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30 results for “domestication traits”
Data from: Geographic variation in leaf traits and palatability of a native plant invader during domestic expansion
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Leaf trait covariation and controls on leaf mass per area (LMA) following cotton domestication
<p class="MsoNormal"><span>The process of domestication has driven dramatic shifts in plant functional traits including leaf mass per area (LMA). It remains unclear whether domestication has produced concerted shifts in the lower-level anatomical traits that underpin LMA and how these traits in turn affect photosynthesis. </span><span>In this study, we investigated controls of LMA and leaf gas exchange by leaf anatomical properties at the cellular, tissue and whole leaf levels, comparing 26 wild and 31 domesticated genotypes of cotton </span><span>(<em>Gossypium</em>). </span><span>As expected, domesticated plants expressed lower LMA, higher photosynthesis and stomatal conductance</span><span>, suggesting a shift towards the 'faster' end of the leaf economics spectrum. At whole-leaf level, variation in LMA was predominantly determined by leaf density (LD) both in wild and domesticated genotypes. At tissue level, higher leaf volume per area (<em>V</em><sub>leaf</sub>) in domesticated genotypes was driven by a simultaneous increase in the volume of epidermal, mesophyll and vascular bundle tissue and airspace, while lower LD resulted from a dilution effect of lower increased volume of palisade tissue and vascular bundle of high mass density by higher increased volume of epidermis and airspace of low mass density. The volume of spongy mesophyll exerted direct control on photosynthesis in domesticated genotypes but only indirect control in wild genotypes. At cellular level, a shift to larger but less numerous cells with thinner cell walls underpinned a lower proportion of cell wall mass, and thus a reduction in LD. </span><span>Taken together, cotton domestication has triggered synergistic shifts in the underlying determinants of LMA but also photosynthesis, at cell, tissue and whole-leaf level, resulting in a marked shift in plant ecological strategy.</span></p>
100 Years of Penaeids Domestication and Meta-analysis of Breeding Traits
<p><strong>Additional files</strong></p> <p><strong>Additional file 1 Table S1</strong></p> <p>Format: csv file</p> <p>Title: Quantitative genetic publications for penaeids genetic improvement programs from 1997 to 2024.</p> <p><strong>Additional file 2 Table S2</strong></p> <p>Format: csv file</p> <p>Title: Summary of heritability estimates on breeding traits in penaeids selective breeding programs.</p> <p><strong>Additional file 3 Table S3</strong></p> <p>Format: csv file</p> <p>Title: Analysis of heritability estimates in penaeids selective breeding programs for disaese resistance, feeding efficiency, growth traits, morphological traits, quality traits, reproductive traits, stress tolerance and survival.</p>
Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
<p class="MsoNormal">Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (<em>Ensete ventricosum</em>), an indigenous African relative of bananas (<em>Musa</em>) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.</p>
Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population
<p><span>Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health</span><span>. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. </span><span>Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is </span><span>critical. </span><span>We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances, and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding </span><span>which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform </span><span>targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes. </span></p>
Data from: Molecular mapping and identification of quantitative trait loci for domestication traits in field cress (Lepidium campestre L.) genome
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Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
Open the record for dataset details and reuse information.
Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population
Open the record for dataset details and reuse information.
Leaf trait covariation and controls on leaf mass per area (LMA) following cotton domestication
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Fig. 6 in Dual domestications and origin of traits in grapevine evolution
Fig. 6. Schematic graph of grapevine evolutionary history. Key events in the evolutionary history of grapevines are shown alongside major events in global climate change and human migration.
Fig. 2 in Dual domestications and origin of traits in grapevine evolution
Fig. 2. Population history of V. sylvestris ecotypes. (A) Geographic isolation and population separation of V. sylvestris ecotypes. Pie charts show mean ancestry proportion at K = 8. Same color scheme as in Fig. 1B is used. (B) Demographic histories of V. sylvestris populations deduced from Stairway Plot 2. Lines indicate medians with 75% and 95% confidence intervals. (C) Population split times among ecotypes with MSMC2. Red bars indicate medians with 95% confidence intervals. (D) Ecological niche modeling of the suitable habitats for V. sylvestris ecotypes. The color scale shows suitability score.
Fig. 1 in Dual domestications and origin of traits in grapevine evolution
Fig. 1. Genetic diversity of global core V. sylvestris and V. vinifera accessions. (A) Geographical locations of the 2448 core grapevine accessions. (B) PCA according to major viticultural regions. Large square/ circle highlights median position. Star shows VS-1 position. (C) Isolationby-distance test of V. sylvestris and V. vinifera accessions. Linear regression with 95% confidence interval is shown. (D) ADMIXTURE clustering of the accessions. (E) Geographic locations of the accessions in each group. Gray represents minor locations. (F) Average proportion of major genetic ancestries in grapevine groups. (G) PC2 versus PC3 projection according to grapevine group.
Fig. 5 in Dual domestications and origin of traits in grapevine evolution
Fig. 5. Selection and evolution of the SDR in the core grapevine accessions. (A) The SDR in VS-1. Red arrows indicate identified recombination sites. (B) SDR genotypes from associated SNPs reveal five recombination sites (dashed lines) and genotype diversity (right). Major and minor haplotypes are shown on the left. (C) Distribution of SDR genotypes in the six major grapevine groups. (D) Recombination history of all SDR haplotypes. (E) Putative dispersal route of the H4 haplotype and the origination of H2 haplotype.
Fig. 3 in Dual domestications and origin of traits in grapevine evolution
Fig. 3. Dual domestications of V. vinifera in Western Asia and the Caucasus. (A) Pairwise fixation index of the major grapevine groups. (B) Outgroup f3 statistics biplot measuring genetic similarity. Rotund, Muscadinia rotundifolia. Stars mark the f3 statistics for CG1/CG2. (C) Estimated split times among Syl-E1/2 and CG1/2 with MSMC2 (left). Red bars indicate medians with 95% confidence intervals. (D) Geographic distribution of CG1 and CG2 in relation to the domestication centers. Human dispersal routes are shown. (E) Shared (sky blue) and unique domestication selective sweep regions (red and dark teal) in V. vinifera.
Fig. 4 in Dual domestications and origin of traits in grapevine evolution
Fig. 4. Stepwise diversification of V. vinifera in Europe. (A and B) Introgression from Syl-W into European V. vinifera groups revealed by TreeMix (A) and confirmed by D-statistic (B). (C) Four population simulation of split times and genetic introgression using Momi2. Median numbers from 100 bootstrap runs are shown. (D) Origination of V. vinifera groups (CG3 to CG6) by the end of the Neolithic. Geographic distributions of CG groups are shown by colored circles. See fig. S24 for details on CG3.
Pod indehiscence is a domestication and aridity resilience trait in common bean
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Is drought tolerance a domestication trait in tepary bean?: Allelic diversity at abiotic stress responsive genes in cultivated Phaseolus acutifolius A. Gray and its wild relatives
<p>Some of the major impacts of climate change are expected in the poorest regions of the world where drought stress and nutrient deficiency are already a main issue. Legumes are an essential food crop for the poorest because of their high dietary protein and micronutrient contents. However, they are generally drought susceptible. Therefore, our goal in this study was to explore allele diversity at abiotic stress responsive candidate genes in the only drought tolerant cultivated bean species of the genus <i>Phaseolus</i>, tepary bean (<i>P. acutifolius</i> A. Gray) and its related species <i>P. parvifolius </i>Freytag. Specifically, we estimated drought tolerance in 52 tepary bean <i>s.l.</i> geo-referenced germplasm accessions from the <i>P. acutifolius</i>–<i>parvifolius</i> clade using climate information, and used this estimated drought stress index to examine allele correlations with <i>Asr2</i>, <i>Dreb2B</i> and ERECTA-encoding candidate genes for drought tolerance. Genetic clustering showed that cultivated and wild <i>P. acutifolius</i> were intermingled with <i>P. acutifolius </i>var.<i> tenuifolius</i> and <i>P. parvifolius</i>, signifying that allele diversity at candidate genes for drought tolerance was not scarce in tepary bean <i>s.l</i>. <i>Dreb2B</i> and ERECTA-encoding genes harbored signatures of directional/purifying selection, likely in favor of adaptive alleles selectively advantageous because each had two SNPs significantly correlated (<i>p-value</i> < 0.05) with habitat drought stress at six and 12 months. These results suggest that tepary bean <i>s.l. </i>is a reservoir of novel alleles at candidate genes for drought tolerance, as expected for a drought-tolerant species that originated in warmer and arid environments. Abiotic stress responsive candidate genes also exhibit comparable patterns of selective signatures when comparing orthologous across species, which speaks for a predominant role of gene sub-functionalization likely due to ecological constrains. Our study therefore corroborates that the candidate gene approach is still an effective alternative for marker validation across a broader genetic basis of germplasm accessions. Further efforts to determine the genetic architecture of drought tolerance will unlock novel alleles hidden in a crop with limited modern relevance as tepary bean, but capable of acting as a donor in backcrossing and genome editing strategies with elite common bean lines aiming to meet the imminent demands of a drier world.</p>
Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL
The domesticated crop maize and its wild progenitor, teosinte, have been used in numerous experiments to investigate the nature of divergent morphologies. This study examines a poorly understood region on the fifth chromosome of maize associated with a number of traits under selection during domestication using a QTL mapping population specific to the fifth chromosome. In contrast with other major domestication loci in maize where large effect, highly pleiotropic, single genes are responsible for phenotypic effects, our study found the region on chromosome five fractionates into multiple QTL regions, none with singularly large effects. The smallest 1.5 LOD support interval for a QTL contained 54 genes, one of which was a MADS MIKCC transcription factor, a family of proteins implicated in many developmental programs. We also used simulated trait datasets to investigate the power of our mapping population to identify QTL for which there is a single underlying causal gene. This analysis showed that while QTL for traits controlled by single genes can be accurately mapped, our population design can detect no more than ~4.5 QTL per trait even when there are 100 causal genes. Thus when a trait is controlled by 5 or more genes in the simulated data, the number of detected QTL can represent a simplification of the underlying causative factors. Our results show how a QTL region with effects on several domestication traits may be due to multiple linked QTL of small effect as opposed to a single gene with large and pleiotropic effects.
Data from: Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host
Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate changes in life history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems were assessed on the domesticated apple, its central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulences in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity.
Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats
<p><span>In the largest DNA-based study of domestic cat to date, 11,036 individuals (10,419 pedigreed cats from 91 breeds and breed types and 617 non-pedigreed cats) were genotyped via commercial panel testing, </span><span>elucidating the distribution and frequency of known genetic variants associated with blood type, disease and physical traits across cat breeds. </span><span>Blood group determining variants, which are relevant clinically and in cat breeding, were genotyped to assess the across breed distribution of blood types A, B and AB.</span> <span>Extensive panel testing identified 13 disease-associated variants in 48 breeds or breed types for which the variant had not previously been observed, strengthening the argument for panel testing across populations. The study also indicates that multiple breed clubs have effectively used DNA testing to reduce disease-associated genetic variants within certain pedigreed cat populations. Appearance-associated genetic variation in all cats is also discussed. Additionally, we combined genotypic data with phenotype information and clinical documentation</span><span>, actively conducted owner and veterinarian interviews, and recruited cats for clinical examination</span><span> to investigate the causality of a number of</span><span> tested variants across different breed backgrounds</span><span>. Lastly, genome-wide informative SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds.</span></p> <p><span>This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 domestic cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.</span></p>
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