Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species

The Plant Journal, Год журнала: 2024, Номер 118(5), С. 1372 - 1387

Опубликована: Фев. 11, 2024

SUMMARY Understanding the genetic basis of population divergence and adaptation is an important goal in genetics evolutionary biology. However, relative roles demographic history, gene flow, and/or selective regime driving genomic divergence, climatic adaptation, speciation non‐model tree species are not yet fully understood. To address this issue, we generated whole‐genome resequencing data Liquidambar formosana L. acalycina , which broadly sympatric but altitudinally segregated Tertiary relict forests subtropical China. We integrated environmental to investigate these two sister species. inferred a scenario allopatric during late Miocene, followed by secondary contact Holocene. identified multiple islands elevated that mainly evolved through hitchhiking recombination rate variation, likely fostered long‐term refugial isolation recent differential introgression low‐recombination regions. also found some candidate genes with divergent selection signatures potentially involved reproductive isolation. Our results contribute better understanding how Tertiary/Quaternary change influenced speciation, introgressive hybridization East Asia's flora. In addition, they should facilitate future evolutionary, conservation genomics, molecular breeding studies genus medicinal ornamental values.

Язык: Английский

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Introductory applied bioinformatics

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 53 - 66

Опубликована: Янв. 1, 2025

Язык: Английский

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Climate Vulnerability Assessment of the Espeletia Complex on Páramo Sky Islands in the Northern Andes

Frontiers in Ecology and Evolution, Год журнала: 2020, Номер 8

Опубликована: Сен. 24, 2020

Some of the largest impacts climate change are expected in environmentally heterogeneous and species rich high mountain ecosystems. Among those, Neotropical alpine grassland above tree line (c. 2,800 m), known as Páramo, is fastest evolving biodiversity hotspot on earth, one most threatened. Yet, predicting responses typically slow-growing, long-lived plant linages this unique ecosystem remains challenging. Here we coupled sensitivity modeling adaptive potential inferences to efficiently assess vulnerability Espeletia, Páramo's iconic, predominant rapidly complex. In order estimate sensitivity, first modeled distribution 28 Espeletia taxa under a niche conservatism scenario using altitude five current (1970-2000) future (2050 RCP 8.5) bioclimatic variables across 36 different Páramo complexes northern Andes (49 % world's area). As an alternative range shifts via migration, also computed capacity these by considering three enhancing factors biodiversity's well environmental limiting populations' plastic response. These predictors showed that diverse Páramos Eastern Cordillera were more vulnerable likely because counteracting effects (r = -0.93 ± 0.01) not sufficient buffer higher losses 0.39 0.01). Agriculture -0.48 0.01), mining -0.36 rural population density -0.23 weakened capacity. results speak for limited persistence migration short-term change, even though past dynamics concert with glacial cycling indicative role shifts. Furthermore, changing climate, together general inability adapt, may eventually constrain rapid diversification Our integrative illustrates how impact populations mega highly threatened such encourages carrying out similar estimates other island-like

Язык: Английский

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Assessing uncertainty in genomic offset forecasts from landscape genomic models (and implications for restoration and assisted migration)

Frontiers in Ecology and Evolution, Год журнала: 2023, Номер 11

Опубликована: Июнь 19, 2023

Introduction Ecological genomic models are increasingly used to guide climate-conscious restoration and conservation practices in the light of accelerating environmental change. Genomic offsets that quantify disruption existing genotype–environment associations under change a promising model-based tool inform such measures. With recent advances, potential applications offset predictions include but not restricted to: (1) assessing situ climate risks, (2) mapping future habitat suitability while accounting for local adaptations, or (3) selecting donor populations recipient areas maximize diversity minimize maladaptation environments assisted migration planning. As any approach, it is crucial understand how arbitrary decisions made during modeling process affect induce uncertainty. Methods Here, we present sensitivity analysis various components influence forecasts offset-based metrics, using red spruce ( Picea rubens ), cool-temperate tree species endemic eastern North America, as case study. We assess effects marker set, climatic predictor scenario, “not-to-exceed” threshold evaluate uncertainty varies across space. Results Climate scenario induced by far largest our forecasts; however, choice set was also important regions Southern Central Appalachians high relevance efforts. While much effort often expended identifying candidate loci, found minor importance. The maximum limit transfers between locations programs has mostly affected magnitude rather than geographic variation predictions. Discussion Overall, model suggest risks entire distributional range strongly underscore help ameliorate these risks. In regard, well along US Canadian east coast seem best candidates both relocation.

Язык: Английский

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Inheritance of Rootstock Effects in Avocado (Persea americana Mill.) cv. Hass

Frontiers in Plant Science, Год журнала: 2020, Номер 11

Опубликована: Дек. 23, 2020

Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes produce a unique tree phenotype. However, interconnection both genotypes obscures individual contributions phenotypic variation (rootstock-mediated heritability), hampering breeding. Therefore, our goal was quantify inheritance rootstock effects on scion traits using avocado ( Persea americana Mill.) cv. Hass as model fruit tree. We characterized 240 diverse from 8 orchards similar management in three regions province Antioquia, northwest Andes Colombia, 13 microsatellite markers simple sequence repeats (SSRs). Parallel this, we recorded 20 (including morphological, biomass/reproductive, and yield quality traits) scions for 3 years (2015–2017). Relatedness among inferred through genetic inputted “genetic prediction” calculate narrow-sense heritabilities h 2 ) traits. used different randomization tests highlight consistently significant heritability estimates. strategy allowed us capture five values that ranged 0.33 0.45 fits r oscillated between 0.58 0.73 across orchards. The results showed significance four complex harvest (i.e., total number fruits, fruits exportation quality, discarded because low weight or thrips damage), whereas only morphological trait had value overall trunk height (an emergent property rootstock–scion interaction). These findings suggest effects, beyond root phenotype, surprisingly wide spectrum “Hass” avocado. They also reinforce utility polymorphic SSRs relatedness reconstruction prediction research is, up date, most cohesive evidence tropical crop. Ultimately, work highlights importance considering broaden basis breeding programs while enhancing understanding consequences grafting.

Язык: Английский

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Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience

Plants, Год журнала: 2021, Номер 10(7), С. 1347 - 1347

Опубликована: Июль 1, 2021

Fruit trees provide essential nutrients to humans by contributing major agricultural outputs and economic growth globally. However, constraints sustainable productivity are the uncontrolled proliferation of population, biotic abiotic stresses. Tree mutation breeding has been substantially improved using different physical chemical mutagens. Nonetheless, tree plant certain crucial bottlenecks including a long life cycle, ploidy level, occurrence sequence polymorphisms, nature parthenocarpic fruit development linkage. Genetic engineering focused on boosting quality traits such as productivity, wood quality, resistance Recent technological advances in genome editing unique opportunity for genetic improvement woody plants. This review examines application CRISPR-Cas system reduce disease susceptibility, alter architecture, enhance improve yields. Examples discussed contemporary engineer easily scorable PDS genes, modify lignin, flowering onset, fertility, architecture

Язык: Английский

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Pests, diseases, and aridity have shaped the genome of Corymbia citriodora

Communications Biology, Год журнала: 2021, Номер 4(1)

Опубликована: Май 10, 2021

Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes eucalypts (Eucalyptus, and Angophora; ~800 species). grown for timber, pulp paper, essential oils in Australia, South Africa, Asia, Brazil, maintaining high-growth rate under marginal conditions due to drought, poor-quality soil, biotic stresses. To dissect genetic basis these desirable traits, we sequenced assembled 408 Mb genome citriodora, anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although two diverged approximately 60 million years ago have different sizes (408 vs 641 Mb), few large intra-chromosomal rearrangements. C. shares an ancient whole-genome duplication event E. but has undergone tandem gene family expansions related terpene biosynthesis, innate pathogen resistance, leaf wax formation, enabling their successful adaptation biotic/abiotic stresses arid Australian continent.

Язык: Английский

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Multi-Omics Techniques in Genetic Studies and Breeding of Forest Plants

Forests, Год журнала: 2023, Номер 14(6), С. 1196 - 1196

Опубликована: Июнь 9, 2023

In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, growing global demand for new plant varieties with higher wood production capacity better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, genomic selection. past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, developed rapidly, providing powerful tools precision genetic breeding plants. Genomics lays a solid foundation understanding complex biological regulatory networks, while other technologies provide different perspectives at levels. Multi-omics integration combines becoming tool genome-wide functional element identification in breeding. This review summarizes progress their applications studies on It will breeders an elementary knowledge multi-omics techniques future programs.

Язык: Английский

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Integrating evolutionary genomics of forest trees to inform future tree breeding amidst rapid climate change

Plant Communications, Год журнала: 2024, Номер 5(10), С. 101044 - 101044

Опубликована: Авг. 7, 2024

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats biodiversity nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems play a crucial role combating mitigating the adverse effects extreme events, despite their own vulnerability these threats. Therefore, understanding monitoring how natural forests respond key priority for conservation. Recent progress evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools address several issues. These include precise delineation species units, inference past histories demographic fluctuations, identification environmentally adaptive variants, measurement genetic load levels. As urgency deal with more stresses grows, genomics history, local adaptation, future responses change, conservation restoration forest will be critical research at nexus global population biology. In this review, we explore application assess using approaches discuss outlook breeding climate-adapted trees.

Язык: Английский

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Integrative Pre-Breeding for Biotic Resistance in Forest Trees

Plants, Год журнала: 2021, Номер 10(10), С. 2022 - 2022

Опубликована: Сен. 26, 2021

Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations’ persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of resistance in tree species. Specifically, we first discuss how assessing genomic architecture stress enables us recognize a more polygenic nature trait typically regarded Mendelian, an expectation Fisherian runaway pathogen–host concerted arms-race model. Secondly, outline innovative pipelines capture harness natural pre-adaptations stresses by merging tools ecology, phylo-geography, omnigenetics fields within predictive platform. Promoting integrative studies promises better understanding co-evolutionary interactions, as well efficient utilization resistant phenotypes.

Язык: Английский

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