Genomic Approaches Research Articles

Phylogenomics reveals the timescale of diversification in Amblycera

AbstractRecently, genomic approaches have helped to resolve phylogenetic questions in many groups of parasitic organisms, including lice (Phthiraptera). However, these approaches have still not been applied to one of the most diverse groups of lice, Amblycera. To fill this gap, we applied phylogenomic methods based on genome‐level exon sequence data to resolve the relationships within and among the families of Amblycera. Our phylogenomic trees support the monophyly of the families Ricinidae and Laemobothriidae. However, the families Trimenoponidae and Gyropidae are not monophyletic, indicating that they should be merged into a single family. The placement of Trinoton is unstable with respect to Boopiidae and Menoponidae, and we suggest recognizing Trinotonidae as a separate family. At the genus level, the genera Colpocephalum, Hohorstiella, Menacanthus and Ricinus were recovered as paraphyletic. Regarding generic complexes, the tree revealed the Menacanthus complex to be monophyletic, but the Colpocephalum complex paraphyletic, including genera not traditionally placed in this group. Dating analysis suggests that the divergence among families of Amblycera occurred shortly after the Cretaceous–Paleogene boundary 66 Mya. Cophylogenetic analyses revealed many host‐switching events during the diversification of Amblycera, indicating that the evolutionary history of Amblycera does not tightly mirror that of its hosts. Ancestral host reconstructions revealed that the ancestral host of Amblycera was most likely a bird, with two host switching events to mammals. By combining phylogenomics, molecular dating and cophylogenetic analyses, we provide the first large‐scale picture of amblyceran evolution, which will serve as a basis for future studies of this group.

Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size.

We are witnessing an ongoing global biodiversity crisis, and an increasing number of mammalian populations are at risk of decline. Species that have survived severe historic bottlenecks, such as the cheetah (Acinonyx jubatus) exhibit symptoms of inbreeding depression including reproductive and developmental defects. Although it has long been suggested that such defects stem from an accumulation of weakly deleterious mutations, the implications of such mutations leading to pseudogenization has not been assessed. Here, we use comparative analysis of eight felid genomes to better understand the impacts of deleterious mutations in the cheetah. We find novel pseudogenization events specific to the cheetah. Through careful curation, we identify 65 genes with previously unreported premature termination codons that likely affect gene function. With the addition of population data (n=6) we find 22 of these premature termination codons in at least one resequenced individual, four of which (DEFB116, ARL13A, CFAP119 and NT5DC4) are also found in a more recent reference genome. Mutations within three of these genes are linked with sterility, including azoospermia, which is common in cheetahs. Our results highlight the power of comparative genomic approaches for the discovery of novel causative variants in declining species.

Epigenetics and individuality: from concepts to causality across timescales.

Traditionally, differences among individuals have been divided into genetic and environmental causes. However, both types of variation can underlie regulatory changes in gene expression - that is, epigenetic changes - that persist across cell divisions (developmental differentiation) and even across generations (transgenerational inheritance). Increasingly, epigenetic variation among individuals is recognized as an important factor in human diseases and ageing. Moreover, non-genetic inheritance can lead to evolutionary changes within populations that differ from those expected by genetic inheritance alone. Despite its importance, causally linking epigenetic variation to phenotypic differences across individuals has proven difficult, particularly when epigenetic variation operates independently of genetic variation. New genomic approaches are providing unprecedented opportunity to measure and perturb epigenetic variation, helping to elucidate the role of epigenetic variation in mediating the genotype-phenotype map. Here, we review studies that have advanced our understanding of how epigenetic variation contributes to phenotypic differences between individuals within and across generations, and provide a unifying framework that allows historical and mechanistic perspectives to more fully inform one another.

Identification of Drug-Targetable Genes for Eczema and Dermatitis Using Integrated Genomic and Proteomic Approaches.

Background: Eczema and dermatitis are common inflammatory skin conditions with significant morbidity. Identifying drug-targetable genes can facilitate the development of effective treatments. Methods: This study analyzed data obtained by meta-analysis of 2 genome-wide association studies on eczema/dermatitis (57,311 cases and 896,779 controls, European ancestry). We identified drug-targetable genes from the Drug-Gene Interaction Database and Finan et al's findings. Cis-expression quantitative trait loci (eQTL) data from human blood and skin tissues were used for Mendelian randomization (MR) analysis. Bayesian colocalization, proteomic MR, and meta-analysis validated the causal relationships. Finally, protein-protein interactions (PPIs) and correlation analysis of potential drug targets and cytokines were performed. Results: We identified 2532 drug-targetable genes; 3378 Single Nucleotide Polymorphism (SNPs) were associated with 1531 genes in blood cis-eQTLs, 664 SNPs with 667 genes in sun-exposed skin eQTLs, and 572 SNPs with 574 genes in nonsun-exposed skin eQTLs. Five genes (SLC22A5, NOTCH4, AGER, HLA-DRB5, and EHMT2) showed causal relationships with eczema/dermatitis across multiple datasets. Single-variable and multi-variable Mendelian randomization (SMR) and multi-SNP SMR analysis identified 8 genes (PIK3R4, DHODH, CXCR2, Interleukin (IL)18, LGALS9, RPS6KB2, SLC22A5, and AGER) across all tissues. Functional Summary Information for Variants in the Online Network (FUSION) analysis confirmed associations for SLC22A5 and AGER. Bayesian colocalization indicated AGER (PPH4: 0.95) as a shared causal variant. Proteomic MR and meta-analysis showed that increased AGER protein levels were associated with a lower risk of eczema or dermatitis (odds ratio: 0.995, 95% confidence interval: 0.997-0.993, P = 0.0002). A PPI network revealed interactions of AGER with NOTCH4 and multiple cytokines, whereas SLC22A5 showed no cytokine interactions. Conclusions: This study identified potential drug-targetable genes, with AGER showing strong potential as a target for reducing eczema/dermatitis risk. These findings provide a basis for developing targeted therapies.

Magnetotactic bacteria from diverse Pseudomonadota families biomineralize intracellular Ca-carbonate.

Intracellular calcium carbonate formation has long been associated with a single genus of giant Gammaproteobacteria, Achromatium. However, this biomineralization has recently received increasing attention after being observed in photosynthetic Cyanobacteriota and in two families of magnetotactic bacteria affiliated with the Alphaproteobacteria. In the latter group, bacteria form not only intracellular amorphous calcium carbonates into large inclusions that are refringent under the light microscope, but also intracellular ferrimagnetic crystals into organelles called magnetosomes. Here new observations suggest that magnetotactic bacteria previously identified in the sediments and water column of Lake Pavin (France) were only a small fraction of the diversity of bacteria producing intracellular amorphous calcium carbonates. To explore this diversity further, we conducted a comprehensive investigation of magnetotactic populations with refractive granules using a combination of environmental microbiology, genomic and mineralogy approaches on cells sorted by micromanipulation. Several species belonging to divergent genera of two Pseudomonadota classes were identified and characterized. Scanning transmission electron microscopy coupled with energy-dispersive X-ray spectrometry support that all these species indeed form intracellular amorphous calcium carbonates. Cryo soft X-ray tomography experiments conducted on ice-vitrified cells, enabled 3D investigation of inclusions volume, which was found to occupy 44 - 68% of the cell volume. Metabolic network modeling highlighted different metabolic abilities of Alpha- and Gammaproteobacteria, including methylotrophy and CO2 fixation via the reverse Krebs cycle or the Calvin-Benson-Bassham cycle. Overall, this study strengthens a convergent evolution scenario for intracellular carbonatogenesis in Bacteria, and further supports that it is promoted by the fixation of CO2 in anoxic environments.

Modeling non-genetic adaptation in tumor cells.

Treatment resistance poses a significant challenge in the care of cancer patients. Hirsch etal. applied computational and genomic approaches, examining gene expression dynamics from a mouse model of melanoma at single-cell resolution to reveal that semi-heritable non-genetic alterations in tumor cell populations confer adaptive resistance to treatment.

Using phenomic selection to predict hybrid values with NIR spectra measured on the parental lines: proof of concept on maize

Key messagePhenomic selection based on parental spectra can be used to predict GCA and SCA in a sparse factorial design.Prediction approaches such as genomic selection can be game changers in hybrid breeding. They allow predicting the genetic values of hybrids without the need for their physical production. This leads to significant reductions in breeding cycle length, and so to the increase in genetic progress. However, these methods are often underutilized in breeding programs due to the substantial cost involved in genotyping thousands of candidate parental lines annually. To address this limitation, we propose a cost-effective alternative based on phenomic selection, where genotyping of parental lines is replaced by NIR spectroscopy. Standard prediction models are then applied for genomic and phenomic selection, using similarity matrices derived from either genotyping data (genomic selection) or NIR spectral data (phenomic selection). Our hypothesis is that the chemical composition of parental tissues captured by NIRS reflects the genetic similarity between parental lines. We evaluated both strategies using a sparse factorial design, whose hybrids have been phenotyped in a multi-environment trial network, and with NIR spectra acquired on the parental lines on two independent environments. Both genomic and phenomic prediction approaches demonstrated moderate-to-high predictive abilities across various cross-validation scenarios. Our results also showcase the capability of phenomic selection to predict Mendelian sampling. This study serves as a proof of concept that low-cost high-throughput phenomics of parental lines can effectively be used to predict maize hybrids in independent trials. This paves the way for widespread adoption of prediction approaches at the very first stages of hybrid breeding, benefiting both major and orphan species.

AI-enabled construction and prediction of atomic models for thin-film heterostructures via materials genome approach

AI-enabled construction and prediction of atomic models for thin-film heterostructures via materials genome approach

De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar.

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next-generation sequencing technologies and the resulting reduction in associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first published reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.157 gigabase, 2980-contig nuclear assembly with an N50 of 101.6 Mb and a 17,108 bp mitogenome. The nuclear assembly had 30× average coverage and was comparable in completeness to other primate reference genomes, with a 96.1% BUSCO completeness score for primate-specific genes. As the first published reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

Genetic and Genomic Approaches to the Study of Drug-Induced Liver Injury.

Idiosyncratic hepatotoxicity induced by prescribed drugs has been known since the early 20th century. Identifying risk factors, including genetic factors, that trigger this drug-induced liver injury (DILI) has been an important priority for many years, both to prevent drugs that cause liver injury being licensed and as a potential means of preventing at-risk patients being prescribed causative drugs. Improved methods for genomic analysis, particularly the development of genome-wide association studies, have facilitated the identification of genomic risk factors for DILI, but, to date, there are only two main examples, liver injury caused by amoxicillin-clavulanate (AC) and by flucloxacillin, where genetic risk factors causing the injury have been identified and replicated with understanding of the underlying mechanism. There has also been progress on identifying genetic risk factors for liver injury caused by other anti-infective agents, herbal remedies and nonsteroidal anti-inflammatory drugs. The majority of genetic risk factors identified to date are specific human leucocyte antigen (HLA) alleles and evidence that these alleles preferentially present self-peptides inappropriately to T cells in the liver has been obtained. Non-HLA genes also contribute to genetic susceptibility, both as co-factors in T-cell responses and, in the case of isoniazid-only, drug metabolism. Polygenic risk scores to predict DILI have been developed, both a simple score that predicts AC injury and complex scores that may be applied to DILI more generally and provide evidence that additional risk factors other than HLA genes exist.

Replication stress increases de novo CNVs across the malaria parasite genome.

Changes in the copy number of large genomic regions, termed copy number variations (CNVs), contribute to important phenotypes in many organisms. CNVs are readily identified using conventional approaches when present in a large fraction of the cell population. However, CNVs that are present in only a few genomes across a population are often overlooked but important; if beneficial under specific conditions, a de novo CNV that arises in a single genome can expand during selection to create a larger population of cells with novel characteristics. While the reach of single cell methods to study de novo CNVs is increasing, we continue to lack information about CNV dynamics in rapidly evolving microbial populations. Here, we investigated de novo CNVs in the genome of the Plasmodium parasite that causes human malaria. The highly AT-rich P. falciparum genome readily accumulates CNVs that facilitate rapid adaptation to new drugs and host environments. We employed a low-input genomics approach optimized for this unique genome as well as specialized computational tools to evaluate the de novo CNV rate both before and after the application of stress. We observed a significant increase in genome-wide de novo CNVs following treatment with a replication inhibitor. These stress-induced de novo CNVs encompassed genes that contribute to various cellular pathways and tended to be altered in clinical parasite genomes. This snapshot of CNV dynamics emphasizes the connection between replication stress, DNA repair, and CNV generation in this important microbial pathogen.

Potential of FGL1 Gene Variation in Increasing the Risk of Liver Side Effects Due to The Use of Nifedipine in Patients with Gestational Hypertension

Hypertension in pregnancy (HIP) affects approximately 10% of all pregnant women worldwide, including preeclampsia, eclampsia, gestational hypertension, and chronic hypertension. This study aims to analyze the potential of the Fibrinogen Like Protein 1 (FGL1) gene in increasing the risk of liver side effects due to the use of Nifedipine in pregnant women with genomic and bioinformatic information approaches. Bioinformatic databases included GWAS and SNPnexus, and gene expression profiles were examined using the GTEx Portal. We prioritized SNPs based on Benign, Possibly damaging, and Probably damaging criteria with the polyphen scoring system. Of the two SNPs (rs167479 and rs2653414) identified, the rs2653414 variant in the FGL1 gene showed probably damaging properties. The results showed that rs2653414 encoding the FGL1 gene has the potential to worsen the condition of hypertension during pregnancy and impact the side effects of using Nifedipine. FGL1 plays a role in liver regeneration, lipid metabolism, and energy utilization. Nifedipine metabolized in the liver can cause hepatitis with severe clinical symptoms. Therefore, routine monitoring of liver function in gestational hypertensive patients receiving Nifedipine therapy is necessary.

Sex evolution path involved in flowering plant family Cucurbitaceae: A review

The predominant sexual system in the plant kingdom is hermaphroditism, where both female and male reproductive organs coexist within a single flower. The major parameters that influence the sexual systems are genetic variation, pollinator availability and type, mating system, ecological factors, geographical isolation, selective pressures, evolutionary history, polyploidy, hybridization and sexual conflict. These factors all play significant roles. Plants may evolve self-fertilization or outcrossing mechanisms based on their specific environmental conditions, reproductive strategies and evolutionary history. The interplay of these factors shapes the diverse range of sexual systems observed in plant species worldwide. The Cucurbitaceae family exhibits a highly specialized sex chromosome differentiation scheme with three major sexual patterns (monoecy, dioecy and hermaphroditism). In the present review, we focus on the evolution of gender in flowering plants of the Cucurbitaceae family, exploring the various paths and drivers involved in the evolution of dioecy. We also shed light on the sex chromosomes and phytohormones that contribute to gender diversification. Several molecular and genomic approaches have been recently applied to uncover the genetic basis of gender differentiation in different flowering plant species.

Prognostic importance of direct assignment of parent-of-origin via long-read genome and epigenome sequencing in retinoblastoma.

Current clinical sequencing methods cannot effectively detect DNA methylation and allele-specific variation to provide parent-of-origin information from the proband alone. Parent-of-origin effects can lead to differential disease and the inability to assign this in de novo cases limits prognostication in the majority of affected individuals with retinoblastoma, a hereditary cancer with suspected parent-of-origin effects. To directly assign parent-of-origin in retinoblastoma patients, genomic DNA was extracted from blood samples for sequencing using a programmable, targeted single-molecule long-read DNA genomic and epigenomic approach. This allowed germline variant calling and simultaneous haplotype-resolved CpG methylation in subjects with familial (n=7) and de novo (n=9) retinoblastoma. Targeted long-read sequencing allowed phasing genomic variation with a differentially methylated region in intron 2 of the RB1 gene to confirm parent-of-origin in known familial samples. Leveraging this approach allowed us to directly assign parent-of-origin rapidly in simple and complex de novo cases from the proband alone. The ability to assign parent-of-origin in all cases of retinoblastoma showed that harboring disease-causing variants on the paternally inherited allele, whether arising familial or de novo, is associated with more advanced cancer staging at presentation and significantly greater risk of chemotherapy failure (P=0.002). This study demonstrates the diagnostic potential of multi-omic long-read profiling to unveil the parent-of-origin effect in hereditary cancer. The approach in this work will be instrumental in assigning parent-of-origin to other genetic diseases using local and distant imprinting signals in the genome. National Eye Institute, NIH (K08EY033789); Gerber Foundation; Research to Prevent Blindness.

Applications of Three Genomic Approaches in Alzheimer's Disease Research

Dementia is a group of diseases that affect brain function and lead to a decline in cognitive abilities. Some types involve the gradual loss of function in brain neurons, such as Alzheimer's disease, which is characterized by progressive memory loss and cognitive dysfunction and is one of the most common neurodegenerative dementias. The growing prevalence, particularly in aging populations, underscores the need for enhanced diagnostic and therapeutic stproportiongies. The application of cutting-edge genomic technologies, encompassing genome-wide association studies (GWAS) to identify genetic variants associated with Alzheimer's disease (AD), whole exome sequencing (WES) to explore protein-coding regions for functional mutations, and single-cell RNA sequencing (scRNA-seq) to dissect cellular heterogeneity at a granular level, has collectively enhanced our insight into the intricate genetic architecture of AD, shedding light on the complex interplay of genes and biological pathways implicated in the disease's pathogenesis. GWAS has identified several risk loci, including the APOE ε4 allele, which plays a crucial role in lipid metabolism and amyloid-β clearance. However, GWAS primarily detects common variants, limiting its ability to explain rare genetic mutations. WES, which focuses on protein-coding regions, has uncovered rare variants in genes such as PSEN1 and PSEN2, which are linked to early-onset familial AD. Despite its strengths, WES overlooks non-coding regions critical for gene regulation. scRNA-seq provides high-resolution insights into cellular heterogeneity, identifying cell subsets and molecular mechanisms involved in AD. This technique has revealed novel therapeutic targets by analyzing gene expression at the single-cell level. However, it faces challenges in data processing and cost. Integrating these approaches offers a more comprehensive view of AD’s pathology, enhancing early diagnosis and personalized treatment. As genomic technologies evolve, they hold great promise for improving our understanding and management of AD.

Genomic-Inbreeding Landscape and Selection Signatures in the Polo Argentino Horse Breed.

Analyzing genetic variability and inbreeding trends is essential for effective breed management in animal populations. To this, the characterization of runs of homozygosity (ROH) provides a good genomic approach to study the phenomena. The Polo Argentino (PA) breed, globally recognized as the best adapted to playing polo, is known for its strong influence of Thoroughbreds, intense selective breeding, and extensive use of reproductive biotechnologies. This study investigates the PA's genomic variability, by characterizing the ROH landscape and identifying ROH islands (ROHi) as potential genomic footprints for the breed. PA horses (n = 506) were genotyped using EquineGGP™ array v5 (70 k). We calculated the inbreeding coefficient based on ROH (FROH-ancestral and recent) using a chromosomal approach. Finally, we identified genomic regions with increased ROH frequency (ROHi) and their associated genes. An average of 79.5 ROH per horse was detected, with a mean length of 4.6 Mb. The average FROH was 0.151, but most of them (54%) corresponded to ancestral inbreeding (ROH < 5.5 Mb). However, 4 ROHi were identified in ECA 1, 3, 7 and 17, containing 67 genes, some of which were related to behavior, neurodevelopment, and metabolic functions. This genomic analysis determined, for the first time, the length and location of homozygosity segments in the PA breed and identified ROHi associated with potential genomic regions and genes for positive selection in the breed.

A population genomics approach to unlock the genetic potential of lablab (Lablab purpureus (L.) Sweet), an underutilized tropical forage crop

BackgroundLablab is one of the conventionally grown multi-purpose crops that originated in Africa. It is an annual or short-lived perennial forage legume which has versatile uses (as a vegetable and dry seeds, as food or feed, or as green manure) but is yet to receive adequate research attention and hence remains underexploited. To develop new and highly productive lablab varieties, using genomics-assisted selection, the present study aimed to identify quantitative trait loci associated with agronomically important traits in lablab and to assess the stability of these traits across two different agro-ecologies in Ethiopia. Here, we resequenced one hundred and forty-two lablab accessions, utilised whole genome genotyping approaches, and conducted multi-locational phenotyping over two years.ResultsThe selected lablab accessions displayed significant agro-morphological variation in eight analysed traits, including plant height, total fresh weight, and total dry weight. Furthermore, the agronomic performance of the accessions was significantly different across locations and years, highlighting substantial genotype-by-environment interactions. The population genetic structure of the lablab accessions, based on ~ 500,000 informative single nucleotide polymorphisms (SNPs), revealed an independent domestication pattern for two-seeded and four-seeded lablab accessions. Finally, based on multi-environmental trial data, a genome-wide association study (GWAS) identified useful SNPs and k-mers for key traits, such as plant height and total dry weight.ConclusionsThe publicly available genomic tools and field evaluation data from this study will offer a valuable resource for plant breeders and researchers to inform a new cycle of lablab breeding. With the aid of these tools, the breeding cycle will be significantly reduced and livestock farmers will have access to improved lablab varieties in a shorter time-frame.

Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis

BackgroundSince the beginning of the pandemic, contact tracing has been one of the most relevant issues to understand SARS-CoV-2 transmission dynamics and, in this context, the analysis of quasispecies may turn out to be a useful tool for outbreak investigations. Analysis of the intra-host single nucleotide variants (iSNVs) found in the nsp2, ORF3, and ORF7 genes of SARS-CoV-2 was conducted in order to correctly identify virus transmission chain among patients hospitalized in Brescia Civic Hospital.MethodsDuring the period between August and October 2023, 13 nasopharyngeal specimens, collected from patients admitted to Brescia Civic Hospital, were tested for SARS-CoV-2 positivity and molecularly characterized. Firstly, a phylogenetic analysis was performed to evaluate if they were epidemiologically linked and, then, the Beta-binomial method was used to estimate the transmission bottleneck size (Nb) and quantify the number of viral particles transmitted from one individual (donor) to another (recipient).ResultsAccording to the molecular characterization of specimens, we identified two transmission clusters in the cardiology unit: the first cluster concerned patients tested positive for the HV.1/EG.5.1.6 lineage, while the second cluster concerned patients tested positive for the FL.10.1 lineage. Moreover, evaluating the bottleneck size, we were able to solve SARS-CoV-2 transmission chain among infected patients.ConclusionOur method shows that it is possible to conduct a tracing study using a genomic approach based on iSNVs analysis.

Transcriptional regulation of the piRNA pathway by Ovo in animal ovarian germ cells.

The gene-regulatory mechanisms controlling the expression of the germline PIWI-interacting RNA (piRNA) pathway components within the gonads of metazoan species remain largely unexplored. In contrast to the male germline piRNA pathway, which in mice is known to be activated by the testis-specific transcription factor A-MYB, the nature of the ovary-specific gene-regulatory network driving the female germline piRNA pathway remains a mystery. Here, using Drosophila as a model, we combined multiple genomics approaches to reveal the transcription factor Ovo as regulator of the germline piRNA pathway in ovarian germ cells. Ectopic expression of Ovo in ovarian somatic cells activates germline piRNA pathway components, including the ping-pong factors Aubergine, Argonaute-3, and Vasa, leading to assembly of perinuclear cellular structures resembling nuage bodies of germ cells. We found that in ovarian somatic cells, transcription of ovo is repressed by l(3)mbt, thus preventing expression of germline piRNA pathway genes in the soma. Cross-species ChIP-seq and motif analyses demonstrate that Ovo is binding to genomic CCGTTA motifs within the promoters of germline piRNA pathway genes, suggesting a regulation by Ovo in ovaries analogous to that of A-MYB in testes. Our results also show consistent engagement of the Ovo transcription factor family at ovarian piRNA clusters across metazoan species, reflecting a deep evolutionary conservation of this regulatory paradigm from insects to humans.

Understanding anaerobic germination in direct-seeded rice: a genomic mapping approach

BackgroundAnaerobic germination is a critical trait for rice cultivation, particularly in regions that experience flooding or waterlogging immediately after sowing. Under direct-seeded conditions, where rice is sown directly into the field without prior transplantation, the ability of seeds to germinate in anaerobic (oxygen-deficient) conditions becomes essential for successful crop establishment. This trait is especially relevant in areas prone to waterlogging, were traditional methods of rice cultivation, such as puddled transplanting, may be less viable. Understanding the genetic basis of anaerobic germination can lead to the development of rice varieties that are better adapted to such challenging conditions, thus supporting more sustainable agricultural practices.ResultsIn this study, a nested association mapping (NAM) population consisting of 384 breeding lines was utilized to identify genomic regions associated with anaerobic germination in rice. Through comprehensive analysis, 19 significant marker-trait associations (MTAs) were identified, including 12 associations specifically linked to percent seed germination under anaerobic conditions. These associations were distributed across six different chromosomes: 3, 4, 5, 6, 7, and 9. Notably, a cluster of single nucleotide polymorphisms (SNPs) spanning a 6.9 Mb genomic region on chromosome 3 (from 21,089,181 to 28,017,712 bp) was consistently associated with percent germination at 15 and 21 days after sowing over multiple years. Similarly, a 6.4 Mb genomic segment on chromosome 6 (from 18,028,538 to 24,492,161 bp) was also associated with percent germination at the same time points. Specific SNPs within this region, namely S6_18028538 and S6_24492161, were linked to germination at 15 and 21 days, respectively. In addition to these findings, one MTA was identified for days to 50% flowering on chromosome 1, and six MTAs were identified for grain yield across chromosomes 1, 2, 5, 8, and 10. The breeding lines that exhibited both high and stable yields, along with anaerobic germination traits, have the potential to be particularly valuable in genomics-assisted breeding programs aimed at improving rice varieties for flood-prone areas.ConclusionsThis study provides crucial insights into the genetic basis of anaerobic germination in rice, highlighting specific genomic regions associated with this trait under direct-seeded conditions. The identification of significant MTAs across multiple chromosomes, particularly the consistent associations found on chromosomes 3 and 6, underscores the potential for developing rice varieties with enhanced tolerance to anaerobic conditions. The high-yielding breeding lines identified in this research, which also exhibit strong anaerobic germination traits, represent valuable genetic resources for breeding programs. These findings support the use of direct-seeded rice (DSR) as a sustainable alternative to traditional puddled transplanting, particularly in regions prone to flooding, thereby contributing to the development of more resilient rice cultivation practices.