Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(5), P. 1227 - 1241

Published: Jan. 18, 2024

Domestication can be considered a specialized mutualism in which domesticator exerts control over the reproduction or propagation (fitness) of domesticated species to gain resources services. The evolution crops by human-associated selection provides powerful set models study recent evolutionary adaptations and their genetic bases. Moreover, domestication dispersal such as rice, maize, wheat during Holocene transformed human social political organization serving key mechanism societies fed themselves. Here we review major themes identify emerging questions three fundamental areas crop research: phenotypes syndromes, architecture underlying evolution, ecology domestication. Current insights on syndrome largely come from research cereal rice work indicates distinct arise different histories. While early studies genetics often identified single large-effect loci traits, evidence supports polygenic bases for many canonical traits shattering plant architecture. Adaptation human-constructed environments also influenced ecological domesticates resource acquisition rates interactions with other organisms root mycorrhizal fungi pollinators. Understanding context will developing resource-efficient implementing more sustainable land management cultivation practices.

Language: Английский

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Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 17, 2025

The innovations of the "Omics Era" have ushered in significant advancements genetic improvement agriculturally important animal species through transforming genetics, genomics and breeding strategies. These were often coordinated, part, by support provided over 30 years 1993-2023 National Research Support Project 8 (NRSP8, Animal Genome Program, NAGRP) affiliate projects focused on enabling genomic discoveries livestock, poultry, aquaculture species. parallel advances demand strategic planning future research priorities. This paper, as an output from May 2023 Aquaculture Genomics, Genetics, Breeding Workshop, provides updated status resources for United States species, highlighting major achievements emerging Finfish shellfish genome omics enhance our understanding architecture heritability performance production traits. Workshop identified present aims genomics/omics to build this progress: (1) advancing reference assembly quality; (2) integrating multi-omics data analysis traits; (3) developing collection integration phenomics data; (4) creating pathways applying information across industries; (5) providing training, extension, outreach application phenome. focuses should emphasize collection, artificial intelligence, identifying causative relationships between genotypes phenotypes, establishing apply tools industries, expansion training programs next-generation workforce facilitate sciences into operations productivity, competitiveness, sustainability. collective vision with focus highlighted priorities is intended continued advancement genomics, genetics community industries. Critical challenges ahead include practical analytical frameworks beyond academic communities that require collaborative partnerships academia, government, industry. scope review encompasses use applications study aquatic animals cultivated human consumption settings throughout their life-cycle.

Language: Английский

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Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 5, 2025

Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model

Language: Английский

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Thrushes in Love: Extensive Gene Flow, With Differential Resistance and Selection, Obscures and Reveals the Evolutionary History of a Songbird Clade

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

ABSTRACT The application of high‐throughput sequencing to phylogenetic analyses is allowing authors reconstruct the true evolutionary history species. This work can illuminate specific mechanisms underlying divergence when combined with gene flow, recombination and selection. We conducted a phylogenomic analysis Catharus , songbird genus considerable potential for variation in migratory behaviour genomic resources. documented discordance among trees constructed mitochondrial, autosomal sex (Z) chromosome partitions. Two were recovered on Z. Both differed from autosomes, one matched mitochondria, other was unique Gene flow species likely generated much this discordance; substantial admixture between ustulatus remaining linked at least two historic events. tree Z reflects ; local same regions reduced recombination. Genes previously connected migration enriched these suggesting transitions non‐migratory states helped generate divergence. Migratory (vs. nonmigratory) formed monophyletic clade subset regions. elevated some adaptive introgression may have occurred, but dominant pattern balancing selection maintaining ancestral polymorphisms important olfaction perhaps, by extension, adaptation temperate climates. illuminates an model speciation demonstrates how differential resistance affect patterns.

Language: Английский

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RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: March 4, 2025

ABSTRACT Tandem repeats play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination and the regulation of gene activity. Analysis their distribution genomes offers a potential means for predicting putative locations, which continues to be challenge genome annotation. Here we present RepeatOBserver ( https://github.com/celphin/RepeatOBserverV1 ), new tool visualising repeat patterns identifying using Fourier transform walks. can identify visualise broad range perfect imperfect (3–5000 bp long) assemblies without any priori knowledge sequences or need optimising parameters. heatmaps distinguish between tandem retrotransposon repeats. We analysed 159 chromosomes with experimentally‐verified positions from 12 plant animal species. find that 93% centromeres occur regions low sequence diversity 97% high abundance lengths. Depending on type predicted by heatmaps, locations either genomic Shannon index sum. also locate other interest including neocentromeres copy variation. Split inverted at inversion boundaries suggest chromosomal inversions mis‐assemblies located. is flexible comprehensive characterisation used variety assemblies.

Language: Английский

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Genomic Insights Into the Origin, Decline and Recovery of the Once Critically Endangered Iberian Lynx

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

ABSTRACT The Iberian lynx was at the brink of extinction by year 2000 but has since then, and thanks to intensive conservation measures, gone through a remarkable recovery, providing much‐welcomed encouraging success story. Genetic issues have probably contributed decline in past, genetic management inbreeding diversity is likely contributing its recent recovery. species an early adopter genomic approaches, combination extreme decline, monitoring programme extensive resources data makes excellent model for genomics. Here, we review how knowledge evolutionary demographic history, evaluation status time, including historical ancient data, this information prompted guided actions. In process, genomics provided valuable insights into dynamics functional variation bottlenecked populations consequences intraspecific interspecific admixtures. more applied terms, subjected ambitious programme, covering captive, remnant reintroduced populations, which succeeded improving thereby Current work aims expanding these contributions with novel while capitalising on genealogical ongoing non‐invasive programme.

Language: Английский

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Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: March 26, 2025

Language: Английский

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Application of Omics in Donkey Meat Research: A Review

Animals, Journal Year: 2025, Volume and Issue: 15(7), P. 991 - 991

Published: March 29, 2025

This review comprehensively examines the molecular basis of donkey meat characteristics and growth-associated genes, integrating findings from multiple omics approaches. study nutritional profile meat, which is rich in protein, essential amino acids, unsaturated fatty acids. Through a systematic literature search across Web Science, Google Scholar, PubMed, Scopus databases (2000-2024), we collected analyzed data 400 research articles using predefined inclusion criteria focused on composition, approaches, quality parameters populations. The also evaluates various factors affecting quality, including breed differences, age, feeding management, storage conditions. Advanced genomic transcriptomic analyses have revealed numerous candidate such as ACTN3, BMP7, NR6A1, Wnt7a, HOXC8, LCORL, TPM2, TPM3, associated with growth traits characteristics, providing valuable insights for genetic improvement programs. Furthermore, discusses authentication methods ensuring preventing adulteration, highlighting integration traditional modern analytical

Language: Английский

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How structural variants shape avian phenotypes: Lessons from model systems

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 23, 2024

Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although advances long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review role SVs shaping phenotypes avian model systems, identify some general patterns type, length their associated traits. found that most so far identified are short indels chickens, which frequently with changes body weight plumage colouration. Overall, we relatively more detected, likely due to a combination prevalence compared large SVs, detection bias, stemming primarily from widespread use short-read sequencing analytical methods. commonly involve non-coding regions, especially introns, when inheritance were reported, dominant discrete summarise several examples convergence across different species, mediated by same or genes types gene can lead various phenotypes. Complex rearrangements supergenes, simultaneously affect link genes, tend pleiotropic effects. Additionally, co-occur single-nucleotide polymorphisms, highlighting need consider all genetic understand basis end summarising expectations for technologies become implemented non-model birds, leading an increase discovery characterisation. The growing interest this subject suggests our understanding effects upcoming years.

Language: Английский

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A review of genetic resources and trends of omics applications in donkey research: focus on China

Frontiers in Veterinary Science, Journal Year: 2024, Volume and Issue: 11

Published: Oct. 11, 2024

Omics methodologies, such as genomics, transcriptomics, proteomics, metabolomics, lipidomics and microbiomics, have revolutionized biological research by allowing comprehensive molecular analysis in livestock animals. However, despite being widely used various animal species, on donkeys has been notably scarce. China, renowned for its rich history donkey husbandry, plays a pivotal role their conservation utilization. China boasts 24 distinct breeds, necessitating efforts, especially smaller breeds facing extinction threats. So far, omics approaches employed studies of milk meat, shedding light composition quality. Similarly, methods utilized to explore the basis associated with growth, meat production, quality traits. also unraveled critical microbiota health nutrition, gut microbiome revealing associations factors pregnancy, age, transportation stress, altitude. Furthermore, applications addressed issues, including infectious diseases reproductive problems. In addition, these provided insights into improvement efficiency research. conclusion, methodologies are essential advancing knowledge about donkeys, genetic diversity, across domains. is still infancy, there need continued enhance breeding, welfare beyond.

Language: Английский

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