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13 results for “Genotype table”
Supplementary Table 1. Raw data of egg quality parameters for 990 egg samples with ATOL (Animal Trait Ontology for Livestock) descriptors, as function of hen age, pen no. and genotype in 15 replicates.
<p>Data table of egg quality parameters</p>
Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables
<p>Extreme <span>environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, </span><span>m</span><span>odern bony fishes have colonized various aquatic environments, including perpetually dark,</span><span> hypoxic, hypersaline and toxic habitats</span><span>. </span><span>Eurasian perch (</span><em>Perca fluviatilis</em><span>) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (associated with >3,000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.</span></p>
Table 1 in Prevalence and new genotypes of Enterocytozoon bieneusi in sheltered dogs and cats in Sichuan province, southwestern China
<p><b>Table 1.</b> Prevalence and genotypes of <i>E. bieneusi</i> in sheltered dogs from different cities and sources in Sichuan province, southwestern China.</p><table><tbody><tr><th>City</th><th>Source</th><th>No. examined</th><th>No. positive</th><th>Prevalence (%)</th><th>OR (95% CI)</th><th><i>p-</i> value</th><th>Genotypes (<i>n</i>)</th></tr></tbody><tbody><tr><th></th><td></td><td></td><td></td><td>(95% CI)</td><td></td><td></td><td></td></tr><tr><th>Chengdu</th><td>Shuangliu</td><td>158</td><td>16</td><td>10.1% (5.4–14.8)</td><td>Reference</td><td></td><td>CD9 (8); PtEb IX (7); SCD-1 (1)</td></tr><tr><th></th><td>Wenjiang</td><td>250</td><td>80</td><td>32.0% (26.2–37.8)</td><td>4.176</td><td>0.000</td><td>CD9 (79); PtEb IX (1)</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>(2.336–7.468)</td><td></td><td></td></tr><tr><th>Ya’ an</th><td>Yucheng</td><td>228</td><td>36</td><td>15.8% (11.1–20.5)</td><td>1.664</td><td>0.112</td><td>CD9 (4); PtEb IX (32)</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>(0.888–3.117)</td><td></td><td></td></tr><tr><th>Panzhihua</th><td>Dongqu</td><td>44</td><td>2</td><td>4.5% (<i>—</i> 1.6–10.7)</td><td>0.423</td><td>0.264</td><td>CD9 (1); PtEb IX (1)</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>(0.093–1.913)</td><td></td><td></td></tr><tr><th>Guangyuan</th><td>Lizhou</td><td>44</td><td>2</td><td>4.5% (<i>—</i> 1.6–10.7)</td><td>0.423</td><td>0.264</td><td>Type IV (1); SCD-2 (1)</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>(0.093–1.913)</td><td></td><td></td></tr><tr><th>Total</th><td></td><td>724</td><td>136</td><td>18.8% (15.9–21.6)</td><td></td><td></td><td>CD9 (92); PtEb IX (41);</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td></td><td></td><td>Type IV (1); SCD-1 (1); SCD-2 (1)</td></tr></tbody></table>
Table 2 in Prevalence and new genotypes of Enterocytozoon bieneusi in sheltered dogs and cats in Sichuan province, southwestern China
<p><b>Table 2.</b> Prevalence and genotypes of <i>E. bieneusi</i> in sheltered cats from different cities and sources in Sichuan province, southwestern China.</p><table><tbody><tr><th>City</th><th>Source</th><th>No. examined</th><th>No. positive</th><th>Prevalence</th><th>OR (95% CI)</th><th><i>p-</i> value</th><th>Genotypes (<i>n</i>)</th></tr></tbody><tbody><tr><th></th><td></td><td></td><td></td><td>(%) (95% CI)</td><td></td><td></td><td></td></tr><tr><th>Chengdu</th><td>Shuangliu</td><td>85</td><td>13</td><td>15.3% (7.6–22.9)</td><td>Reference</td><td></td><td>CD9 (10); D (2); PtEb IX (1)</td></tr><tr><th>Ya’ an</th><td>Yucheng</td><td>23</td><td>3</td><td>13.0% (<i>—</i> 0.7–26.8)</td><td>0.831 (0.215–3.203)</td><td>0.788</td><td>CD9 (1); D (2)</td></tr><tr><th>Panzhihua</th><td>Dongqu</td><td>48</td><td>6</td><td>12.5% (3.1–21.9)</td><td>0.791 (0.280–2.237)</td><td>0.791</td><td>Type IV (6)</td></tr><tr><th>Total</th><td></td><td>156</td><td>22</td><td>14.1% (8.6–19.6)</td><td></td><td></td><td>CD9 (11); Type IV (6);</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td></td><td></td><td>D (4); PtEb IX (1)</td></tr></tbody></table>
Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables
Open the record for dataset details and reuse information.
Table 2 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
<p><b>Table 2</b> Summary of the annotation of the sweetpotato unigenes.</p><table><tbody><tr><th></th><th>Number of unigenes</th><th>Percentage (%)</th></tr></tbody><tbody><tr><th>Total unigenes</th><td>109,401</td><td></td></tr><tr><th>Annotated in NR</th><td>41,729</td><td>38.14</td></tr><tr><th>Annotated in NT</th><td>21,004</td><td>19.19</td></tr><tr><th>Annotated in KO</th><td>12,524</td><td>11.44</td></tr><tr><th>Annotated in SwissProt</th><td>29,444</td><td>26.91</td></tr><tr><th>Annotated in PFAM</th><td>30,212</td><td>27.61</td></tr><tr><th>Annotated in GO</th><td>31,304</td><td>28.61</td></tr><tr><th>Annotated in KOG</th><td>14,349</td><td>13.11</td></tr><tr><th>All annotated unigenes</th><td>47,749</td><td>43.64</td></tr></tbody></table>
Table 3 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
<p><b>Table 3</b> Summary of EST-SSRs in the sweetpotato transcriptome.</p><table><tbody><tr><th>Searching item</th><th>Numbers</th></tr></tbody><tbody><tr><th>Total number of sequences examined</th><td>109,401</td></tr><tr><th>Total size of examined sequences (bp)</th><td>75,954,853</td></tr><tr><th>Total number of identified SSRs</th><td>9549</td></tr><tr><th>Number of SSR containing sequences</th><td>8334</td></tr><tr><th>Number of sequences containing more than 1 SSR</th><td>1025</td></tr><tr><th>Number of SSRs present in compound formation</th><td>399</td></tr><tr><th>Di-nucleotide</th><td>5086</td></tr><tr><th>Tri-nucleotide</th><td>4092</td></tr><tr><th>Tetra-nucleotide</th><td>336</td></tr><tr><th>Penta-nucleotide</th><td>19</td></tr><tr><th>Hexa-nucleotide</th><td>16</td></tr></tbody></table>
Table 1 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
<p><b>Table 1</b> Length distribution of the assembled transcripts and unigenes.</p><table><tbody><tr><th>Nucleotides length (bp)</th><th>Transcripts</th><th>Unigenes</th></tr></tbody><tbody><tr><th>200–500 bp</th><td>90,099</td><td>67,643</td></tr><tr><th>500–1000 bp</th><td>38,799</td><td>21,181</td></tr><tr><th>1000–2000 bp</th><td>30,015</td><td>13,149</td></tr><tr><th>>2000 bp</th><td>17,254</td><td>7428</td></tr><tr><th>Total</th><td>176,167</td><td>109,401</td></tr><tr><th>Min length</th><td>201</td><td>201</td></tr><tr><th>Mean length</th><td>847</td><td>694</td></tr><tr><th>Median length</th><td>486</td><td>385</td></tr><tr><th>Max length</th><td>15,618</td><td>15,618</td></tr><tr><th>N50</th><td>1430</td><td>1127</td></tr><tr><th>N90</th><td>333</td><td>277</td></tr><tr><th>Total nucleotides</th><td>149,175,171</td><td>75,954,853</td></tr></tbody></table>
Pinna nobilis genotype table (Occitan coast)
<p>The fan mussel, <em>Pinna nobilis</em>, endemic to the Mediterranean Sea, is a critically endangered species facing mass mortality events in almost all of its populations, following the introduction of the parasite <em>Haplosporidium pinnae</em>. Such a unique pandemic in a marine organism, which spreads rapidly and with mortality rates reaching 100 %, could lead to the potential extinction of the species. Only few regions, involving lagoon habitats, remain healthy throughout entire Mediterranean Sea. This dataset was used to describes the genetic structure of <em>P. nobilis</em> across the Gulf of Lion, including confined locations such as lagoons and ports. This dataset contains the genotype, at 22 microsatellite loci, of total of 960 samples that were collected among 16 sites distributed at 8 localities.</p> <p>The results of the study are available in Peyran et al. (2021).</p> <p>Peyran, C., Boissin, E., Morage, T., Nebot-Colomer, E., Iwankow, G., & Planes, S. (2021). Genetic homogeneity of the critically endangered fan mussel, Pinna nobilis, throughout lagoons of the Gulf of Lion (North-Western Mediterranean Sea). <em>Scientific reports</em>, <em>11</em>(1), 1-12.</p> <p>Corresponding author: claire.peyran@gmail.com</p>
Task 4.1 Table 4.1.1_Seed index of soybean genotypes at NARDI in 2019
<p>At NARDI more than 100 genotypes from two core collections (Fundulea and Turda) were analysed for germination parameters.</p>
Table S1: Fetal phenotype and genotype
<p>Legend to supplementary Table 1</p> <p>This table contains the 28 fetal cases on whom WES was performed. For each case, the fetal phenotype and the organ system involved are described, as well as the sample type from which the DNA was extracted, the applied gene panel and the result. For the positive cases, the gestational age at ultrasound, the affected gene and variant, the inheritance mode, the associated syndrome, the fetal phenotype as described in the literature and the outcome of the pregnancy are listed as well.</p> <p>AC: amniocytes; AD: autosomal dominant; AR: autosomal recessive; CNS: central nervous system; CV: chorionic villi; hom: homozygous; IF: incidental finding; IUGR: intrauterine growth restriction; LB: live birth; norm: normal; NT: nuchal translucency; pat: paternal; path: pathogenic; TOP: termination of pregnancy; US: ultrasound; VSD: ventricular septal defect; WES: whole exome sequencing; WESSD: WES with skeletal dysplasia panel</p>
Task 4.3 Table 4.3.2_Progeny from cross GQ4X (nodulating x non-nodulating soybean) and nod_genotype status of progeny
<p>Soybean lines lacking N2-fixation.</p>
Biology and Fertility Life Table of Soybean Looper in Soybean Genotypes
<p>Dados brutos da biologia do Looper de soja em genótipos de soja</p>
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