Heredity最新文献_第10页

Efficient genomics-based ‘end-to-end’ selective tree breeding framework 基于基因组学的高效 "端到端 "选择性树木育种框架

IF 3.8 2区生物学

Heredity Pub Date : 2024-01-03 DOI: 10.1038/s41437-023-00667-w

Yousry A. El-Kassaby, Eduardo P. Cappa, Charles Chen, Blaise Ratcliffe, Ilga M. Porth

{"title":"Efficient genomics-based ‘end-to-end’ selective tree breeding framework","authors":"Yousry A. El-Kassaby, Eduardo P. Cappa, Charles Chen, Blaise Ratcliffe, Ilga M. Porth","doi":"10.1038/s41437-023-00667-w","DOIUrl":"10.1038/s41437-023-00667-w","url":null,"abstract":"Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 2","pages":"98-105"},"PeriodicalIF":3.8,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-023-00667-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139084412","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}

引用次数: 0

AI-informed conservation genomics 人工智能保护基因组学。

IF 3.8 2区生物学

Heredity Pub Date : 2023-12-27 DOI: 10.1038/s41437-023-00666-x

Cock van Oosterhout

引用次数: 0

Projection of current and future distribution of adaptive genetic units in an alpine ungulate 预测高山蹄类动物适应性基因单元当前和未来的分布情况

IF 3.8 2区生物学

Heredity Pub Date : 2023-12-11 DOI: 10.1038/s41437-023-00661-2

Amélie Hoste, Thibaut Capblancq, Thomas Broquet, Laure Denoyelle, Charles Perrier, Elena Buzan, Nikica Šprem, Luca Corlatti, Barbara Crestanello, Heidi Christine Hauffe, Loïc Pellissier, Glenn Yannic

{"title":"Projection of current and future distribution of adaptive genetic units in an alpine ungulate","authors":"Amélie Hoste, Thibaut Capblancq, Thomas Broquet, Laure Denoyelle, Charles Perrier, Elena Buzan, Nikica Šprem, Luca Corlatti, Barbara Crestanello, Heidi Christine Hauffe, Loïc Pellissier, Glenn Yannic","doi":"10.1038/s41437-023-00661-2","DOIUrl":"10.1038/s41437-023-00661-2","url":null,"abstract":"Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate—the Northern chamois (Rupicapra rupicapra)—could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 1","pages":"54-66"},"PeriodicalIF":3.8,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138580632","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}

引用次数: 0

Gene expression and alternative splicing contribute to adaptive divergence of ecotypes 基因表达和替代剪接有助于生态型的适应性分化

IF 3.8 2区生物学

Heredity Pub Date : 2023-12-09 DOI: 10.1038/s41437-023-00665-y

Peter A. Innes, April M. Goebl, Chris C. R. Smith, Kaylee Rosenberger, Nolan C. Kane

{"title":"Gene expression and alternative splicing contribute to adaptive divergence of ecotypes","authors":"Peter A. Innes, April M. Goebl, Chris C. R. Smith, Kaylee Rosenberger, Nolan C. Kane","doi":"10.1038/s41437-023-00665-y","DOIUrl":"10.1038/s41437-023-00665-y","url":null,"abstract":"Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 3","pages":"120-132"},"PeriodicalIF":3.8,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138580930","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}

引用次数: 0

Aneuploidy during development in facultative parthenogenetic Drosophila 兼性孤雌生殖果蝇发育过程中的非整倍性。

IF 3.8 2区生物学

Heredity Pub Date : 2023-11-28 DOI: 10.1038/s41437-023-00664-z

A. L. Sperling, D. M. Glover

{"title":"Aneuploidy during development in facultative parthenogenetic Drosophila","authors":"A. L. Sperling, D. M. Glover","doi":"10.1038/s41437-023-00664-z","DOIUrl":"10.1038/s41437-023-00664-z","url":null,"abstract":"From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval brains of facultatively parthenogenetic Drosophila. We identified a background of aneuploidy in D. mercatorum strains and found increased levels of aneuploidy in the larval brain tissue of animals arising parthenogenetically versus those arising from sexual reproduction. There is also intra-individual variation in germline-derived aneuploidy within the same strain. To determine if this is a general feature of facultative parthenogenesis in drosophilids, we compared sexually reproduced and parthenogenetic offspring from an engineered facultative parthenogenetic strain of D. melanogaster. In addition to germline-derived aneuploidy, this revealed somatic aneuploidy that increased by up to fourfold in parthenogens compared to sexually reproduced offspring. Therefore, the genetic combination identified in D. mercatorum that causes facultative parthenogenesis in D. melanogaster results in aneuploidy, which indicates that the loss of mitotic control resulting in parthenogenesis causes subsequent genome variation within the parthenogenetic offspring. Our findings challenge the assumption that parthenogenetic offspring are near genetic replicas of their mothers.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 2","pages":"89-97"},"PeriodicalIF":3.8,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-023-00664-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138451377","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}

引用次数: 0

Alternative splicing and environmental adaptation in wild house mice 野生家鼠的选择性剪接与环境适应。

IF 3.8 2区生物学

Heredity Pub Date : 2023-11-27 DOI: 10.1038/s41437-023-00663-0

David N. Manahan, Michael W. Nachman

{"title":"Alternative splicing and environmental adaptation in wild house mice","authors":"David N. Manahan, Michael W. Nachman","doi":"10.1038/s41437-023-00663-0","DOIUrl":"10.1038/s41437-023-00663-0","url":null,"abstract":"A major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identify cis-acting splicing quantitative trait loci (cis-sQTL), and we identified cis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in mRNA abundance, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 3","pages":"133-141"},"PeriodicalIF":3.8,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138444499","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}

引用次数: 0

Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil 景观对巴西东北部高地森林飞地两种鸟类种群基因组变异的当代和历史影响。

IF 3.8 2区生物学

Heredity Pub Date : 2023-11-20 DOI: 10.1038/s41437-023-00662-1

Henrique Batalha-Filho, Silvia Britto Barreto, Mario Henrique Barros Silveira, Cristina Yumi Miyaki, Sandra Afonso, Nuno Ferrand, Miguel Carneiro, Fernando Sequeira

{"title":"Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil","authors":"Henrique Batalha-Filho, Silvia Britto Barreto, Mario Henrique Barros Silveira, Cristina Yumi Miyaki, Sandra Afonso, Nuno Ferrand, Miguel Carneiro, Fernando Sequeira","doi":"10.1038/s41437-023-00662-1","DOIUrl":"10.1038/s41437-023-00662-1","url":null,"abstract":"Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 2","pages":"77-88"},"PeriodicalIF":3.8,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138176022","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}

引用次数: 0

Heritability and developmental plasticity of growth in an oviparous lizard 卵生蜥蜴生长的遗传力和发育可塑性。

IF 3.8 2区生物学

Heredity Pub Date : 2023-11-15 DOI: 10.1038/s41437-023-00660-3

Fonti Kar, Shinichi Nakagawa, Daniel W. A. Noble

{"title":"Heritability and developmental plasticity of growth in an oviparous lizard","authors":"Fonti Kar, Shinichi Nakagawa, Daniel W. A. Noble","doi":"10.1038/s41437-023-00660-3","DOIUrl":"10.1038/s41437-023-00660-3","url":null,"abstract":"Selective processes act on phenotypic variation although the evolutionary potential of a trait relies on the underlying heritable variation. Developmental plasticity is an important source of phenotypic variation, but it can also promote changes in genetic variation, yet we have a limited understanding of how they are both impacted. Here, we quantified the influence of developmental temperature on growth in delicate skinks (Lampropholis delicata) and partitioned total phenotypic variance using an animal model fitted with a genomic relatedness matrix. We measured mass for 261 individuals (nhot = 125, ncold = 136) over 16 months (nobservations = 3002) and estimated heritability and maternal effects over time. Our results show that lizards reared in cold developmental temperatures had consistently higher mass across development compared to lizards that were reared in hot developmental temperatures. However, developmental temperature did not impact the rate of growth. On average, additive genetic variance, maternal effects and heritability were higher in the hot developmental temperature treatment; however, these differences were not statistically significant. Heritability increased with age, whereas maternal effects decreased upon hatching but increased again at a later age, which could be driven by social competition or intrinsic changes in the expression of variation as an individual’s growth. Our work suggests that the evolutionary potential of growth is complex, age-dependent and not overtly affected by extremes in natural nest temperatures.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 2","pages":"67-76"},"PeriodicalIF":3.8,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-023-00660-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134648848","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}

引用次数: 0

Marsupials have monoallelic MEST expression with a conserved antisense lncRNA but MEST is not imprinted 有袋动物具有单等位基因的MEST表达和保守的反义lncRNA，但MEST不印迹。

IF 3.8 2区生物学

Heredity Pub Date : 2023-11-11 DOI: 10.1038/s41437-023-00656-z

Teruhito Ishihara, Shunsuke Suzuki, Trent A. Newman, Jane C. Fenelon, Oliver W. Griffith, Geoff Shaw, Marilyn B. Renfree

{"title":"Marsupials have monoallelic MEST expression with a conserved antisense lncRNA but MEST is not imprinted","authors":"Teruhito Ishihara, Shunsuke Suzuki, Trent A. Newman, Jane C. Fenelon, Oliver W. Griffith, Geoff Shaw, Marilyn B. Renfree","doi":"10.1038/s41437-023-00656-z","DOIUrl":"10.1038/s41437-023-00656-z","url":null,"abstract":"The imprinted isoform of the Mest gene in mice is involved in key mammalian traits such as placental and fetal growth, maternal care and mammary gland maturation. The imprinted isoform has a distinct differentially methylated region (DMR) at its promoter in eutherian mammals but in marsupials, there are no differentially methylated CpG islands between the parental alleles. Here, we examined similarities and differences in the MEST gene locus across mammals using a marsupial, the tammar wallaby, a monotreme, the platypus, and a eutherian, the mouse, to investigate how imprinting of this gene evolved in mammals. By confirming the presence of the short isoform in all mammalian groups (which is imprinted in eutherians), this study suggests that an alternative promoter for the short isoform evolved at the MEST gene locus in the common ancestor of mammals. In the tammar, the short isoform of MEST shared the putative promoter CpG island with an antisense lncRNA previously identified in humans and an isoform of a neighbouring gene CEP41. The antisense lncRNA was expressed in tammar sperm, as seen in humans. This suggested that the conserved lncRNA might be important in the establishment of MEST imprinting in therian mammals, but it was not imprinted in the tammar. In contrast to previous studies, this study shows that MEST is not imprinted in marsupials. MEST imprinting in eutherians, therefore must have occurred after the marsupial-eutherian split with the acquisition of a key epigenetic imprinting control region, the differentially methylated CpG islands between the parental alleles.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 1","pages":"5-17"},"PeriodicalIF":3.8,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89718084","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}

引用次数: 0

Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia 澳大利亚坚脊线虫的两个同域谱系共有Ambrosiella共生体，但没有沃尔巴克氏体。

IF 3.8 2区生物学

Heredity Pub Date : 2023-11-10 DOI: 10.1038/s41437-023-00659-w

James R. M. Bickerstaff, Bjarte H. Jordal, Markus Riegler

{"title":"Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia","authors":"James R. M. Bickerstaff, Bjarte H. Jordal, Markus Riegler","doi":"10.1038/s41437-023-00659-w","DOIUrl":"10.1038/s41437-023-00659-w","url":null,"abstract":"Sympatric lineages of inbreeding species provide an excellent opportunity to investigate species divergence patterns and processes. Many ambrosia beetle lineages (Curculionidae: Scolytinae) reproduce by predominant inbreeding through sib mating in nests excavated in woody plant parts wherein they cultivate symbiotic ambrosia fungi as their sole source of nutrition. The Xyleborini ambrosia beetle species Cnestus solidus and Cnestus pseudosolidus are sympatrically distributed across eastern Australia and have overlapping morphological variation. Using multilocus sequencing analysis of individuals collected from 19 sites spanning their sympatric distribution, we assessed their phylogenetic relationships, taxonomic status and microbial symbionts. We found no genetic differentiation between individuals morphologically identified as C. solidus and C. pseudosolidus confirming previous suggestions that C. pseudosolidus is synonymous to C. solidus. However, within C. solidus we unexpectedly discovered the sympatric coexistence of two morphologically indistinguishable but genetically distinct lineages with small nuclear yet large mitochondrial divergence. At all sites except one, individuals of both lineages carried the same primary fungal symbiont, a new Ambrosiella species, indicating that fungal symbiont differentiation may not be involved in lineage divergence. One strain of the maternally inherited bacterial endosymbiont Wolbachia was found at high prevalence in individuals of the more common lineage but not in the other, suggesting that it may influence host fitness. Our data suggest that the two Australian Cnestus lineages diverged allopatrically, and one lineage then acquired Wolbachia. Predominant inbreeding and Wolbachia infection may have reinforced reproductive barriers between these two lineages after their secondary contact contributing to their current sympatric distribution.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 1","pages":"43-53"},"PeriodicalIF":3.8,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-023-00659-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209133","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}

引用次数: 0