Heredity最新文献

{"title":"FISH mapping in Xenopus pygmaeus refines understanding of genomic rearrangements and reveals jumping NORs in African clawed frogs.","authors":"Barbora Bergelová, Václav Gvoždík, Martin Knytl","doi":"10.1038/s41437-025-00749-x","DOIUrl":"https://doi.org/10.1038/s41437-025-00749-x","url":null,"abstract":"<p><p>Chromosomal rearrangements are fundamental evolutionary drivers leading to genomic diversification. African clawed frogs (genus Xenopus, subgenera Silurana and Xenopus) represent an allopolyploid model system with conserved chromosome numbers in species with the same ploidy within each subgenus. Two significant interchromosomal rearrangements have been identified: a translocation between chromosomes 9 and 2, found in subgenus Silurana, and a fusion between chromosomes 9 and 10, probably widespread in subgenus Xenopus. Here, we study the allotetraploid Xenopus pygmaeus (subgenus Xenopus) based on in-depth karyotype analysis using chromosome measurements and fluorescent in situ hybridization (FISH). We designed FISH probes for genes associated with translocation and fusion to test for the presence of the two main types of rearrangements. We also examined the locations of 5S and 28S ribosomal tandem repeats, with the former often associated with telomeric regions and the latter with nucleolus organizer regions (NORs). The translocation-associated gene mapping did not detect the translocation in X. pygmaeus, supporting the hypothesis that the translocation is restricted to Silurana, but instead identified a pericentromeric inversion on chromosome 2S. The fusion-associated gene mapping confirmed the fusion of chromosomes 9 and 10, supporting this fusion as an ancestral state in subgenus Xenopus. As expected, the 5S repeats were found predominantly in telomere regions on almost all chromosomes. The nucleolar 28S repeats were localized on chromosome 6S, a position previously found only in the closely related species X. parafraseri, whereas other, phylogenetically more distant species have NORs located on different chromosomes. We therefore hypothesize that a jumping mechanism could explain the relatively frequent changes in the location of NORs during Xenopus evolution.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system.","authors":"Sen Xu, Swatantra Neupane, Hongjun Wang, Thinh Phu Pham, Marelize Snyman, Trung V Huynh, Li Wang","doi":"10.1038/s41437-025-00750-4","DOIUrl":"10.1038/s41437-025-00750-4","url":null,"abstract":"<p><p>The effective use of CRISPR technologies in emerging model organisms faces significant challenges in efficiently generating heritable mutations and in understanding the genomic consequences of induced DNA damages and the inheritance patterns of induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for gene editing in the microcrustacean Daphnia pulex; 2) assessing the editing dynamics of Cas9 and Cas12a nucleases in the scarlet knock-out mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet gene. Our reengineered microinjection method results in efficient biallelic editing with both nucleases. Our data suggest site-specific DNA cleavage mostly occurs in a stepwise fashion. Indels dominate the induced mutations. A few, unexpected on-site large deletions (>1 kb) are also observed. Notably, genome-wide analyses reveal no off-target mutations. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progeny. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes involved in human neurodegenerative diseases.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program.","authors":"Cathrine Kiel Skovbjerg, Pernille Sarup, Ellen Wahlström, Jens Due Jensen, Jihad Orabi, Lotte Olesen, Just Jensen, Ahmed Jahoor, Guillaume Ramstein","doi":"10.1038/s41437-025-00751-3","DOIUrl":"https://doi.org/10.1038/s41437-025-00751-3","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deforestation-induced Hybridization in Philippine Frogs Creates a Distinct Phenotype With an Inviable Genotype.","authors":"Kin Onn Chan, Paul M Hime, Rafe M Brown","doi":"10.1038/s41437-025-00748-y","DOIUrl":"https://doi.org/10.1038/s41437-025-00748-y","url":null,"abstract":"<p><p>Hybridization plays a major role in the evolutionary history of many taxa and can generate confounding patterns affecting many downstream applications. In this study, we empirically demonstrate how hybridization obfuscates phylogenetic inference (via the artefactual branch effect), species boundaries, and taxonomy in an adaptive radiation of frogs. Philippine narrow-mouthed frogs of the genus Kaloula exhibit a wide range of phenotypic and ecological adaptations but their evolutionary history and taxonomy remain poorly understood. In particular, the Kaloula conjuncta complex contains numerous subspecies with unresolved taxonomic boundaries and unclear evolutionary relationships. Within this complex, Kaloula conjuncta stickeli, until now was considered a rare, enigmatic, and phenotypically distinct subspecies that had not been encountered since its original description nearly 80 years ago. Here, we show that K. c. stickeli shares alleles with K. conjuncta meridionalis and another species outside the conjuncta group, K. picta. Using target-capture sequencing and a robust analytical framework, we show that despite having a unique phenotype, K. c. stickeli is likely an inviable F1 hybrid between K. c. meridionalis and K. picta and thus, does not warrant taxonomic recognition. Our results show how industry-standard approaches in systematic inference and integrative taxonomy-morphological, phylogenomic, clustering, and distance-based methods-can generate misleading results for identifying and understanding affinities of hybrids. In contrast, we demonstrate how network multispecies coalescent and population genetic approaches are more effective at accurately inferring reticulated evolutionary history. We also propose a rare phenomenon of deforestation-induced hybridization, which could have important consequences in light of large-scale Southeast Asian forest destruction.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143433128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing stable SNPs and genomic prediction insights across environments enhance breeding strategies of productivity, defense, and climate-adaptability traits in white spruce.","authors":"Eduardo P Cappa, Charles Chen, Jennifer G Klutsch, Jaime Sebastian-Azcona, Blaise Ratcliffe, Xiaojing Wei, Letitia Da Ros, Yang Liu, Sudarshana Reddy Bhumireddy, Andy Benowicz, Shawn D Mansfield, Nadir Erbilgin, Barb R Thomas, Yousry A El-Kassaby","doi":"10.1038/s41437-025-00747-z","DOIUrl":"10.1038/s41437-025-00747-z","url":null,"abstract":"<p><p>Exploring the relationship between phenotype, genotype, and environment is essential in quantitative genetics. Considering the complex genetic architecture of economically important traits, integrating genotype-by-environment interactions in a genome-wide association (GWAS) and genomic prediction (GP) framework is imperative. This integration is crucial for identifying robust markers with stability across diverse environments and improving the predictive accuracy of individuals' performance within specific target environments. We conducted a multi-environment GWAS and GP analysis for 30 productivity, defense, and climate-adaptability traits on 1540 white spruce trees from Alberta, Canada, genotyped for 467,224 SNPs and growing across three environments. We identified 563 significant associations (p-value < 1.07 ×10^-05) across the studied traits and environments, with 105 SNPs showing overlapping associations in two or three environments. Wood density, myrcene, total monoterpenes, α-pinene, and catechin exhibited the highest overlap (>50%) across environments. Gas exchange traits, including intercellular CO₂ concentration and intrinsic water use efficiency, showed the highest number of significant associations (>38%) but less stability (<1.2%) across environments. Predictive ability (PA) varied significantly (0.03-0.41) across environments for 20 traits, with stable carbon isotope ratio having the highest average PA (0.36) and gas exchange traits the lowest (0.07). Only two traits showed differences in prediction bias (PB) across environments, with 80% of site-trait PB falling within a narrow range (0.90 to 1.10). Integrating multi-environment GWAS and GP analyses proved useful in identifying site-specific markers, understanding environmental impacts on PA and PB, and ultimately providing indirect insights into the environmental factors that influenced this white spruce breeding program.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143406673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Horizontal transfer of accessory chromosomes in fungi - a regulated process for exchange of genetic material?","authors":"Michael Habig, Satish Kumar Patneedi, Remco Stam, Henrik Hjarvard De Fine Licht","doi":"10.1038/s41437-025-00746-0","DOIUrl":"https://doi.org/10.1038/s41437-025-00746-0","url":null,"abstract":"<p><p>Horizontal transfer of entire chromosomes has been reported in several fungal pathogens, often significantly impacting the fitness of the recipient fungus. All documented instances of horizontal chromosome transfers (HCTs) showed a marked propensity for accessory chromosomes, consistently involving the transfer of an accessory chromosome while other chromosomes were seldom, if ever, co-transferred. The mechanisms underlying HCTs, as well as the factors regulating the specificity of HCTs for accessory chromosomes, remain unclear. In this perspective, we provide an overview of the observed propensity in reported cases of horizontal chromosome transfers. We hypothesize the existence of a signal that distinguishes mobile, i.e., horizontally transferred, accessory chromosomes from the rest of the donor genome. Recent findings in Metarhizium robertsii and Magnaporthe oryzae, suggest that a mobile accessory chromosome may contain putative histones and/or histone modifiers, which could generate such a signal. Based on this, we propose that mobile accessory chromosomes may encode the machinery required for their own horizontal transmission, implying that HCT could be a regulated process. Finally, we present evidence of substantial differences in codon usage bias between core and accessory chromosomes in 14 out of 19 analysed fungal species and strains. Such differences in codon usage bias could indicate past horizontal transfers of these accessory chromosomes. Interestingly, HCT was previously unknown for many of these species, suggesting that the horizontal transfer of accessory chromosomes may be more widespread than previously thought, and therefore an important factor in fungal genome evolution.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA.","authors":"Emma Falkeid Eriksen, Adam Jon Andrews, Svein Vatsvåg Nielsen, Per Persson, Estrella Malca, Vedat Onar, Veronica Aniceti, Gäel Piquès, Federica Piattoni, Francesco Fontani, Martin Wiech, Keno Ferter, Oliver Kersten, Giada Ferrari, Alessia Cariani, Fausto Tinti, Elisabetta Cilli, Lane M Atmore, Bastiaan Star","doi":"10.1038/s41437-025-00745-1","DOIUrl":"https://doi.org/10.1038/s41437-025-00745-1","url":null,"abstract":"<p><p>Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinship clustering within an ecologically diverse killer whale metapopulation","authors":"Chérine D. Baumgartner,&nbsp;Eve Jourdain,&nbsp;Sebastian Bonhoeffer,&nbsp;Katrine Borgå,&nbsp;Mads P. Heide-Jørgensen,&nbsp;Richard Karoliussen,&nbsp;Jan T. Laine,&nbsp;Aqqalu Rosing-Asvid,&nbsp;Anders Ruus,&nbsp;Sara B. Tavares,&nbsp;Fernando Ugarte,&nbsp;Filipa I. P. Samarra,&nbsp;Andrew D. Foote","doi":"10.1038/s41437-024-00740-y","DOIUrl":"10.1038/s41437-024-00740-y","url":null,"abstract":"Metapopulation dynamics can be shaped by foraging ecology, and thus be sensitive to shifts in prey availability. Genotyping 204 North Atlantic killer whales at 1346 loci, we investigated whether spatio-temporal population structuring is linked to prey type and distribution. Using population-based methods (reflecting evolutionary means), we report a widespread metapopulation connected across ecological groups based upon nuclear genome SNPs, yet spatial structuring based upon mitogenome haplotypes. These contrasting patterns of markers with maternal and biparental inheritance are consistent with matrilineal site fidelity and philopatry, and male-mediated gene flow among demes. Connectivity between fish-eating and ‘mixed-diet’ (eating both fish and mammal prey) killer whales, marks a deviation within a species renowned for its marked structure associated with ecology. However, relatedness estimates suggest distinct spatial clusters, and heterogeneity in recent gene flow between them. The contrasting patterns between inference of structure and inference of relatedness suggest that gene flow has been partially restricted over the past two to three generations (50–70 years). This coincides with the collapse of North Atlantic herring stocks in the late 1960s and the subsequent cessation of their seasonal connectivity. Statistically significant association between diet types and assignment of Icelandic killer whales to relatedness-based clusters indicated limited gene flow was maintained through Icelandic ‘mixed-diet’ whales when herring-mediated connectivity was diminished. Thus, conservation of dietary variation within this metapopulation is critical to ensure genetic health. Our study highlights the role of resource dynamics and foraging ecology in shaping population structure and emphasises the need for transnational management of this widespread migratory species and its prey.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"109-119"},"PeriodicalIF":3.1,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00740-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incorporating spatial and genetic competition into breeding pipelines with the R package gencomp","authors":"Saulo F. S. Chaves,&nbsp;Filipe M. Ferreira,&nbsp;Getulio C. Ferreira,&nbsp;Salvador A. Gezan,&nbsp;Kaio Olimpio G. Dias","doi":"10.1038/s41437-024-00743-9","DOIUrl":"10.1038/s41437-024-00743-9","url":null,"abstract":"Genetic competition can obscure the true merit of selection candidates, potentially leading to altered genotype rankings and a divergence between expected and actual genetic gains. Despite a wealth of literature on genetic competition in plant and animal breeding, the separation of genetic values into direct genetic effects (DGE, related to a genotype’s merit) and indirect genetic effects (IGE, related to the effects of a genotype’s alleles on its neighbor''s phenotype) in linear mixed models is often overlooked, likely due to the complexity involved. To address this, we introduce gencomp, a new R package designed to simplify the use of (spatial-) genetic competition models in crop and tree breeding routines. gencomp includes functions for constructing the genetic competition matrix, fitting (spatial-) genetic competition models via the variance-component approach, and extracting key results such as variance components, heritabilities, competition classes, and total genetic values. For tree breeding, gencomp also calculates the merit of different clonal mixtures using the estimated DGE and IGE of the selection candidates. In this paper, we first present the theoretical foundation of the methods implemented in the package. We then demonstrate the use of gencomp with two datasets: one simulated from a Eucalyptus spp. trial and a real potato dataset. We used both datasets to demonstrate the influence of genetic competition in variance component estimates, heritabilities and selection. Despite the dependency on ASReml-R, a paid resource, gencomp is a user-friendly tool that can popularize genetic competition models, contributing to more informed decision-making in plant breeding.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"129-141"},"PeriodicalIF":3.1,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00743-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evolution of preferred male traits, female preference and the G matrix: \"Toto, I've a feeling we're not in Kansas anymore\".","authors":"Derek A Roff","doi":"10.1038/s41437-024-00744-8","DOIUrl":"https://doi.org/10.1038/s41437-024-00744-8","url":null,"abstract":"<p><p>Female preference exerts selection on male traits. How such preferences affect male traits, how female preferences change and the genetic correlation between male traits and female preference were examined by an experiment in which females were either mated to males they preferred (S lines) or to males chosen at random from the population (R lines). Female preference was predicted to increase the time spent calling by males. Thirteen other song components were measured. Preference for individual traits was greatest for time spent calling(CALL), volume(VOL) and chirp rate(CHIRP) but the major contributors in the multivariate function were CALL and CHIRP, the univariate influence of VOL arising from correlations to these traits. Estimation of β, the standardized selection differential, for CALL resulting from female preference showed that it was under strong direct selection. However, contrary to prediction, CALL did not change over the course of the experiment whereas VOL, CHIRP and other song components did. Simulation of the experiment using the estimated G matrix showed that lack of change in CALL resulted from indirect genetic effects negating direct effects. Changes in song components were largely due to indirect effects. This experiment showed that female preference may exert strong selection on traits but how they respond to such selection will depend greatly upon the G matrix. As predicted, female preference declined in the R lines. The genetic correlations between preference and preferred traits did not decline significantly more in the R lines, suggesting correlations resulted from both linkage disequilibrium and pleiotropy.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142970578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}