Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

Planta, Journal Year: 2023, Volume and Issue: 257(2)

Published: Jan. 9, 2023

Language: Английский

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Cutting edge tools in the field of soil microbiology

Current Research in Microbial Sciences, Journal Year: 2024, Volume and Issue: 6, P. 100226 - 100226

Published: Jan. 1, 2024

The study of the whole genetic material contained within microbial populations found in a certain environment is made possible by metagenomics. This technique enables thorough knowledge variety, function, and interactions communities that are notoriously difficult to research. Due limitations conventional techniques such as culturing PCR-based methodologies, soil microbiology particularly challenging field. Metagenomics has emerged an effective for overcoming these obstacles shedding light on dynamic nature soil. review focuses principle metagenomics techniques, their potential applications diversity analysis. effectiveness target-based determining function individual genes microorganisms ecosystems also highlighted. Targeted metagenomics, including high-throughput sequencing stable-isotope probing, essential studying taxa complex ecosystems. Shotgun may reveal bacteria, composition, impacted land use management. Sanger, Next Generation Sequencing, Illumina, Ion Torrent revolutionise microbiome Oxford Nanopore Technology (ONT) Pacific Biosciences (PacBio)'s third fourth generation systems long-read technology. GeoChip, clone libraries, metabarcoding help comprehend communities. article indicates improve environmental management agriculture despite existing limitations.Metagenomics revolutionised research revealing complete diversity, anticipated continue defining future some limitations, difficulty locating appropriate method specific genes.

Language: Английский

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Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(8), P. 2207 - 2222

Published: Feb. 16, 2022

The last decade has witnessed huge technological advances in genomics, particularly DNA sequencing. Here, we review the actual and potential application of genomics supporting situ conservation crop wild relatives (CWRs). In addition to helping prioritization protection CWR taxa sites, genome analysis is allowing identification novel alleles that need be prioritized for conservation. Genomics enabling sources important adaptive traits can guide establishment or enrichment genetic reserves. Genomic tools also have developing a robust framework monitoring reporting genome-based indicators diversity changes associated with factors such as land use climate change. These been demonstrated an role managing populations, sustainable access utilization diversity, enhancing accelerated domestication new crops forensic thus preventing misappropriation resources. Despite this great potential, many policy makers managers failed recognize appreciate accelerate support management biodiversity CWRs underpin global food security. Funding inadequate genomic expertise among practitioners remain major hindrances widespread

Language: Английский

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The Diversity of Eucheumatoid Seaweed Cultivars in the Philippines

Reviews in Fisheries Science & Aquaculture, Journal Year: 2022, Volume and Issue: 31(1), P. 47 - 65

Published: April 12, 2022

Collectively known as eucheumatoids, Eucheuma denticulatum, Kappaphycus alvarezii, K. malesianus, and striatus are the main farmed seaweed species in Philippines. The success of farming for over five decades country is due, part, to high diversity cultivars maintained by Filipino farmers. Notwithstanding fact that many eucheumatoid presently (and consistently) recognized farmers, there has been no attempt summarize current state local traditional knowledge about this group, especially with reference taxonomy, cultivar designation distribution. Factors based on present day what genetic identification Philippines were also discussed. A total 66 across 58 provinces documented. Most these morphologically identified either alvarezii or striatus, however, majority yet be genetically identified. In due higher demand kappa-carrageenan extract compared from iota type, widely cultivated than E. denticulatum. Only southern malesianus currently cultivated. diverse study suggest farmers possess important can useful future crop selection breeding.

Language: Английский

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Role of Seed Banks in Supporting Ecosystem and Biodiversity Conservation and Restoration

Diversity, Journal Year: 2023, Volume and Issue: 15(8), P. 896 - 896

Published: July 29, 2023

The world is witnessing massive land degradation caused by climate change and various anthropogenic activities. There has been a significant increase in habitat restoration efforts, with demand for seeds to restore these degraded ecosystems some cases outstripping supply. Traditionally, activities have mainly sourced through collections from the wild, but growing seed demand, this increasingly becoming unsustainable. In order ensure responsible practice, practitioners need explore other options of economical, ethical sustainable sourcing seeds. Ex situ banks can leverage their technical infrastructural capacity play greater more direct role supporting biodiversity ecosystem conservation restoration, particularly supply quality ecologically genetically suitable seed. paper, we review whether ex possess competence challenges they are likely face efforts. focuses on collecting, field-based bulking, handling storage, control as well experience facilitating germplasm exchange. availability high-quality documented provenance broad genetic diversity arguably greatest resource asset that restoration.

Language: Английский

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Progress in Plant Genome Sequencing

Applied Biosciences, Journal Year: 2022, Volume and Issue: 1(2), P. 113 - 128

Published: July 4, 2022

The genome sequence of any organism is key to understanding the biology and utility that organism. Plants have diverse, complex sometimes very large nuclear genomes, mitochondrial genomes much smaller more highly conserved chloroplast genomes. Plant sequences underpin our plant serve as a platform for genetic selection improvement crop plants achieve food security. development technology can capture volumes data at low costs with high accuracy has driven acceleration sequencing advancements. More recently, long read been advance supporting accurate assembly chromosome-level This review explored progress in outcomes date. support conservation biodiversity, adaptations climate change improvements sustainability agriculture, which nutritional

Language: Английский

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Conservation Approaches of Plant Genetic Resources

Sustainable development and biodiversity, Journal Year: 2024, Volume and Issue: unknown, P. 643 - 681

Published: Jan. 1, 2024

Language: Английский

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Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: June 6, 2023

Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We identified introgressions using these genotyping-by-sequencing and whole-genome On the basis our results, we provide information about predicted at 1-Mb resolution for 9,172 samples as a resource breeders scientists. recommend that all plant genetic resources, including collections, be combination variant calling introgression prediction. This is necessary to identify potential duplicates in efficiently reliably, select promising germplasms potentially beneficial further characterization prospective breeding application.

Language: Английский

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Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo

Annals of Botany, Journal Year: 2024, Volume and Issue: 133(7), P. 917 - 930

Published: March 5, 2024

Plant breeders are increasingly turning to crop wild relatives (CWRs) ensure food security in a rapidly changing environment. However, CWR populations confronted with various human-induced threats, including hybridization their nearby cultivated crops. This might be particular problem for coffee species, which often occur near cultivation areas. Here, we briefly review the evidence Coffea arabica (cultivated as Arabica coffee) and canephora Robusta then focused on C. Yangambi region Democratic Republic of Congo. There, examined geographical distribution incidence between individuals within rainforest.

Language: Английский

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The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(8)

Published: June 7, 2024

We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled haploid consensus of 1.67 Gb as 28.7 K scaffolds with scaffold N50 74.9 Mb. annotated repeat content in 74.8% genome. Long terminal repeats (LTRs) covered 44.0% Copia families predominant at 22.9% followed by Gypsy 14.2%. Both elements were common ancestral peaks LTRs, most abundant element was containing nested Copia/Angela sequence similarity, reflecting complex evolutionary history activity. Gene annotation produced 33,257 genes 68,942 transcripts, which 99% functionally annotated. BUSCO scores proteins 96.0% complete 77.6% single copy 18.4% duplicates. Whole duplication synonymous mutation rates tarplant sunflower (Helianthus annuus) shared that correspond last Asteraceae polyploidization event subsequent divergence from ancestor ∼27 MYA. Regions high-density tandem identified, pointing potentially important loci environmental adaptation this species.

Language: Английский

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