ND virus (NDV) have impacted poultry breeders all over the world. Immunization and biosecurity measures are used to reduce ND; however, vaccination has been shown to offer protection against clinical signs but not against virus proliferation and shedding, which could have an adverse effect on the environment. The genetic basis for inherent resistance to NDV has been established, and genetic selection on existing resistance-related genetic variation can help to mitigate virus propagation. Further, understanding the genes and processes that drive the response to NDV will lay the groundwork for genetic improvement in poultry. The majority of studies on NDV susceptibility make use of phenotypic indicators such as body weight, morbidity, mortality, antibody response, and viral load. According to recent advancements in molecular genetic research, many different genes are diversely regulated in different chicken lines to NDV infection, which might be used in the future to establish disease-resistant breeding approaches. It is possible that many more genes linked to illness and resistance are still to be discovered, because the precise mechanism of resistance is not entirely understood. The enhanced genetic knowledge of chickens and the development of more advanced transgenic techniques would lead to pathogen resistance. Hence, this paper summarizes the current understanding of genetic resistance to Newcastle Disease, and we additionally highlight a few possible genes/markers connected with NDV that may improve chicken resistance to NDV infections and can be used to produce NDV-resistant chicken breeds/strains in the near future.

This study focused on improving the milk fat percentage for crossbred dairy cows in smallholder systems, using GEBV. The data were collected from 2507 animals between 2016 and 2023 under BAIF’s Enhanced Genetic Gains program in Pune, India. After refining the dataset, 33,845 records from 1896 animals were analyzed. The result showed that 75.54% of farms had either one or two animals. Prior to quality control, the mean milk fat percentage was 3.94%, but it decreased to 3.83% after data pruning, which necessitated removing the outliers. Genetic analysis involved 1478 animals genotyped for 49,911 SNPs after applying a rigorous quality control process, and imputation improved the accuracy of genomic data, boosting allele frequency correlation from 0.594 to 0.882. The study revealed that the additive genetic variance, phenotypic variance, and error variance were calculated as 0.012, 0.118, and 0.106, respectively. The heritability was estimated at 0.10, suggesting cautious use for breeding improvements. The GEBV ranged from 0.096 to 3.10%, which offers breeders a practical tool for selecting high-fat-producing cows. This research provides valuable insights into optimizing milk quality and advancing genetic improvement strategies in smallholder dairy systems.

Objective: The poultry industry is significantly impacted by viral infections, particularly Newcastle Disease Virus (NDV), which leads to substantial economic losses. It is essential to comprehend how the sequence of development affects biological pathways and how early exposure to infections might affect immune responses. Methods: This study employed transcriptome analysis to investigate host–pathogen interactions by analyzing gene expression changes in NDV-infected chicken embryos’ lungs. Result: RNA-Seq reads were aligned with the chicken reference genome (Galgal7), revealing 594 differentially expressed genes: 264 upregulated and 330 downregulated. The most overexpressed genes, with logFC between 8.15 and 8.75, included C8A, FGG, PIT54, FETUB, APOC3, and FGA. Notably, downregulated genes included BPIFB3 (−4.46 logFC) and TRIM39.1 (−4.26 logFC). The analysis also identified 29 novel transcripts and 20 lncRNAs that were upregulated. Gene Ontology and KEGG pathways’ analyses revealed significant alterations in gene expression related to immune function, metabolism, cell cycle, nucleic acid processes, and mitochondrial activity due to NDV infection. Key metabolic genes, such as ALDOB (3.27 logFC), PRPS2 (2.66 logFC), and XDH (2.15 logFC), exhibited altered expression patterns, while DCK2 (−1.99 logFC) and TK1 (−2.11 logFC) were also affected. Several immune-related genes showed significant upregulation in infected lung samples, including ALB (6.15 logFC), TLR4 (1.86 logFC), TLR2 (2.79 logFC), and interleukin receptors, such as IL1R2 (3.15 logFC) and IL22RA2 (1.37 logFC). Conversely, genes such as CXCR4 (−1.49 logFC), CXCL14 (−2.57 logFC), GATA3 (−1.51 logFC), and IL17REL (−2.93 logFC) were downregulated. The higher expression of HSP genes underscores their vital role in immune responses. Conclusion: Comprehension of these genes’ interactions is essential for regulating viral replication and immune responses during infections, potentially aiding in the identification of candidate genes for poultry breed improvement amidst NDV challenges.

The objective of this study was to investigate the transcriptomic profiling of differentially ex-pressed genes between a commercial layer breed and an indigenous Indian breed. RNA was ex-tracted from NDV-infected and uninfected embryo lung tissue samples of Aseel, Kadaknath, and White Leghorn chickens. RNA-Seq was performed, and reads were aligned to the chicken refer-ence genome (Galgal7). A total of 594 genes were significantly differentially expressed, with 264 upregulated and 330 downregulated in infected embryos. Highly overexpressed genes in infect-ed conditions included C8A, FGG, PIT54, FETUB, APOC3, FGA, SPIA1, AvBD13, APOH, AMBP, TTR, PLA2G12B. Additionally, 29 novel transcripts and 20 lncRNAs were upregulated. White Leghorn embryos showed distinct expression patterns for CAV1 and GATA3, while Kadaknath healthy embryos had higher levels of CYTB, HBBA, ND4, ND4L, and ND5, indicating breed uniqueness. The analysis revealed significant gene involvement through Gene Ontology and KEGG pathways, highlighting alterations in gene expression related to immune function, me-tabolism, cell cycle, nucleic acid processes, and mitochondrial activity due to NDV infection. ALDOB, PRPS2, XDH, DCK2, and TK1 genes, which were involved in several metabolic path-ways, clearly displayed an altered expression pattern in the infected embryo. Additionally, ALB, TLR4, TLR2, TLR21, IL1R2, IL22RA2, HSP90AA, HSPB9(p60), and HSPB8 were significantly up-regulated in infected lung samples, while CXCR4, CXCL14, GATA3, IL17REL, and IL22RA1 were downregulated. Notably, higher expression of HSPs in Kadaknath suggests heat tolerance. This research provides insights into the genetic differences between commercial and local breeds and reveals the impact of NDV infection on metabolic processes, potentially identifying candidate genes for breed improvement.

Newcastle disease (ND) is highly contagious and usually causes severe illness that affects Aves all over the world, including domestic poultry. Depending on the virus’s virulence, it can impact the nervous, respiratory, and digestive systems and cause up to 100% mortality. The chIFITM genes are activated in response to viral infection. The current study was conducted to quantify the mRNA of chIFITM genes in vitro in response to ND viral infection. It also examined its ability to inhibit ND virus replication in chicken embryo fibroblast (CEF) cells of the Aseel and Kadaknath breeds. Results from the study showed that the expression of all chIFITM genes was significantly upregulated throughout the period in the infected CEF cells of both breeds compared to uninfected CEF cells. In CEF cells of the Kadaknath breed, elevated levels of expression of the chIFITM3 gene dramatically reduced ND viral growth, and the viral load was 60% lower than in CEF cells of the Aseel breed. The expression level of the chIFITMs in Kadaknath ranged from 2.39 to 11.68 log₂ folds higher than that of control CEFs and was consistently (p < 0.01) higher than Aseel CEFs. Similar to this, theIFN-γ gene expresses strongly quickly and peaks at 13.9 log₂ fold at 48 hpi. Based on these cellular experiments, the Kadaknath breed exhibits the potential for greater disease tolerance than Aseel. However, to gain a comprehensive understanding of disease resistance mechanisms in chickens, further research involving in vivo investigations is crucial.