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84 results for “Landraces”
Data from: Finding a needle in a haystack: distinguishing Mexican maize landraces using a small number of SNPs
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Vegetative characters of Agave landraces used for the production of pulque in Tlaxcala.
<p>Raw data of 19 morphological variables of vegetative characters of nine Agave landraces (N=478 individuals) used for the production of pulque in 10 localities of Tlaxcala. These data were used to analyze and describe the morphological diversity of these varieties.</p> <p>Nine <em>Agave</em> landraces used for pulque production in 10 localities Tlaxcala were analyzed: <em>Agave salmiana</em> subsp. <em>salmiana</em> ‘Amarillo’, ‘Ayoteco’, ‘Colorado’, ‘Chalqueño’, ‘Chino’, ‘Manso’, ‘Prieto’, and ‘Xilomelt’ and <em>Agave mapisaga</em> var. <em>mapisaga</em> ‘Palmilla’. Twenty-two populations of 13–35 individuals were included in the study (N = 478 individuals). Both landraces and wild individuals were identified at the species and subspecies level following García-Mendoza’s (2011) and Gentry’s (1982) taxonomic keys. Twenty morphological variables were measured in de field between 2018 and 2019.</p> <p> </p>
Evaluation of rice landraces for brown planthopper resistance based on phenotypic reactions and biochemical attributes [DataSet]
<p>Data set for the publication: Evaluation of rice landraces for brown planthopper resistance based on phenotypic reactions and biochemical attributes</p>
Data from: Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations
A possible consequence of planting GMOs in centers of crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence of the transgenic 35S promoter in maize landraces sampled in 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample taken from the same region in 2003 and 2004 could not confirm the existence of transgenes, thereby casting doubt on the earlier results. These two studies were based on different sampling and analytical procedures and are thus hard to compare. Here we present new molecular data for this region that confirm the presence of transgenes in three of 23 localities sampled in 2001. Transgene sequences were not detected in samples taken in 2002 from nine localities, while directed samples taken in 2004 from two of the positive 2001 localities were again found to contain transgenic sequences. These findings suggest the persistence or re-introduction of transgenes up until 2004 in this area. We address variability in recombinant sequence detection by analyzing the consistency of current molecular assays. We also present theoretical results on the limitations of estimating the probability of transgene detection in samples taken from landraces. The inclusion of a limited number of female gametes, but more importantly, aggregated transgene distributions may significantly lower detection probabilities. Our analytical and sampling considerations help explain discrepancies among different detection efforts, including the one presented here, and provide considerations for the establishment of monitoring protocols to detect the presence of transgenes among structured populations of landraces.
Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces
Background: Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal. Results: We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage. Conclusions: We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.
Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers
<p>Ethiopia is a center of diversity for barley (<i>Hordeum vulgare </i>L.) and it is grown across different agro-ecologies of the country. Unraveling population structure and gene flow status on temporal scales assists an evaluation of the consequences of physical, demographic as well as overall environmental changes on the stability and persistence of populations. Here, we examine spatial and temporal genetic variation within and among barley landrace samples collected over a period of four decades (1976-2017), using simple sequence repeat (SSR) markers. Our objective was to evaluate spatial and temporal changes in barley population connectivity associated with the closure of geographic origin and time periods. Low to strong genetic diversity was observed among the landraces and STRUCTURE, Neighbour joining tree and Discriminant Analysis of Principal Component analysis revealed three clusters. The cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance increases along with geographic distance. The grouping of landraces based on altitudinal classes was influenced by geographic proximity. From AMOVA year categories, it was observed that within population genetic diversity much higher than between population genetic diversity and that the temporal differentiation is considerably smaller. The low to strong genetic differentiation between landraces from various geographic origins could be attributed to gene flow across the region as a consequence of seed exchange among farmers. Nevertheless, we found some connectivity between changes in population dynamics as well as contemporary gene flow. The results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of barley germplasms. Furthermore, our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that <i>in-situ</i> conservation strategies based on farmers use can conserve the genetic identity of landraces while allowing adaptation to local-environments.</p>
Investigating gas-exchange performance between wheat landraces and commercial varieties
<p>Improvement of photosynthetic traits in crops to increase yield potential and crop resilience has recently become a major breeding target. Synthetic biology and genetic technologies offer unparalleled opportunities to create new genetics for photosynthetic traits driven by existing fundamental knowledge. However, large "gene bank" collections of germplasm comprising of historical collections of crop species and their relatives offer a wealth of opportunities to find novel allelic variation in the key steps of photosynthesis, to identify new mechanisms and to accelerate genetic progress in crop breeding programs. Here we explore the available genetic resources in food and fibre crops, strategies to selectively target allelic variation in genes underpinning key photosynthetic processes and deployment of this variation via gene editing in modern elite material.</p>
Data from: Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations
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Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers
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Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces
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Data from: Genome-environment associations in sorghum landraces predict adaptive traits
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Investigating gas-exchange performance between wheat landraces and commercial varieties
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Genome-wide epistatic interaction networks affecting feed efficiency in Duroc and Landrace pigs
GEO Series GSE144064. Sus scrofa. 109 samples. Type: Genome variation profiling by genome tiling array.
Transcriptomic and Co-expression Network Analyses on Diverse Wheat Landraces Identifies Candidate Master Regulators of the Response to Early Drought
GEO Series GSE225797. Triticum aestivum. 28 samples. Type: Expression profiling by high throughput sequencing.
Differences in gene expression profiles for subcutaneous adipose, liver, and skeletal muscle tissues between Meishan and Landrace pigs with different backfat thicknesses
GEO Series GSE97711. Sus scrofa. 102 samples. Type: Expression profiling by array.
Raw data of testicular small RNA-Seq in Hezuo pigs and Landrace pigs at two different ages
GEO Series GSE192462. Sus scrofa. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Sustainable cultivation of melon landraces: effects of grafting on the accumulation of flavor-related compounds
<p>Melon landraces are highly appreciated by consumers who pay price premiums to compensate for lower yields, enabling thus supporting on-farm conservation. However, susceptibility to soilborne diseases poses a significant challengeHowever, they are highly susceptible to soilborne diseases. This study analyses the impact of Cucurbita and Cucumis rootstocks on the accumulation of flavor-related metabolites in several Spanish landraces of the Ibericus melon group, as a strategy to promote their sustainable cultivation. Scion genotype was the main factor conditioning the accumulation of sugars and acids both under standard and salineunder organic farming conditions in different environments. The effects of grafting on organic acid accumulation were negligible, while the effects on sugar profile content were limited butand volatile profile were significant, and. The latter effects were dependent on specific scion-rootstock combinations, though wild Cucumis (e.g. Fian) rootstocks represent an interesting alternative that should be furtherto be studied. The effect on the accumulation of volatiles was limited, and again depended on specific scion-rootstock combinations, and on the specific landrace population studied.. The rootstock effect even differed between populations of the same landrace.</p> <p>Additional data available thorugh contcts with correspondence author.</p> <p>Manuscript Published in Food chemistry.</p>
VALORIZATION OF DIFFERENT LANDRACE AND COMMERCIAL SORGHUM (Sorghum bicolor (L.) Moench) STRAW VARIETIES BY ANAEROBIC DIGESTION
<p>The provided data are the raw or primary data used to create the figures and tables in the article: VALORIZATION OF DIFFERENT LANDRACE AND COMMERCIAL SORGHUM (Sorghum bicolor (L.) Moench) STRAW VARIETIES BY ANAEROBIC DIGESTION.</p> <p> </p>
Raw datas of the transcriptome in testes of Hezuo pigs and Landrace pigs at two different ages
GEO Series GSE171756. Sus scrofa. 12 samples. Type: Expression profiling by high throughput sequencing.
Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses
GEO Series GSE232367. Triticum aestivum. 30 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.