Cyber-agricultural systems for crop breeding and sustainable production

Trends in Plant Science, Journal Year: 2023, Volume and Issue: 29(2), P. 130 - 149

Published: Aug. 28, 2023

The cyber-agricultural system (CAS) represents an overarching framework of agriculture that leverages recent advances in ubiquitous sensing, artificial intelligence, smart actuators, and scalable cyberinfrastructure (CI) both breeding production agriculture. We discuss the progress perspective three fundamental components CAS - modeling, actuation emerging concept agricultural digital twins (DTs). also how CI is becoming a key enabler In this review we shed light on significance revolutionizing crop by enhancing efficiency, productivity, sustainability, resilience to changing climate. Finally, identify underexplored promising future directions for research development.

Language: Английский

---

Digitized collections elucidate invasion history and patterns of awn polymorphism inMicrostegium vimineum

American Journal of Botany, Journal Year: 2022, Volume and Issue: 109(5), P. 689 - 705

Published: April 18, 2022

Abstract Premise Digitized collections can help illuminate the mechanisms behind establishment and spread of invasive plants. These databases provide a record traits in space time that allows for investigation abiotic biotic factors influence species. Methods Over 1100 digitized herbarium records were examined to investigate invasion history trait variation Microstegium vimineum . Presence–absence awns was investigated quantify geographic patterns this polymorphic trait, which serves several functions grasses, including diaspore burial dispersal germination sites. Floret further quantified, genomic analyses contemporary samples conducted M. 's introduction into North America. Results Herbarium revealed similar awn polymorphism native invaded ranges , with awned forms predominating at higher latitudes awnless lower latitudes. data suggested initial form southeastern United States, followed by putative secondary from eastern Pennsylvania. Awned have longer florets, floret size varies significantly latitude. There is evidence transition zone short‐awned specimens mid‐latitudes. Genomic two distinct clusters corresponding forms, admixture. Conclusions Our results demonstrate power elucidate problematic weed America and, together data, reveal possible key success: presence or absence an awn.

Language: Английский

---

Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Published: Sept. 7, 2023

Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct analyze their genomes. The aDNA is commonly obtained remains found in paleontological archaeological sites, conserved museums other archival collections. Herbarium collections represent a great source phenotypic genotypic information, exploitation allowed infer clarify previously unsolved taxonomic systematic relationships. Moreover, specimens offered new study phenological traits plants disentangle biogeography evolutionary scenarios species. More recently, advances molecular technologies went parallel with decreasing costs next-generation sequencing (NGS) approaches, that paved way utilization for whole-genome studies. Although many studies have been carried out combining modern analytic techniques specimens, this research field still relatively unexplored, due need improving strategies manipulation exploitation. higher susceptibility degradation contamination during conservation occurrence biochemical post-mortem damages, can result more challenging reconstruction original sequence. Here, we review methodological approaches developed plant materials, such as best practices extraction, amplification genotyping. We also focus some overcome main problems related

Language: Английский

---

A lack of population structure characterizes the invasive Lonicera japonica in West Virginia and across eastern North America1,2

The Journal of the Torrey Botanical Society, Journal Year: 2023, Volume and Issue: 150(3)

Published: July 12, 2023

Invasive plant species cause massive ecosystem damage globally yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, the ubiquity invasive across landscape make them highly accessible for invasion history dynamics associated with their introduction, establishment, spread, ecological interactions. Here we focus on Lonicera japonica, one most damaging vine North America. We leveraged data contemporary field reconstruct characterize patterns genomic variation eastern USA, using a straightforward method generating nucleotide polymorphism recently published, chromosome-level genome species. found an overall lack structure among sites northern West Virginia, as well central USA. Heterozygosity differentiation were both low based FST analysis molecular variance, principal components analysis, cluster-based analyses. also evidence high inbreeding coefficients significant linkage disequilibrium, line ability this otherwise outcrossing, perennial propagate vegetatively. Our findings corroborate earlier allozyme suggest that intentional, human-assisted spread explains structure, was planted erosion control ornamental, escaping cultivation repeatedly

Language: Английский

---

Grass awns: Morphological diversity arising from developmental constraint

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102663 - 102663

Published: Nov. 16, 2024

Grasses dominate agriculturally and ecologically. One hypothesized driver of this dominance is grasses' facility for grain dispersal rapid seedling establishment. Dispersal establishment are aided by the awned lemma - a modified bract associated with grass flowers. Awns have diverse forms, many proposed functions, been gained lost repeatedly in evolution. Here we hypothesize that evolution awn emergence underpinned deep conservation developmental genes. likely homologous to leaf blades. Because blades essential, every species has latent program available development. This may be reactivated lemmas, resulting frequent appearance awns. awns inessential, they can without dire consequences fitness, loss diversity Replicated reveals how potentiate diversity. also present powerful opportunity dissect mechanisms

Language: Английский

---

Mitochondrial genome sequencing and analysis of the invasiveMicrostegium vimineum: a resource for systematics, invasion history, and management

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 11, 2023

Abstract Premise of the Research Plants remain underrepresented among species with sequenced mitochondrial genomes (mitogenomes), due to difficulty in assembly short-read technology. Invasive lag behind crops and other economically important this respect, representing a lack tools for management land conservation efforts. Methodology The mitogenome Microstegium vimineum , one most damaging invasive plant North America, was analyzed using long-read data, providing resource biologists managers. We conducted analyses genome content, phylogenomic grasses relatives based on coding regions, an analysis single nucleotide polymorphism grass species. Pivotal Results is 478,010 bp length characterized by two large, inverted repeats, direct repeat. However, could not be circularized, arguing against “master circle” structure. Long-read assemblies data subsets revealed several alternative genomic conformations, predominantly associated large repeats. Plastid-like sequences comprise 2.4% genome, further evidence Class I II transposable element-like sequences. Phylogenetic placed M. species, excluding nudum but weak support. Analysis polymorphic sites across 112 accessions from native ranges complex invasion history. Conclusions present in-depth structure, phylogenetic relationships, range-wide variation vimineum’s US range. typical andropogonoid grasses, yet sequence extensive. Our findings suggest multiple introductions over last century, subsequent spread, secondary contact, long-distance dispersal, possibly post-invasion selection awn phenotypes. Efforts produce resources including genomes, will continue provide their effective management, help predict prevent future invasions.

Language: Английский

---

A lack of population structure characterizes the invasiveLonicera japonicain West Virginia and across eastern North America

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 2, 2023

ABSTRACT Invasive plant species cause massive ecosystem damage globally, yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, the ubiquity invasive across landscape make them highly accessible for invasion history dynamics associated with their introduction, establishment, spread, ecological interactions. Here we focus on Lonicera japonica , one most damaging vine North America. We leveraged data contemporary field reconstruct characterize patterns genomic variation eastern USA, using a straightforward method generating nucleotide polymorphism recently published, chromosome-level genome species. found an overall lack structure among sites northern West Virginia, as well central USA. Heterozygosity differentiation were both low based Fst analysis molecular variance, principal components analysis, cluster-based analyses. also evidence high inbreeding coefficients significant linkage disequilibrium, line ability this otherwise outcrossing, perennial propagate vegetatively. Our findings corroborate earlier allozyme suggest that intentional, human-assisted spread explains structure, was planted erosion control ornamental, escaping cultivation repeatedly Finally, discuss how genomics can be incorporated into experiential undergraduate education way integrate teaching research.

Language: Английский

---

Mitochondrial Genome Sequencing and Analysis of the Invasive Microstegium vimineum: A Resource for Systematics, Invasion History, and Management

International Journal of Plant Sciences, Journal Year: 2023, Volume and Issue: 184(7), P. 525 - 540

Published: May 17, 2023

Premise of research. Plants remain underrepresented among species with sequenced mitochondrial genomes (mitogenomes) because the difficulty in assembly short-read technology. Invasive lag behind crops and other economically important this respect, resulting a lack tools for management land conservation efforts.Methodology. The mitogenome Microstegium vimineum, one most damaging invasive plant North America, was analyzed using long-read data, providing resource biologists managers. We conducted analyses genome content, phylogenomic grasses relatives based on coding regions, an analysis single-nucleotide polymorphism grass species.Pivotal results. is 478,010 bp length characterized by two large inverted repeats direct repeat. However, could not be circularized, arguing against “master circle” structure. Long-read assemblies data subsets revealed several alternative genomic conformations, predominantly associated repeats. Plastid-like sequences comprise 2.4% genome, further evidence class I II transposable element-like sequences. Phylogenetic placed M. vimineum species, excluding Leptathera (Microstegium) nudum, but weak support. Analysis polymorphic sites across 112 accessions from native ranges complex invasion history.Conclusions. present in-depth structure, phylogenetic relationships, range-wide variation vimineum’s US range. typical andropogonoid grasses, yet sequence extensive. Our findings suggest multiple introductions to over last century, subsequent spread, secondary contact, long-distance dispersal, possible postinvasion selection awn phenotypes. Efforts produce resources including genomes, will continue provide their effective help predict prevent future invasions.

Language: Английский

---