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31 results for “domestication selection”
Artificial selection on cis-element of Abl contributes cocoon yield increase in domestic silkworm
<p><span>The silkworm (</span><em><span>Bombyx mori</span></em><span>) is an important silk-producing domestic insect.</span><span> The quality and yield of the silk produced by <em>B. mori </em>exceeds that of its ancestor, the wild silkworm <em>B. mandarina</em>. However, to date little is known about the molecular mechanisms underlying domestication-related increases in silk yield. Here, we identified a gene associated with both domestication and silk-related quantitative trait locus (QTL): Abelson tyrosine protein kinase (<em>Abl</em>). </span><span>Population genomic data for <em>B. mori</em> and <em>B. mandarina</em> identified obvious signatures of artificial selection in the genomic region bearing the <em>Abl</em></span><span><em> </em>gene. T</span><span>here were two fixed nucleotide substitutions (−244 and −1311) in the </span><span>tran</span><span>scription factor binding motif of the upstream regulatory region of <em>B. mori Abl</em>.</span> <span>Compared to <em>Abl </em>in the wild silkworm <em>B. mandarina</em>, <em>B. mori Abl</em> exhibited significantly greater promoter activity and was upregulated in the silk gland from the last day of the 5<sup>th</sup> larval instar to pupal stage (P0). Compared to the wild type, CRISPR/Cas9-generated <em>Abl </em>loss-of-function mutants </span><span>exhibited a higher sensitivity to diseases, shorter developmental duration, and reductions in economically important silk traits, including cocoon weight, pupal weight, and cocoon layer thickness. Comparison of silk-gland transcriptomes between the wild type and the mutant indicated that genes enriched in ribosome biosynthesis, splicing, RNA transport, and the carbon metabolism were significantly downregulated in the mutants. Weighted gene co-expression network analysis (WGCNA) confirmed that genes related to ribosome biosynthesis were pivotal, driving the significant differentiation in silk yield between <em>B. mori</em> and <em>B. mandarina</em>. Here, we demonstrated that artificial selection acts on the cis-elements of silk-trait QTL gene <em>Abl </em>in a novel case (the domestic silkworm), and that this selection pressure increased <em>Abl </em>promoter activity and expression level. By promoting protein translation and synthesis, artificial selection further enhanced the robustness of silkworm larvae and improved cocoon silk synthesis.</span></p>
Enhancing crop domestication through genomic selection, a case study of intermediate wheatgrass
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Artificial selection on cis-element of Abl contributes cocoon yield increase in domestic silkworm
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Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication
<p>Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds.</p> <p>Results: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments.</p> <p>Conclusions: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.</p>
Data from: Reduction of the pectoral spine and girdle in domesticated Channel Catfish is likely caused by changes in selection pressure
Locked pectoral spines of the Channel Catfish Ictalurus punctatus more than double the fish's width and complicate ingestion by gape-limited predators. The spine mates with the pectoral girdle, a robust structure that anchors the spine. This study demonstrates that both spine and girdle exhibit negative allometric growth and that pectoral spines and girdles are lighter in domesticated than in wild Channel Catfish. This finding could be explained by changes in selection pressure for spine growth during domestication or by an epigenetic effect in which exposure to predators in wild fish stimulates pectoral growth. We tested the epigenetic hypothesis by exposing domesticated Channel Catfish fingerlings to Largemouth Bass Micropterus salmoides predators for 13 weeks. Spines and girdles grow isometrically in the fingerlings, and regression analysis indicates no difference in proportional pectoral growth between control and predator-exposed fish. Therefore a change in selection pressure likely accounts for smaller pectoral growth in domesticated Channel Catfish. Decreasing spine growth in older fish suggests anti-predator functions are most important in smaller fish. Additionally, growth of the appendicular and axial skeleton is controlled differentially, and mechanical properties of the spine and not just its length are an important component of this defensive adaptation.
Data from: Supplementary stocking selects for domesticated genotypes
Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.
Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.
Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.)
<p>Domestication is considered a model of adaptation that can be used to draw conclusions about the <em>modus operandi</em> of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 <em>Pisum sativum</em> (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild <em>P. sativum</em> revealed five distinct groups with a notable geographic pattern. <em>Pisum abyssinicum</em> clustered unequivocally within the <em>P. sativum</em> complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in <em>P. sativum</em> ssp. <em>sativum</em> and three in <em>P. abyssinicum</em>. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild <em>P. sativum</em> is structured into well-diverged subgroups. Although <em>Pisum sativum</em> ssp<em>. humile</em> is not supported as a taxonomic entity, the so-called 'southern <em>humile</em>' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.</p>
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
<p>A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as <em>Cannabis</em> <em>sativa </em>(<em>C. sativa</em>), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of <em>C. sativa</em>. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high <span>𝐹̅</span>ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene <em>SMALLER TRICHOMES</em> <em>WITH VARIABLE BRANCHES 2 </em>to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in <em>C. sativa</em>.</p>
Data from: Genomic signatures of artificial selection during early domestication of a wood crop
<p>To determine how a century of artificial selection has changed the genome of <i>E. grandis</i>, we generated SNP genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors.</p>
Data from: Supplementary stocking selects for domesticated genotypes
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Data from: Defining the role of the MADS-box gene, Zea agamous like1, a target of selection during maize domestication
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Data from: Ecotypic differentiation under farmers’ selection: molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes
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Data from: Reduction of the pectoral spine and girdle in domesticated Channel Catfish is likely caused by changes in selection pressure
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Data from: Genomic signatures of artificial selection during early domestication of a wood crop
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Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
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The influences of progenitor filtering, domestication selection and the boundaries of nature on the domestication of grain crops
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Data from: A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.)
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Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
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Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication
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